Cellular tumor antigen p53
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein–DNA Homooligomer Protein × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts | Chain A； UniProt 55–254 Chain B； UniProt 55–254 | Fragment：P53 DNA BINDING DOMAIN | DNA × 2 ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 20 ACT ACETATE ION × 4 | X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 8.8；292 K；0.02 M Citric acid, 0.08 M BIS-TRIS propane, 16% w/v Polyethylene glycol 3,350 | Resolution 1.60 Å R-free 0.188 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 5MCV | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1A1U SOLUTION STRUCTURE DETERMINATION OF A P53 MUTANT DIMERIZATION DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
324–358（35 aa）
Fragment：OLIGOMERIZATION
Chain C
324–358（35 aa）
Fragment：OLIGOMERIZATION
|
Mutation：M40K, F41I, L44Y Mutation：M40K, F41I, L44Y | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；313 K
|
Resolution not provided |
| 1AIE P53 TETRAMERIZATION DOMAIN CRYSTAL STRUCTURE Deposited 1997-04-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
326–356（31 aa）
Fragment：TETRAMERIZATION DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；1.4 M SODIUM CITRATE, 100 MM HEPES, PH 8.0
|
Resolution 1.50 Å R-free 0.252 |
| 1C26 CRYSTAL STRUCTURE OF P53 TETRAMERIZATION DOMAIN Deposited 1999-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
325–356（32 aa）
Fragment：TETRAMERIZATION DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.8；298 K；3.0 M SODIUM FORMATE 0.5 M AMMONIUM SULFATE 50 MM TRIS-HCL PH 8.8, VAPOR DIFFUSION, HANGING DROP at 298 K
|
Resolution 1.70 Å |
| 1DT7 SOLUTION STRUCTURE OF THE C-TERMINAL NEGATIVE REGULATORY DOMAIN OF P53 IN A COMPLEX WITH CA2+-BOUND S100B(BB) Deposited 2000-01-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain X
367–388（22 aa）
Fragment：C-TERMINAL PEPTIDE
Chain Y
367–388（22 aa）
Fragment：C-TERMINAL PEPTIDE
|
Not recorded | CA CALCIUM ION × 4 |
SOLUTION NMR
NMR measurement conditions
pH 6.5；310 K；Ionic strength (raw mmCIF value) 25 mM；Pressure ambient
NMR sample composition
3-6 mM S100 (subunit concentration), 0.1 mM EDTA, 0.34 mM NaN3, 5 mM DTT, 17 mM NaCl, 10 mM d11-tris-HCl, 7% D2O, 6-13 mM CaCl2, 4.8-10 mM p53 peptide | 7% D2O, 93% H2O
|
Resolution not provided |
| 1GZH Crystal structure of the BRCT domains of human 53BP1 bound to the p53 tumor supressor Deposited 2002-05-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
95–292（198 aa）
Fragment：DNA BINDING REGION, RESIDUES 95-292
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.4；50 MM TRIS PH 7.4, 250 MM AMMONIUM SULFATE, 25% POLYETHYLENE GLYCOL 4000
|
Resolution 2.60 Å R-free 0.288 |
| 1GZH Crystal structure of the BRCT domains of human 53BP1 bound to the p53 tumor supressor Deposited 2002-05-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
95–292（198 aa）
Fragment：DNA BINDING REGION, RESIDUES 95-292
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.4；50 MM TRIS PH 7.4, 250 MM AMMONIUM SULFATE, 25% POLYETHYLENE GLYCOL 4000
|
Resolution 2.60 Å R-free 0.288 |
| 1H26 CDK2/CyclinA in complex with an 11-residue recruitment peptide from p53 Deposited 2002-07-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
376–386（11 aa）
Fragment：RESIDUES 376-386
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；0.8M KCL, 1.2M (NH4)2SO4, 40MM HEPES PH 7.0. PROTEIN CONCENTRATION = 10MG/ML
|
Resolution 2.24 Å R-free 0.268 |
| 1HS5 NMR SOLUTION STRUCTURE OF DESIGNED P53 DIMER Deposited 2000-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
324–357（34 aa）
Fragment：RESIDUES 324-357
Chain B
324–357（34 aa）
Fragment：RESIDUES 324-357
|
Mutation：M340Q, L344R Mutation：M340Q, L344R | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；300 K；Ionic strength (raw mmCIF value) 25mM；Pressure ambient
NMR sample composition
2mM U-15N,13C; 25mM sodium phosphate; 150mM sodium chloride | 90% H2O/10% D2O
|
Resolution not provided |
| 1JSP NMR Structure of CBP Bromodomain in complex with p53 peptide Deposited 2001-08-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
367–386（20 aa）
Fragment：C-terminal fragment
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；298 K；Pressure ambient
NMR measurement conditions
pH 6.5；298 K；Pressure ambient
NMR measurement conditions
pH 6.5；298 K；Pressure ambient
NMR measurement conditions
pH 6.5；298 K；Pressure ambient
NMR sample composition
0.5mM CBP bromodomain U-15N; 0.5mM P53 peptide; 100mM phosphate buffer; pH 6.5 | 90% H2O/10% D2O
NMR sample composition
0.5mM CBP bromodomain U-15N,13C; 0.5mM P53 peptide;100mM phosphate buffer; pH 6.5 | 90% H2O/10% D2O
NMR sample composition
0.5mM CBP bromodomain U-15N,13C; 0.5mM P53 peptide;100mM phosphate buffer; pH 6.5 | 99.9%D2O
NMR sample composition
0.5mM CBP bromodomain U-15N,13C,75% 2H; 0.5mM P53 peptide;100mM phosphate buffer; pH 6.5 | 90% H2O/10% D2O
|
Resolution not provided |
| 1KZY Crystal Structure of the 53bp1 BRCT Region Complexed to Tumor Suppressor P53 Deposited 2002-02-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
95–289（195 aa）
Fragment：DNA-BINDING CORE DOMAIN
Chain B
95–289（195 aa）
Fragment：DNA-BINDING CORE DOMAIN
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG4000, sodium citrate, ammonium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.50 Å R-free 0.256 |
| 1MA3 Structure of a Sir2 enzyme bound to an acetylated p53 peptide Deposited 2002-07-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
372–389（18 aa）
Fragment：Regulatory C-terminal tail (residues 372-389)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；PEG 8000, PEG 1000 and Sodium Chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.254 |
| 1OLG HIGH-RESOLUTION SOLUTION STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR Deposited 1994-06-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
319–360（42 aa）
Chain B
319–360（42 aa）
Chain C
319–360（42 aa）
Chain D
319–360（42 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 1OLH HIGH-RESOLUTION SOLUTION STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR Deposited 1994-06-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
319–360（42 aa）
Chain B
319–360（42 aa）
Chain C
319–360（42 aa）
Chain D
319–360（42 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 1PES NMR SOLUTION STRUCTURE OF THE TETRAMERIC MINIMUM TRANSFORMING DOMAIN OF P53 Deposited 1994-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
325–355（31 aa）
Chain B
325–355（31 aa）
Chain C
325–355（31 aa）
Chain D
325–355（31 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 1PET NMR SOLUTION STRUCTURE OF THE TETRAMERIC MINIMUM TRANSFORMING DOMAIN OF P53 Deposited 1994-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
325–355（31 aa）
Chain B
325–355（31 aa）
Chain C
325–355（31 aa）
Chain D
325–355（31 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 1SAE HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR (SAC STRUCTURES) Deposited 1995-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
319–360（42 aa）
Chain B
319–360（42 aa）
Chain C
319–360（42 aa）
Chain D
319–360（42 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 1SAF HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR (SAD STRUCTURES) Deposited 1995-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
319–360（42 aa）
Chain B
319–360（42 aa）
Chain C
319–360（42 aa）
Chain D
319–360（42 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 1SAK HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR (SAC STRUCTURES) Deposited 1995-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
319–360（42 aa）
Chain B
319–360（42 aa）
Chain C
319–360（42 aa）
Chain D
319–360（42 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 1SAL HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR (SAD STRUCTURES) Deposited 1995-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
319–360（42 aa）
Chain B
319–360（42 aa）
Chain C
319–360（42 aa）
Chain D
319–360（42 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 1TSR P53 CORE DOMAIN IN COMPLEX WITH DNA Deposited 1995-07-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric |
Chain A
94–312（219 aa）
Chain B
94–312（219 aa）
Chain C
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 3 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.20 Å |
| 1TUP TUMOR SUPPRESSOR P53 COMPLEXED WITH DNA Deposited 1995-07-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric |
Chain A
94–312（219 aa）
Chain B
94–312（219 aa）
Chain C
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 3 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.20 Å |
| 1UOL Crystal structure of the human p53 core domain mutant M133L/V203A/N239Y/N268D at 1.9 A resolution. Deposited 2003-09-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA BINDING (CORE) DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.2；pH 7.20
|
Resolution 1.90 Å R-free 0.230 |
| 1UOL Crystal structure of the human p53 core domain mutant M133L/V203A/N239Y/N268D at 1.9 A resolution. Deposited 2003-09-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA BINDING (CORE) DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.2；pH 7.20
|
Resolution 1.90 Å R-free 0.230 |
| 1XQH Crystal structure of a ternary complex of the methyltransferase SET9 (also known as SET7/9) with a P53 peptide and SAH Deposited 2004-10-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
369–377（9 aa）
Fragment：mono-methylated p53 peptide
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.8；291 K；PEG3350, Tris-HCL, pH 7.8, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.75 Å R-free 0.223 |
| 1XQH Crystal structure of a ternary complex of the methyltransferase SET9 (also known as SET7/9) with a P53 peptide and SAH Deposited 2004-10-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
369–377（9 aa）
Fragment：mono-methylated p53 peptide
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.8；291 K；PEG3350, Tris-HCL, pH 7.8, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.75 Å R-free 0.223 |
| 1YCQ XENOPUS LAEVIS MDM2 BOUND TO THE TRANSACTIVATION DOMAIN OF HUMAN P53 Deposited 1996-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
13–29（17 aa）
Fragment：RESIDUES 13 - 29
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å R-free 0.253 |
| 1YCR MDM2 BOUND TO THE TRANSACTIVATION DOMAIN OF P53 Deposited 1996-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
15–29（15 aa）
Fragment：RESIDUES 15 - 29
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.60 Å R-free 0.276 |
| 1YCS P53-53BP2 COMPLEX Deposited 1996-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
94–292（199 aa）
Fragment：RESIDUES 97 - 287
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.20 Å R-free 0.286 |
| 2AC0 Structural Basis of DNA Recognition by p53 Tetramers (complex I) Deposited 2005-07-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: octameric |
Chain A
94–293（200 aa）
Fragment：residues 94-293
Chain B
94–293（200 aa）
Fragment：residues 94-293
Chain C
94–293（200 aa）
Fragment：residues 94-293
Chain D
94–293（200 aa）
Fragment：residues 94-293
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；Ammonium Formate, PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.217 |
| 2ADY Structural Basis of DNA Recognition by p53 Tetramers (complex IV) Deposited 2005-07-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: octameric |
Chain A
94–293（200 aa）
Fragment：residues 94-293
Chain B
94–293（200 aa）
Fragment：residues 94-293
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；Ammonium Fluoride, PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.50 Å R-free 0.251 |
| 2AHI Structural Basis of DNA Recognition by p53 Tetramers (complex III) Deposited 2005-07-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: octameric |
Chain A
94–293（200 aa）
Fragment：residues 94-293
Chain B
94–293（200 aa）
Fragment：residues 94-293
Chain C
94–293（200 aa）
Fragment：residues 94-293
Chain D
94–293（200 aa）
Fragment：residues 94-293
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；Ammonium Chloride, PEG 3350, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.85 Å R-free 0.225 |
| 2ATA Structural Basis of DNA Recognition by p53 Tetramers (complex II) Deposited 2005-08-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: octameric |
Chain A
94–293（200 aa）
Fragment：residues 94-293
Chain B
94–293（200 aa）
Fragment：residues 94-293
Chain C
94–293（200 aa）
Fragment：residues 94-293
Chain D
94–293（200 aa）
Fragment：residues 94-293
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；Lithium Chloride, PEG 3350, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.20 Å R-free 0.215 |
| 2B3G p53N (fragment 33-60) bound to RPA70N Deposited 2005-09-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
33–60（28 aa）
Fragment：residues 33-60
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.9；298 K；Na3 Citrate, Hepes, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.90
|
Resolution 1.60 Å R-free 0.239 |
| 2BIM human p53 core domain mutant M133L-V203A-N239Y-N268D-R273H Deposited 2005-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING (CORE) DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.98 Å R-free 0.223 |
| 2BIM human p53 core domain mutant M133L-V203A-N239Y-N268D-R273H Deposited 2005-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING (CORE) DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.98 Å R-free 0.223 |
| 2BIN human p53 core domain mutant M133L-H168R-V203A-N239Y-N268D Deposited 2005-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING (CORE) DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å R-free 0.236 |
| 2BIO human p53 core domain mutant M133L-V203A-N239Y-R249S-N268D Deposited 2005-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING (CORE) DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å R-free 0.234 |
| 2BIP human p53 core domain mutant M133L-H168R-V203A-N239Y-R249S-N268D Deposited 2005-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING (CORE) DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.235 |
| 2BIQ human p53 core domain mutant T123A-M133L-H168R-V203A-N239Y-R249S- N268D Deposited 2005-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING (CORE) DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.255 |
| 2F1X Crystal structure of the TRAF-like domain of HAUSP/USP7 bound to a p53 peptide Deposited 2005-11-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
360–368（9 aa）
Fragment：p53 peptide fusion with HAUSP N terminal
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG2000 monomethylether, calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.263 |
| 2F1X Crystal structure of the TRAF-like domain of HAUSP/USP7 bound to a p53 peptide Deposited 2005-11-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
360–368（9 aa）
Fragment：p53 peptide fusion with HAUSP N terminal
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG2000 monomethylether, calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.263 |
| 2GS0 NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the activation domain of p53 Deposited 2006-04-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
20–73（54 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；300 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate；Pressure ambient
NMR sample composition
1.0 mM Tfb1 U-15N,
1.0 mM p53 unlabeled,
1.00 mM EDTA,
20 mM phosphate buffer;
90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
1.0 mM Tfb1 U-15N,13C,
1.0 mM p53 unlabeled,
1.00 mM EDTA,
20 mM phosphate buffer;
100% D20 | 100% D20
NMR sample composition
1.0 mM p53 U-15N,
1.0 mM Tfb1 unlabeled,
1.00 mM EDTA,
20 mM phosphate buffer;
90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
1.0 mM p53 U-15N,
1.0 mM Tfb1 unlabeled,
1.00 mM EDTA,
20 mM phosphate buffer;
100% D20 | 100% D20
|
Resolution not provided |
| 2H2D The Structural Basis for Sirtuin Substrate Affinity Deposited 2006-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
372–389（18 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 9.6；298 K；20% PEG 3350, 0.1 M CHES pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 9.60
|
Resolution 1.70 Å R-free 0.237 |
| 2H2F The Structural basis for Sirtuin Substrate affinity Deposited 2006-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
372–389（18 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 9.6；298 K；20% PEG, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 9.60
|
Resolution 2.20 Å R-free 0.246 |
| 2H4J Sir2-deacetylated peptide (from enzymatic turnover in crystal) Deposited 2006-05-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
372–389（18 aa）
|
Not recorded | ZN ZINC ION × 1 NCA NICOTINAMIDE × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9.6；293 K；CHES, PEG3350, PH9.6, acetylated peptide. Crystals were soaked in cryo + 5mM NAD, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.246 |
| 2J0Z p53 tetramerization domain wild type Deposited 2006-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
326–356（31 aa）
Fragment：TETRAMERIZATION DOMAIN, RESIDUES 326-356
Chain B
326–356（31 aa）
Fragment：TETRAMERIZATION DOMAIN, RESIDUES 326-356
Chain C
326–356（31 aa）
Fragment：TETRAMERIZATION DOMAIN, RESIDUES 326-356
Chain D
326–356（31 aa）
Fragment：TETRAMERIZATION DOMAIN, RESIDUES 326-356
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.2；300 K；Pressure 1.0
NMR sample composition
5% D2O/95% WATER
|
Resolution not provided |
| 2J10 p53 tetramerization domain mutant T329F Q331K Deposited 2006-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
326–356（31 aa）
Fragment：TETRAMERIZATION DOMAIN, RESIDUES 326-356
Chain B
326–356（31 aa）
Fragment：TETRAMERIZATION DOMAIN, RESIDUES 326-356
Chain C
326–356（31 aa）
Fragment：TETRAMERIZATION DOMAIN, RESIDUES 326-356
Chain D
326–356（31 aa）
Fragment：TETRAMERIZATION DOMAIN, RESIDUES 326-356
|
Mutation：YES Mutation：YES Mutation：YES Mutation：YES | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.2；300 K；Pressure 1.0
NMR sample composition
5% D2O/95% WATER
|
Resolution not provided |
| 2J11 p53 tetramerization domain mutant Y327S T329G Q331G Deposited 2006-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
326–356（31 aa）
Fragment：TETRAMERIZATION DOMAIN, RESIDUES 326-356
Chain B
326–356（31 aa）
Fragment：TETRAMERIZATION DOMAIN, RESIDUES 326-356
Chain C
326–356（31 aa）
Fragment：TETRAMERIZATION DOMAIN, RESIDUES 326-356
Chain D
326–356（31 aa）
Fragment：TETRAMERIZATION DOMAIN, RESIDUES 326-356
|
Mutation：YES Mutation：YES Mutation：YES Mutation：YES | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.2；300 K；Pressure 1.0
NMR sample composition
5% D2O/95% WATER
|
Resolution not provided |
| 2J1W Human p53 core domain mutant M133L-V143A-V203A-N239Y-N268D Deposited 2006-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING CORE DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.206 |
| 2J1W Human p53 core domain mutant M133L-V143A-V203A-N239Y-N268D Deposited 2006-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING CORE DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.206 |
| 2J1X Human p53 core domain mutant M133L-V203A-Y220C-N239Y-N268D Deposited 2006-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING CORE DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.65 Å R-free 0.206 |
| 2J1X Human p53 core domain mutant M133L-V203A-Y220C-N239Y-N268D Deposited 2006-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING CORE DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.65 Å R-free 0.206 |
| 2J1Y Human p53 core domain mutant M133L-V203A-N239Y-G245S-N268D Deposited 2006-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
Fragment：DNA-BINDING CORE DOMAIN, RESIDUES 94-293
|
Mutation：YES | ZN ZINC ION × 1 CA CALCIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.69 Å R-free 0.218 |
| 2J1Y Human p53 core domain mutant M133L-V203A-N239Y-G245S-N268D Deposited 2006-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–293（200 aa）
Fragment：DNA-BINDING CORE DOMAIN, RESIDUES 94-293
|
Mutation：YES | ZN ZINC ION × 1 CA CALCIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.69 Å R-free 0.218 |
| 2J1Y Human p53 core domain mutant M133L-V203A-N239Y-G245S-N268D Deposited 2006-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
94–293（200 aa）
Fragment：DNA-BINDING CORE DOMAIN, RESIDUES 94-293
|
Mutation：YES | ZN ZINC ION × 1 CA CALCIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.69 Å R-free 0.218 |
| 2J1Y Human p53 core domain mutant M133L-V203A-N239Y-G245S-N268D Deposited 2006-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
94–293（200 aa）
Fragment：DNA-BINDING CORE DOMAIN, RESIDUES 94-293
|
Mutation：YES | ZN ZINC ION × 1 CA CALCIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.69 Å R-free 0.218 |
| 2J1Z Human p53 core domain mutant M133L-V203A-N239Y-N268D-F270L Deposited 2006-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING CORE DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.213 |
| 2J1Z Human p53 core domain mutant M133L-V203A-N239Y-N268D-F270L Deposited 2006-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING CORE DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.213 |
| 2J20 Human p53 core domain mutant M133L-V203A-N239Y-N268D-R273C Deposited 2006-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING CORE DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.206 |
| 2J20 Human p53 core domain mutant M133L-V203A-N239Y-N268D-R273C Deposited 2006-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING CORE DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.206 |
| 2J21 Human p53 core domain mutant M133L-V203A-N239Y-N268D-R282W Deposited 2006-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING CORE DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.60 Å R-free 0.224 |
| 2J21 Human p53 core domain mutant M133L-V203A-N239Y-N268D-R282W Deposited 2006-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING CORE DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.60 Å R-free 0.224 |
| 2K8F Structural Basis for the Regulation of p53 Function by p300 Deposited 2008-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–39（39 aa）
Fragment：UNP residues 1-39
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.3；308 K；Ionic strength (raw mmCIF value) 200；Pressure ambient
NMR sample composition
1.1 mM TAZ2, 1.0 mM [U-100% 15N] TAD(1-39), 1.0 mM [U-100% 13C; U-100% 15N] TAD(1-39), 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1.0 mM [U-100% 15N] TAZ2, 1.1 mM TAD(1-39), 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1.0 mM [U-100% 13C; U-100% 15N] TAZ2, 1.1 mM TAD(1-39), 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1.0 mM TAZ2, 1.1 mM TAD(1-39), 100% D2O | 100% D2O
|
Resolution not provided |
| 2L14 Structure of CBP nuclear coactivator binding domain in complex with p53 TAD Deposited 2010-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
13–61（49 aa）
Fragment：p53 TAD
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition
0.5 mM [U-99% 15N] CBP nuclear coactivator binding domain, 0.5 mM [U-99% 15N] p53 TAD, 0.5 mM [U-99% 13C; U-99% 15N] CBP nuclear coactivator binding domain, 0.5 mM [U-99% 13C; U-99% 15N] p53 TAD, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2LY4 HMGB1-facilitated p53 DNA binding occurs via HMG-box/p53 transactivation domain interaction and is regulated by the acidic tail Deposited 2012-09-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–93（93 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient
NMR sample composition
10 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 0.5 mM PMSF, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2MEJ Solution Structure of the Complex Between BCL-xL and the p53 Core Domain determined with PRE restraints Deposited 2013-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
96–312（217 aa）
Fragment：UNP residues 96-312
|
Not recorded | ZN ZINC ION × 1 |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition
0.6 mM [U-98% 13C; U-98% 15N; U-98% 2H] p53, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
0.1 mM [U-98% 15N; U-98% 2H] BCL-xL, 0.1 mM p53, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
0.6 mM [U-98% 13C; U-98% 15N; U-98% 2H] p53, 0.65 mM BCL-xL, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
0.1 mM [U-98% 15N; U-98% 2H] p53, 0.1 mM BCL-xL_C151MTSL, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
0.1 mM [U-98% 15N; U-98% 2H] p53, 0.1 mM BCL-xL_C151MTSL, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
0.1 mM [U-98% 15N; U-98% 2H] p53, 0.1 mM BCL-xL_C151S_S122C MTSL, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
0.1 mM [U-98% 15N; U-98% 2H] p53, 0.1 mM BCL-xL_C151S_S122C MTSL, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
0.1 mM [U-98% 15N; U-98% 2H] p53, 0.1 mM BCL-xL_C151S_S2C MTSL, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
0.1 mM [U-98% 15N; U-98% 2H] p53, 0.1 mM BCL-xL_C151S_S2C MTSL, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
0.1 mM [U-98% 15N; U-98% 2H] BCL-xL, 0.1 mM Co_p53, 93% H2O/7% D2O | 93% H2O/7% D2O
|
Resolution not provided |
| 2MWO Solution structure of 53BP1 tandem Tudor domains in complex with a p53K370me2 peptide Deposited 2014-11-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
363–377（15 aa）
Fragment：DNA-binding repression region residues 363-377
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.5；298 K；Ionic strength (raw mmCIF value) 25；Pressure ambient
NMR sample composition
25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 13C; U-100% 15N] 53BP1-Tudor, 6.0 mM p53K370me2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 13C; U-100% 15N] 53BP1-Tudor, 6.0 mM p53K370me2, 100% D2O | 100% D2O
NMR sample composition
25 mM sodium phosphate, 1.5 mM sodium azide, 5.0 mM 53BP1-Tudor, 2.0 mM [U-100% 13C; U-100% 15N] p53Kc370me2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
25 mM sodium phosphate, 1.5 mM sodium azide, 5.0 mM 53BP1-Tudor, 2.0 mM [U-100% 13C; U-100% 15N] p53Kc370me2, 100% D2O | 100% D2O
NMR sample composition
25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 15N] 53BP1-Tudor, 6.0 mM p53K370me2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
35 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM p53K370me2, 100% D2O | 100% D2O
NMR sample composition
25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 13C; U-100% 15N] p53Kc370me2, 100% D2O | 100% D2O
|
Resolution not provided |
| 2MWP Solution structure of 53BP1 tandem Tudor domains in complex with a p53K382me2 peptide Deposited 2014-11-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
376–387（12 aa）
Fragment：DNA-binding repression region residues 376-387
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.5；298 K；Ionic strength (raw mmCIF value) 25；Pressure ambient
NMR sample composition
25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 13C; U-100% 15N] 53BP1-Tudor, 6.0 mM p53K382me2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 13C; U-100% 15N] 53BP1-Tudor, 6.0 mM p53K382me2, 100% D2O | 100% D2O
NMR sample composition
25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM 53BP1-Tudor, 0.5 mM [U-100% 13C; U-100% 15N] p53Kc382me2, 100% D2O | 100% D2O
NMR sample composition
25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 15N] 53BP1-Tudor, 6.0 mM p53K382me2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
25 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM p53K382me2, 100% D2O | 100% D2O
NMR sample composition
25 mM sodium phosphate, 1.5 mM sodium azide, 0.5 mM [U-100% 13C; U-100% 15N] p53Kc382me2, 100% D2O | 100% D2O
|
Resolution not provided |
| 2MWY Mdmx-p53 Deposited 2014-12-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
15–29（15 aa）
Fragment：residues 15-23
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure ambient
NMR sample composition
1.0 mM [U-100% 13C; U-100% 15N] protein 1, 1.2 mM protein 2, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2MZD Characterization of the p300 Taz2-p53 TAD2 Complex and Comparison with the p300 Taz2-p53 TAD1 Complex Deposited 2015-02-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
35–59（25 aa）
Fragment：UNP residues 35-59
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.3；308 K；Ionic strength (raw mmCIF value) 200；Pressure ambient
NMR sample composition
1.1 mM Taz2 domain of Histone Acetyltransferase p300, 1.0 mM [U-100% 13C; U-100% 15N] TAD2 sub-domain of Cellular Tumor Antigen p53, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1.0 mM [U-100% 15N] Taz2 domain of Histone Acetyltransferase p300, 1.1 mM TAD2 sub-domain of Cellular Tumor Antigen p53, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1.0 mM [U-100% 13C; U-100% 15N] Taz2 domain of Histone Acetyltransferase p300, 1.1 mM TAD2 sub-domain of Cellular Tumor Antigen p53, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1.0 mM Taz2 domain of Histone Acetyltransferase p300, 1.1 mM TAD2 sub-domain of Cellular Tumor Antigen p53, 100% D2O | 100% D2O
|
Resolution not provided |
| 2OCJ Human p53 core domain in the absence of DNA Deposited 2006-12-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：core domain (residues 94-312)
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；2 ul protein solution (5 mg/ml protein in 20 mM Tris, pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 ul reservoir buffer consisting of 100 mM Hepes, pH 7.6, 10 mM DTT, and 14-21% (w/v) polyethylene glycol (PEG) 4000 above 500 ul reservoir buffer. Colorless plate-shaped crystals were obtained within a few days. VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.05 Å R-free 0.246 |
| 2OCJ Human p53 core domain in the absence of DNA Deposited 2006-12-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：core domain (residues 94-312)
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；2 ul protein solution (5 mg/ml protein in 20 mM Tris, pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 ul reservoir buffer consisting of 100 mM Hepes, pH 7.6, 10 mM DTT, and 14-21% (w/v) polyethylene glycol (PEG) 4000 above 500 ul reservoir buffer. Colorless plate-shaped crystals were obtained within a few days. VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.05 Å R-free 0.246 |
| 2OCJ Human p53 core domain in the absence of DNA Deposited 2006-12-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
94–312（219 aa）
Fragment：core domain (residues 94-312)
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；2 ul protein solution (5 mg/ml protein in 20 mM Tris, pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 ul reservoir buffer consisting of 100 mM Hepes, pH 7.6, 10 mM DTT, and 14-21% (w/v) polyethylene glycol (PEG) 4000 above 500 ul reservoir buffer. Colorless plate-shaped crystals were obtained within a few days. VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.05 Å R-free 0.246 |
| 2OCJ Human p53 core domain in the absence of DNA Deposited 2006-12-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
94–312（219 aa）
Fragment：core domain (residues 94-312)
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；2 ul protein solution (5 mg/ml protein in 20 mM Tris, pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 ul reservoir buffer consisting of 100 mM Hepes, pH 7.6, 10 mM DTT, and 14-21% (w/v) polyethylene glycol (PEG) 4000 above 500 ul reservoir buffer. Colorless plate-shaped crystals were obtained within a few days. VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.05 Å R-free 0.246 |
| 2PCX Crystal structure of p53DBD(R282Q) at 1.54-angstrom Resolution Deposited 2007-03-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–292（199 aa）
Fragment：p53 DBD DOMAIN
|
Mutation：R282Q | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；300 K；0.1M ammonium acetate, 25% PEG 3350, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
|
Resolution 1.54 Å R-free 0.232 |
| 2RUK Solution structure of the complex between p53 transactivation domain 2 and TFIIH p62 PH domain Deposited 2014-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
41–62（22 aa）
Fragment：p53 transactivation domain, UNP residues 41-62
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；305 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient
NMR sample composition
0.4 mM [U-99% 13C; U-99% 15N] TFIIH p62 PH domain-1, 0.48 mM p53 TAD2-2, 20 mM potassium phosphate-3, 5 mM [U-2H] DTT-4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.4 mM [U-99% 13C; U-99% 15N] TFIIH p62 PH domain-5, 0.48 mM p53 TAD2-6, 20 mM potassium phosphate-7, 5 mM [U-2H] DTT-8, 100% D2O | 100% D2O
|
Resolution not provided |
| 2VUK Structure of the p53 core domain mutant Y220C bound to the stabilizing small-molecule drug PhiKan083 Deposited 2008-05-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；294 K；SITTING DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES PH 7.2, 19 % PEG 4000, 5 MM DTT. CRYSTALS WERE SOAKED WITH 10 MM PHIKAN083 IN CRYO BUFFER CONTAINING 100 MM HEPES PH 7.2, 10 MM SODIUM PHOSPHATE PH 7.2, 19 % PEG 4000, 20 % GLYCEROL, 150 MM KCL.
|
Resolution 1.50 Å R-free 0.208 |
| 2VUK Structure of the p53 core domain mutant Y220C bound to the stabilizing small-molecule drug PhiKan083 Deposited 2008-05-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 P83 1-(9-ethyl-9H-carbazol-3-yl)-N-methylmethanamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；294 K；SITTING DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES PH 7.2, 19 % PEG 4000, 5 MM DTT. CRYSTALS WERE SOAKED WITH 10 MM PHIKAN083 IN CRYO BUFFER CONTAINING 100 MM HEPES PH 7.2, 10 MM SODIUM PHOSPHATE PH 7.2, 19 % PEG 4000, 20 % GLYCEROL, 150 MM KCL.
|
Resolution 1.50 Å R-free 0.208 |
| 2WGX HUMAN P53 CORE DOMAIN MUTANT M133L-V203A-Y236F-N239Y-T253I-N268D Deposited 2009-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；294 K；SITTING DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML IN 25 MM SODIUM PHOSPHATE PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES PH 7.2, 19 % PEG 4000, 5 MM DTT.
|
Resolution 1.75 Å R-free 0.199 |
| 2WGX HUMAN P53 CORE DOMAIN MUTANT M133L-V203A-Y236F-N239Y-T253I-N268D Deposited 2009-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；294 K；SITTING DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML IN 25 MM SODIUM PHOSPHATE PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES PH 7.2, 19 % PEG 4000, 5 MM DTT.
|
Resolution 1.75 Å R-free 0.199 |
| 2X0U STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO A 2-amino substituted benzothiazole scaffold Deposited 2009-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；294 K；SITTING DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES PH 7.2, 19% PEG 4000, 5 MM DTT. SOAKING BUFFER: SATURATED SOLUTION OF SMALL MOLECULE LIGAND IN 100 MM HEPES PH 7.2, 10 MM SODIUM PHOSPHATE PH 7.2, 19% PEG 4000, 20% GLYCEROL, 150 MM KCL.
|
Resolution 1.60 Å R-free 0.193 |
| 2X0U STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO A 2-amino substituted benzothiazole scaffold Deposited 2009-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 X0U 6,7-DIHYDRO[1,4]DIOXINO[2,3-F][1,3]BENZOTHIAZOL-2-AMINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；294 K；SITTING DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES PH 7.2, 19% PEG 4000, 5 MM DTT. SOAKING BUFFER: SATURATED SOLUTION OF SMALL MOLECULE LIGAND IN 100 MM HEPES PH 7.2, 10 MM SODIUM PHOSPHATE PH 7.2, 19% PEG 4000, 20% GLYCEROL, 150 MM KCL.
|
Resolution 1.60 Å R-free 0.193 |
| 2X0V STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO 4-(trifluoromethyl)benzene-1,2-diamine Deposited 2009-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；294 K；SITTING DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES PH 7.2, 19 % PEG 4000, 5 MM DTT. SOAKING BUFFER: SATURATED SOLUTION OF SMALL MOLECULE LIGAND IN 100 MM HEPES PH 7.2, 10 MM SODIUM PHOSPHATE PH 7.2, 19 % PEG 4000, 20 % GLYCEROL, 150 MM KCL.
|
Resolution 1.80 Å R-free 0.189 |
| 2X0V STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO 4-(trifluoromethyl)benzene-1,2-diamine Deposited 2009-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 X0V 4-(TRIFLUOROMETHYL)BENZENE-1,2-DIAMINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；294 K；SITTING DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES PH 7.2, 19 % PEG 4000, 5 MM DTT. SOAKING BUFFER: SATURATED SOLUTION OF SMALL MOLECULE LIGAND IN 100 MM HEPES PH 7.2, 10 MM SODIUM PHOSPHATE PH 7.2, 19 % PEG 4000, 20 % GLYCEROL, 150 MM KCL.
|
Resolution 1.80 Å R-free 0.189 |
| 2X0W STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO 5,6-dimethoxy- 2-methylbenzothiazole Deposited 2009-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES PH 7.2, 19% PEG 4000, 5 MM DTT. SOAKING BUFFER: SATURATED SOLUTION OF SMALL MOLECULE LIGAND IN 100 MM HEPES PH 7.2, 10 MM SODIUM PHOSPHATE PH 7.2, 19% PEG 4000, 20% GLYCEROL, 150 MM KCL.
|
Resolution 2.10 Å R-free 0.228 |
| 2X0W STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO 5,6-dimethoxy- 2-methylbenzothiazole Deposited 2009-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 X0W 5,6-DIMETHOXY-2-METHYL-1,3-BENZOTHIAZOLE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES PH 7.2, 19% PEG 4000, 5 MM DTT. SOAKING BUFFER: SATURATED SOLUTION OF SMALL MOLECULE LIGAND IN 100 MM HEPES PH 7.2, 10 MM SODIUM PHOSPHATE PH 7.2, 19% PEG 4000, 20% GLYCEROL, 150 MM KCL.
|
Resolution 2.10 Å R-free 0.228 |
| 2XWR Crystal structure of the DNA-binding domain of human p53 with extended N terminus Deposited 2010-11-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
89–293（205 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 89-293
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；290 K；SITTING DROP VAPOR DIFFUSION AT 17 DEGREE C. PROTEIN SOLUTION: 5.4 MG/ML IN 25 MM SODIUM PHOSPHATE, PH 7.2, 220 MM NACL, AND 5 MM DTT. RESERVOIR SOLUTION: 100 MM BIS-TRIS, PH 5.5, 23% PEG 3350, 200 MM AMMONIUM SULFATE.
|
Resolution 1.68 Å R-free 0.209 |
| 2XWR Crystal structure of the DNA-binding domain of human p53 with extended N terminus Deposited 2010-11-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
89–293（205 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 89-293
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；290 K；SITTING DROP VAPOR DIFFUSION AT 17 DEGREE C. PROTEIN SOLUTION: 5.4 MG/ML IN 25 MM SODIUM PHOSPHATE, PH 7.2, 220 MM NACL, AND 5 MM DTT. RESERVOIR SOLUTION: 100 MM BIS-TRIS, PH 5.5, 23% PEG 3350, 200 MM AMMONIUM SULFATE.
|
Resolution 1.68 Å R-free 0.209 |
| 2YBG Structure of Lys120-acetylated p53 core domain Deposited 2011-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-293
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
PROTEIN SOLUTION: 5 MG/ML PROTEIN IN 20 MM CITRATE BUFFER PH 6.1, 150 MM NACL, 10 MM DTT. CRYSTALLIZATION BUFFER: 26% (W/V) PEG 3350, 43 MM SODIUM ACETATE AND 100 MM HEPES, PH 7.5
|
Resolution 1.90 Å R-free 0.226 |
| 2YBG Structure of Lys120-acetylated p53 core domain Deposited 2011-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–293（200 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-293
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
PROTEIN SOLUTION: 5 MG/ML PROTEIN IN 20 MM CITRATE BUFFER PH 6.1, 150 MM NACL, 10 MM DTT. CRYSTALLIZATION BUFFER: 26% (W/V) PEG 3350, 43 MM SODIUM ACETATE AND 100 MM HEPES, PH 7.5
|
Resolution 1.90 Å R-free 0.226 |
| 2YBG Structure of Lys120-acetylated p53 core domain Deposited 2011-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
94–293（200 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-293
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
PROTEIN SOLUTION: 5 MG/ML PROTEIN IN 20 MM CITRATE BUFFER PH 6.1, 150 MM NACL, 10 MM DTT. CRYSTALLIZATION BUFFER: 26% (W/V) PEG 3350, 43 MM SODIUM ACETATE AND 100 MM HEPES, PH 7.5
|
Resolution 1.90 Å R-free 0.226 |
| 2YBG Structure of Lys120-acetylated p53 core domain Deposited 2011-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
94–293（200 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-293
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
PROTEIN SOLUTION: 5 MG/ML PROTEIN IN 20 MM CITRATE BUFFER PH 6.1, 150 MM NACL, 10 MM DTT. CRYSTALLIZATION BUFFER: 26% (W/V) PEG 3350, 43 MM SODIUM ACETATE AND 100 MM HEPES, PH 7.5
|
Resolution 1.90 Å R-free 0.226 |
| 2YDR CpOGA D298N in complex with p53-derived O-GlcNAc peptide Deposited 2011-03-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
144–154（11 aa）
Fragment：RESIDUES 144-154
|
Not recorded | CD CADMIUM ION × 18 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.6 M NAAC, 0.175 M CDSO4, 0.1 M HEPES PH 7.5
|
Resolution 2.75 Å R-free 0.219 |
| 2Z5S Molecular basis for the inhibition of p53 by Mdmx Deposited 2007-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
15–29（15 aa）
Fragment：TRANSACTIVATION DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；280 K；30% PEG 300, 0.1M MES pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K
|
Resolution 2.30 Å R-free 0.310 |
| 2Z5S Molecular basis for the inhibition of p53 by Mdmx Deposited 2007-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Q
15–29（15 aa）
Fragment：TRANSACTIVATION DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；280 K；30% PEG 300, 0.1M MES pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K
|
Resolution 2.30 Å R-free 0.310 |
| 2Z5S Molecular basis for the inhibition of p53 by Mdmx Deposited 2007-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain R
15–29（15 aa）
Fragment：TRANSACTIVATION DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；280 K；30% PEG 300, 0.1M MES pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K
|
Resolution 2.30 Å R-free 0.310 |
| 2Z5T Molecular basis for the inhibition of p53 by Mdmx Deposited 2007-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
15–29（15 aa）
Fragment：TRANSACTIVATION DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；280 K；30% PEG 300, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K
|
Resolution 2.30 Å R-free 0.264 |
| 2Z5T Molecular basis for the inhibition of p53 by Mdmx Deposited 2007-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Q
15–29（15 aa）
Fragment：TRANSACTIVATION DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；280 K；30% PEG 300, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K
|
Resolution 2.30 Å R-free 0.264 |
| 2Z5T Molecular basis for the inhibition of p53 by Mdmx Deposited 2007-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain R
15–29（15 aa）
Fragment：TRANSACTIVATION DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；280 K；30% PEG 300, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K
|
Resolution 2.30 Å R-free 0.264 |
| 3D05 Human p53 core domain with hot spot mutation R249S (II) Deposited 2008-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
Fragment：p53 Core Domain, UNP residues 94-293
|
Mutation：R249S | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.2M Sodium Acetate, 20% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.264 |
| 3D06 Human p53 core domain with hot spot mutation R249S (I) Deposited 2008-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
Fragment：p53 Core Domain, UNP residues 94-293
|
Mutation：R249S | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.15M Sodium acetate, 20% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.20 Å R-free 0.202 |
| 3D07 Human p53 core domain with hot spot mutation R249S (III) Deposited 2008-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
Fragment：p53 Core Domain, UNP residues 94-293
|
Mutation：R249S | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.2M Sodium Acetate, 20% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.20 Å R-free 0.256 |
| 3D07 Human p53 core domain with hot spot mutation R249S (III) Deposited 2008-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–293（200 aa）
Fragment：p53 Core Domain, UNP residues 94-293
|
Mutation：R249S | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.2M Sodium Acetate, 20% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.20 Å R-free 0.256 |
| 3D08 Human p53 core domain with hot spot mutation R249S and second-site suppressor mutation H168R Deposited 2008-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
Fragment：p53 Core Domain, UNP residues 94-293
|
Mutation：R249S, H168R | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.2M Sodium acetate, 20% PEG3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.40 Å R-free 0.212 |
| 3D09 Human p53 core domain with hot spot mutation R249S and second-site suppressor mutations H168R and T123A Deposited 2008-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
Fragment：p53 Core Domain, UNP residues 94-293
|
Mutation：R249S, H168R, T123A | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.2M Sodium Acetate, 20% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.262 |
| 3D0A Human p53 core domain with hot spot mutation R249S and second site suppressor mutation H168R in sequence-specific complex with DNA Deposited 2008-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
94–293（200 aa）
Fragment：P53 core domain, UNP residues 94-293
Chain B
94–293（200 aa）
Fragment：P53 core domain, UNP residues 94-293
|
Mutation：R249S, H168R Mutation：R249S, H168R | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.2 M ammonium formate, 20% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.241 |
| 3D0A Human p53 core domain with hot spot mutation R249S and second site suppressor mutation H168R in sequence-specific complex with DNA Deposited 2008-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain C
94–293（200 aa）
Fragment：P53 core domain, UNP residues 94-293
Chain D
94–293（200 aa）
Fragment：P53 core domain, UNP residues 94-293
|
Mutation：R249S, H168R Mutation：R249S, H168R | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.2 M ammonium formate, 20% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.241 |
| 3DAB Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain Deposited 2008-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
15–29（15 aa）
Fragment：UNP residues 15-29
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；25% PEG3350, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
|
Resolution 1.90 Å R-free 0.257 |
| 3DAB Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain Deposited 2008-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
15–29（15 aa）
Fragment：UNP residues 15-29
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；25% PEG3350, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
|
Resolution 1.90 Å R-free 0.257 |
| 3DAB Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain Deposited 2008-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
15–29（15 aa）
Fragment：UNP residues 15-29
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；25% PEG3350, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
|
Resolution 1.90 Å R-free 0.257 |
| 3DAB Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain Deposited 2008-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
15–29（15 aa）
Fragment：UNP residues 15-29
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；25% PEG3350, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
|
Resolution 1.90 Å R-free 0.257 |
| 3DAC Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain Deposited 2008-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
17–37（21 aa）
Fragment：UNP residues 17-37
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；30% PEG300, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP
|
Resolution 1.80 Å R-free 0.243 |
| 3DAC Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain Deposited 2008-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
17–37（21 aa）
Fragment：UNP residues 17-37
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；30% PEG300, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP
|
Resolution 1.80 Å R-free 0.243 |
| 3IGK Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 2) Deposited 2009-07-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
94–293（200 aa）
Fragment：P53 core domain, unp residues 94-293
|
Mutation：H168R, R249S | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.16M SODIUM ACETATE, 16% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.214 |
| 3IGL Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 1) Deposited 2009-07-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
94–293（200 aa）
Fragment：P53 core domain, unp residues 94-293
|
Not recorded | ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.16M SODIUM ACETATE, 16% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.212 |
| 3KMD Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer Deposited 2009-11-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
92–291（200 aa）
Fragment：UNP residues 92-291, DNA binding domain
Chain B
92–291（200 aa）
Fragment：UNP residues 92-291, DNA binding domain
Chain C
92–291（200 aa）
Fragment：UNP residues 92-291, DNA binding domain
Chain D
92–291（200 aa）
Fragment：UNP residues 92-291, DNA binding domain
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
hanging drop；pH 6.68；291 K；16% PEG 4000, 142mM Nacl, pH 6.68, hanging drop, temperature 291K
|
Resolution 2.15 Å R-free 0.239 |
| 3KZ8 Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 3) Deposited 2009-12-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
94–293（200 aa）
Fragment：P53 core domain, UNP residues 94-293
Chain B
94–293（200 aa）
Fragment：P53 core domain, UNP residues 94-293
|
Not recorded | ZN ZINC ION × 4 IOD IODIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.20M AMMONIUM IODIDE, 20% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.91 Å R-free 0.266 |
| 3LW1 Binary complex of 14-3-3 sigma and p53 pT387-peptide Deposited 2010-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
385–393（9 aa）
Fragment：UNP residues 385-393
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 6 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M HEPES, 0.2M calcium chloride, 28% PEG 400, 5% glycerol, 2mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.28 Å R-free 0.151 |
| 3PDH Structure of Sir2Tm bound to a propionylated peptide Deposited 2010-10-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
372–389（18 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；Crystals were obtained from 1:1 mix of protein and the well solution (9.5% (w/v) PEG3350, 100 mM CHES buffer), pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.210 |
| 3Q01 An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity Deposited 2010-12-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
94–291（198 aa）
Fragment：p53 DNA-binding (Res 94-291) and Oligomerization (Res 322-356) domains
Chain A
322–356（35 aa）
Fragment：p53 DNA-binding (Res 94-291) and Oligomerization (Res 322-356) domains
Chain B
94–291（198 aa）
Fragment：p53 DNA-binding (Res 94-291) and Oligomerization (Res 322-356) domains
Chain B
322–356（35 aa）
Fragment：p53 DNA-binding (Res 94-291) and Oligomerization (Res 322-356) domains
|
Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322T, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322T, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322T, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322T, L323M, M340Q, L344R, G356T | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2M ammonium acetate, 0.1M HEPES, pH 7.5, 45% v/v 2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.10 Å R-free 0.282 |
| 3Q05 An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity Deposited 2010-12-15 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
94–291（198 aa）
Fragment：p53 DNA-binding (Res 94-291) and Oligomerization (Res 321-356) domains
Chain A
321–356（36 aa）
Fragment：p53 DNA-binding (Res 94-291) and Oligomerization (Res 321-356) domains
Chain B
94–291（198 aa）
Fragment：p53 DNA-binding (Res 94-291) and Oligomerization (Res 321-356) domains
Chain B
321–356（36 aa）
Fragment：p53 DNA-binding (Res 94-291) and Oligomerization (Res 321-356) domains
Chain C
94–291（198 aa）
Fragment：p53 DNA-binding (Res 94-291) and Oligomerization (Res 321-356) domains
Chain C
321–356（36 aa）
Fragment：p53 DNA-binding (Res 94-291) and Oligomerization (Res 321-356) domains
Chain D
94–291（198 aa）
Fragment：p53 DNA-binding (Res 94-291) and Oligomerization (Res 321-356) domains
Chain D
321–356（36 aa）
Fragment：p53 DNA-binding (Res 94-291) and Oligomerization (Res 321-356) domains
|
Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322A, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322A, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322A, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322A, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322A, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322A, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322A, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322A, L323M, M340Q, L344R, G356T | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.15M DL-Malic Acid [pH 7.0], 20% Polyethylene Glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.40 Å R-free 0.267 |
| 3Q06 An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity Deposited 2010-12-15 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
96–292（197 aa）
Fragment：p53 DNA-binding (Res 96-292) and Oligomerization (Res 321-356) domains
Chain A
321–354（34 aa）
Fragment：p53 DNA-binding (Res 96-292) and Oligomerization (Res 321-356) domains
Chain B
96–292（197 aa）
Fragment：p53 DNA-binding (Res 96-292) and Oligomerization (Res 321-356) domains
Chain B
321–354（34 aa）
Fragment：p53 DNA-binding (Res 96-292) and Oligomerization (Res 321-356) domains
Chain C
96–292（197 aa）
Fragment：p53 DNA-binding (Res 96-292) and Oligomerization (Res 321-356) domains
Chain C
321–354（34 aa）
Fragment：p53 DNA-binding (Res 96-292) and Oligomerization (Res 321-356) domains
Chain D
96–292（197 aa）
Fragment：p53 DNA-binding (Res 96-292) and Oligomerization (Res 321-356) domains
Chain D
321–354（34 aa）
Fragment：p53 DNA-binding (Res 96-292) and Oligomerization (Res 321-356) domains
|
Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, M340Q, L344R, G356T | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.15M DL-Malic Acid pH 7.0, 20% Polyethylene Glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.20 Å R-free 0.314 |
| 3SAK HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR (SAC STRUCTURES) Deposited 1999-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
319–360（42 aa）
Fragment：OLIGOMERIZATION DOMAIN, RESIDUES 319 - 360
Chain B
319–360（42 aa）
Fragment：OLIGOMERIZATION DOMAIN, RESIDUES 319 - 360
Chain C
319–360（42 aa）
Fragment：OLIGOMERIZATION DOMAIN, RESIDUES 319 - 360
Chain D
319–360（42 aa）
Fragment：OLIGOMERIZATION DOMAIN, RESIDUES 319 - 360
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
308 K
|
Resolution not provided |
| 3TG5 Structure of SMYD2 in complex with p53 and SAH Deposited 2011-08-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
365–375（11 aa）
Fragment：UNP residues 365-375
|
Not recorded | GOL GLYCEROL × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；0.1M Hepes (pH 7.5), 25% PEG 3350, VAPOR DIFFUSION, temperature 293K
|
Resolution 2.30 Å R-free 0.263 |
| 3TS8 Crystal structure of a multidomain human p53 tetramer bound to the natural CDKN1A(p21) p53-response element Deposited 2011-09-12 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
94–291（198 aa）
Fragment：p53 DNA-binding (UNP residues 94-291) and Oligomerization (UNP residues 321-356) domains
Chain A
321–356（36 aa）
Fragment：p53 DNA-binding (UNP residues 94-291) and Oligomerization (UNP residues 321-356) domains
Chain B
94–291（198 aa）
Fragment：p53 DNA-binding (UNP residues 94-291) and Oligomerization (UNP residues 321-356) domains
Chain B
321–356（36 aa）
Fragment：p53 DNA-binding (UNP residues 94-291) and Oligomerization (UNP residues 321-356) domains
Chain C
94–291（198 aa）
Fragment：p53 DNA-binding (UNP residues 94-291) and Oligomerization (UNP residues 321-356) domains
Chain C
321–356（36 aa）
Fragment：p53 DNA-binding (UNP residues 94-291) and Oligomerization (UNP residues 321-356) domains
Chain D
94–291（198 aa）
Fragment：p53 DNA-binding (UNP residues 94-291) and Oligomerization (UNP residues 321-356) domains
Chain D
321–356（36 aa）
Fragment：p53 DNA-binding (UNP residues 94-291) and Oligomerization (UNP residues 321-356) domains
|
Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322t, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322t, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322t, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322t, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322t, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322t, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322t, L323M, M340Q, L344R, G356T Mutation：C135V, C141V, W146Y, C182S, V203A, R209P, C229Y, H233Y, Y234F, N235K, Y236F, T253V, N268D, P322t, L323M, M340Q, L344R, G356T | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.2 M potassium tartrate tetrahydrate, 20% Polyethylene Glycol 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.283 |
| 3ZME Structure of the p53 core domain mutant Y220C bound to the small molecule PhiKan7242 Deposited 2013-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：Y220C | ZN ZINC ION × 1 QC5 2-(4-(4-fluorophenyl)-5-(1H-pyrrol-1-yl)-1H-pyrazol-1-yl)-N,N-dimethylethanamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；294 K；CRYSTALLIZATION CONDITIONS: SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 40 MM COMPOUND (PK7204) IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL. SOAKING TIME: 3 HOURS.
|
Resolution 1.35 Å R-free 0.175 |
| 3ZME Structure of the p53 core domain mutant Y220C bound to the small molecule PhiKan7242 Deposited 2013-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：Y220C | ZN ZINC ION × 1 QC5 2-(4-(4-fluorophenyl)-5-(1H-pyrrol-1-yl)-1H-pyrazol-1-yl)-N,N-dimethylethanamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；294 K；CRYSTALLIZATION CONDITIONS: SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 40 MM COMPOUND (PK7204) IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL. SOAKING TIME: 3 HOURS.
|
Resolution 1.35 Å R-free 0.175 |
| 4AGL Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan784 Deposited 2012-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | P84 2,4-BIS(IODANYL)-6-[[METHYL-(1-METHYLPIPERIDIN-4-YL)AMINO]METHYL]PHENOL × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.70 Å R-free 0.193 |
| 4AGL Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan784 Deposited 2012-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | P84 2,4-BIS(IODANYL)-6-[[METHYL-(1-METHYLPIPERIDIN-4-YL)AMINO]METHYL]PHENOL × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.70 Å R-free 0.193 |
| 4AGM Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan5086 Deposited 2012-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | P86 2-{[4-(DIETHYLAMINO)PIPERIDIN-1-YL]METHYL}-4,6-DIIODOPHENOL × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.52 Å R-free 0.197 |
| 4AGM Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan5086 Deposited 2012-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | P86 2-{[4-(DIETHYLAMINO)PIPERIDIN-1-YL]METHYL}-4,6-DIIODOPHENOL × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.52 Å R-free 0.197 |
| 4AGN Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan5116 Deposited 2012-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 NXG 2-{[4-(DIETHYLAMINO)PIPERIDIN-1-YL]METHYL}-4-(3-HYDROXYPROP-1-YN-1-YL)-6-IODOPHENOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.60 Å R-free 0.194 |
| 4AGN Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan5116 Deposited 2012-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 NXG 2-{[4-(DIETHYLAMINO)PIPERIDIN-1-YL]METHYL}-4-(3-HYDROXYPROP-1-YN-1-YL)-6-IODOPHENOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.60 Å R-free 0.194 |
| 4AGO Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan5174 Deposited 2012-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | P74 TERT-BUTYL [3-(3-{[4-(DIETHYLAMINO)PIPERIDIN-1-YL]METHYL}-4-HYDROXY-5-IODOPHENYL)PROP-2-YN-1-YL]CARBAMATE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.45 Å R-free 0.217 |
| 4AGO Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan5174 Deposited 2012-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | P74 TERT-BUTYL [3-(3-{[4-(DIETHYLAMINO)PIPERIDIN-1-YL]METHYL}-4-HYDROXY-5-IODOPHENYL)PROP-2-YN-1-YL]CARBAMATE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.45 Å R-free 0.217 |
| 4AGP Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan5176 Deposited 2012-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | P51 2-{[4-(diethylamino)piperidin-1-yl]methyl}-6-iodo-4-(3-phenoxyprop-1-yn-1-yl)phenol × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.50 Å R-free 0.187 |
| 4AGP Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan5176 Deposited 2012-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | P51 2-{[4-(diethylamino)piperidin-1-yl]methyl}-6-iodo-4-(3-phenoxyprop-1-yn-1-yl)phenol × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.50 Å R-free 0.187 |
| 4AGQ Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan5196 Deposited 2012-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | P96 2-{[4-(diethylamino)piperidin-1-yl]methyl}-6-iodo-4-[3-(phenylamino)prop-1-yn-1-yl]phenol × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 13 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.42 Å R-free 0.192 |
| 4AGQ Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan5196 Deposited 2012-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | P96 2-{[4-(diethylamino)piperidin-1-yl]methyl}-6-iodo-4-[3-(phenylamino)prop-1-yn-1-yl]phenol × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 13 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.42 Å R-free 0.192 |
| 4BUZ SIR2 COMPLEX STRUCTURE MIXTURE OF EX-527 INHIBITOR AND REACTION PRODUCTS OR OF REACTION SUBSTRATES P53 PEPTIDE AND NAD Deposited 2013-06-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
379–386（8 aa）
Fragment：RESIDUES 379-386
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；8.5
|
Resolution 1.90 Å R-free 0.194 |
| 4BV2 CRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH THE INHIBITOR EX-527, 2'-O-ACETYL-ADP-RIBOSE AND DEACETYLATED P53-PEPTIDE Deposited 2013-06-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain H
376–388（13 aa）
Fragment：RESIDUES 380-384
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；20% PEG 6000, 0.1 M BIS-TRIS PH5.9
|
Resolution 3.30 Å R-free 0.318 |
| 4BV2 CRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH THE INHIBITOR EX-527, 2'-O-ACETYL-ADP-RIBOSE AND DEACETYLATED P53-PEPTIDE Deposited 2013-06-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
376–388（13 aa）
Fragment：RESIDUES 380-384
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；20% PEG 6000, 0.1 M BIS-TRIS PH5.9
|
Resolution 3.30 Å R-free 0.318 |
| 4BV2 CRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH THE INHIBITOR EX-527, 2'-O-ACETYL-ADP-RIBOSE AND DEACETYLATED P53-PEPTIDE Deposited 2013-06-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
376–388（13 aa）
Fragment：RESIDUES 380-384
|
Not recorded | ZN ZINC ION × 1 OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；20% PEG 6000, 0.1 M BIS-TRIS PH5.9
|
Resolution 3.30 Å R-free 0.318 |
| 4BV2 CRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH THE INHIBITOR EX-527, 2'-O-ACETYL-ADP-RIBOSE AND DEACETYLATED P53-PEPTIDE Deposited 2013-06-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
376–388（13 aa）
Fragment：RESIDUES 380-384
|
Not recorded | ZN ZINC ION × 1 OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；20% PEG 6000, 0.1 M BIS-TRIS PH5.9
|
Resolution 3.30 Å R-free 0.318 |
| 4FZ3 Crystal structure of SIRT3 in complex with acetyl p53 peptide coupled with 4-amino-7-methylcoumarin Deposited 2012-07-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
379–382（4 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.85M HEPES-NA, 8.5%(V/V) ISO-PROPANOL, 17%(W/V) PEG4000, 15%(V/V) GLYCEROL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
|
Resolution 2.10 Å R-free 0.282 |
| 4HFZ Crystal Structure of an MDM2/P53 Peptide Complex Deposited 2012-10-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
15–29（15 aa）
Fragment：residues 15-29
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.2 M (NH4)2SO4, pH 4.6 and 30% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.69 Å R-free 0.247 |
| 4HFZ Crystal Structure of an MDM2/P53 Peptide Complex Deposited 2012-10-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
15–29（15 aa）
Fragment：residues 15-29
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.2 M (NH4)2SO4, pH 4.6 and 30% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.69 Å R-free 0.247 |
| 4HJE Crystal structure of p53 core domain in complex with DNA Deposited 2012-10-12 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
92–291（200 aa）
Fragment：UNP residues 92-291
Chain B
92–291（200 aa）
Fragment：UNP residues 92-291
Chain C
92–291（200 aa）
Fragment：UNP residues 92-291
Chain D
92–291（200 aa）
Fragment：UNP residues 92-291
|
Not recorded | ZN ZINC ION × 4 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.91 Å R-free 0.228 |
| 4IBQ Human p53 core domain with hot spot mutation R273C Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273C | ZN ZINC ION × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；20% PEG 3350, 0.1M K-Acetate, 0.1M KF, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.80 Å R-free 0.163 |
| 4IBQ Human p53 core domain with hot spot mutation R273C Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273C | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；20% PEG 3350, 0.1M K-Acetate, 0.1M KF, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.80 Å R-free 0.163 |
| 4IBQ Human p53 core domain with hot spot mutation R273C Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273C | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；20% PEG 3350, 0.1M K-Acetate, 0.1M KF, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.80 Å R-free 0.163 |
| 4IBQ Human p53 core domain with hot spot mutation R273C Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273C | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；20% PEG 3350, 0.1M K-Acetate, 0.1M KF, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.80 Å R-free 0.163 |
| 4IBS Human p53 core domain with hot spot mutation R273H (form I) Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273H | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；12% PEG 3350, 0.12M Mg-Formate, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.78 Å R-free 0.181 |
| 4IBS Human p53 core domain with hot spot mutation R273H (form I) Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273H | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；12% PEG 3350, 0.12M Mg-Formate, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.78 Å R-free 0.181 |
| 4IBS Human p53 core domain with hot spot mutation R273H (form I) Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273H | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；12% PEG 3350, 0.12M Mg-Formate, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.78 Å R-free 0.181 |
| 4IBS Human p53 core domain with hot spot mutation R273H (form I) Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273H | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；12% PEG 3350, 0.12M Mg-Formate, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.78 Å R-free 0.181 |
| 4IBT Human p53 core domain with hot spot mutation R273H and second-site suppressor mutation T284R Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273H, T284R | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；20% PEG 3350, 0.2M NaF, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.70 Å R-free 0.182 |
| 4IBT Human p53 core domain with hot spot mutation R273H and second-site suppressor mutation T284R Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273H, T284R | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；20% PEG 3350, 0.2M NaF, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.70 Å R-free 0.182 |
| 4IBT Human p53 core domain with hot spot mutation R273H and second-site suppressor mutation T284R Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273H, T284R | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；20% PEG 3350, 0.2M NaF, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.70 Å R-free 0.182 |
| 4IBT Human p53 core domain with hot spot mutation R273H and second-site suppressor mutation T284R Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273H, T284R | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；20% PEG 3350, 0.2M NaF, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.70 Å R-free 0.182 |
| 4IBU Human p53 core domain with hot spot mutation R273C and second-site suppressor mutation T284R in sequence-specific complex with DNA Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: octameric |
Chain A
94–293（200 aa）
Fragment：DNA binding domain
Chain B
94–293（200 aa）
Fragment：DNA binding domain
Chain C
94–293（200 aa）
Fragment：DNA binding domain
Chain D
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273C, T284R Mutation：R273C, T284R Mutation：R273C, T284R Mutation：R273C, T284R | ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 16 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；1:2 PROTEIN/DNA RATIO, 14% PEG 3350, 0.14M Li-Acetate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.197 |
| 4IBV Human p53 core domain with hot spot mutation R273C and second-site suppressor mutation S240R in sequence-specific complex with DNA Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273C, S240R | EDO 1,2-ETHANEDIOL × 14 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；1:2.4 PROTEIN/DNA RATIO, 16% PEG 3350, 0.18M NH4F, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.229 |
| 4IBW Human p53 core domain with hot spot mutation R273H and second-site suppressor mutation T284R in sequence-specific complex with DNA Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273H, T284R | ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 34 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；1:2.4 PROTEIN/DNA RATIO, 14% PEG 3350, 0.14M NH4F, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.79 Å R-free 0.188 |
| 4IBY Human p53 core domain with hot spot mutation R273H and second-site suppressor mutation S240R Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273H, S240R | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；20% PEG 3350, 0.2M Na2HPO4, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.45 Å R-free 0.200 |
| 4IBY Human p53 core domain with hot spot mutation R273H and second-site suppressor mutation S240R Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273H, S240R | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；20% PEG 3350, 0.2M Na2HPO4, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.45 Å R-free 0.200 |
| 4IBZ Human p53 core domain with hot spot mutation R273C and second-site suppressor mutation T284R Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273C, T284R | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；12% PEG 3350, 0.12M NH4-Acetate, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.92 Å R-free 0.233 |
| 4IBZ Human p53 core domain with hot spot mutation R273C and second-site suppressor mutation T284R Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273C, T284R | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 5 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；12% PEG 3350, 0.12M NH4-Acetate, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.92 Å R-free 0.233 |
| 4IBZ Human p53 core domain with hot spot mutation R273C and second-site suppressor mutation T284R Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273C, T284R | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；12% PEG 3350, 0.12M NH4-Acetate, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.92 Å R-free 0.233 |
| 4IBZ Human p53 core domain with hot spot mutation R273C and second-site suppressor mutation T284R Deposited 2012-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273C, T284R | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 6 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；12% PEG 3350, 0.12M NH4-Acetate, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.92 Å R-free 0.233 |
| 4IJT Human p53 core domain with hot spot mutation R273H (form II) Deposited 2012-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
Fragment：DNA binding domain
|
Mutation：R273H | ZN ZINC ION × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；1:1.5 PROTEIN/DNA RATIO, 20% PEG 3350, 0.2M KCl, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.78 Å R-free 0.194 |
| 4KVP Human p53 Core Domain Mutant V157F Deposited 2013-05-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：p53 Core Domain
|
Mutation：V157F | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；2 microliter protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliter reservoir buffer (25% (w/v) polyethylene glycol (PEG) 2000 monomethyl ether (MME)), pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.50 Å R-free 0.210 |
| 4KVP Human p53 Core Domain Mutant V157F Deposited 2013-05-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：p53 Core Domain
|
Mutation：V157F | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；2 microliter protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliter reservoir buffer (25% (w/v) polyethylene glycol (PEG) 2000 monomethyl ether (MME)), pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.50 Å R-free 0.210 |
| 4KVP Human p53 Core Domain Mutant V157F Deposited 2013-05-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
94–312（219 aa）
Fragment：p53 Core Domain
|
Mutation：V157F | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；2 microliter protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliter reservoir buffer (25% (w/v) polyethylene glycol (PEG) 2000 monomethyl ether (MME)), pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.50 Å R-free 0.210 |
| 4KVP Human p53 Core Domain Mutant V157F Deposited 2013-05-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
94–312（219 aa）
Fragment：p53 Core Domain
|
Mutation：V157F | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；2 microliter protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliter reservoir buffer (25% (w/v) polyethylene glycol (PEG) 2000 monomethyl ether (MME)), pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.50 Å R-free 0.210 |
| 4LO9 Human p53 Core Domain Mutant N235K Deposited 2013-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：p53 Core Domain (UNP residues 94-312)
|
Mutation：N235K | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；2 microliter protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliter reservoir buffer(100 mM HEPES, 30 % (w/v) polyethylene glycol (PEG) 6000, pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.50 Å R-free 0.247 |
| 4LO9 Human p53 Core Domain Mutant N235K Deposited 2013-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：p53 Core Domain (UNP residues 94-312)
|
Mutation：N235K | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；2 microliter protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliter reservoir buffer(100 mM HEPES, 30 % (w/v) polyethylene glycol (PEG) 6000, pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.50 Å R-free 0.247 |
| 4LO9 Human p53 Core Domain Mutant N235K Deposited 2013-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
94–312（219 aa）
Fragment：p53 Core Domain (UNP residues 94-312)
|
Mutation：N235K | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；2 microliter protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliter reservoir buffer(100 mM HEPES, 30 % (w/v) polyethylene glycol (PEG) 6000, pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.50 Å R-free 0.247 |
| 4LO9 Human p53 Core Domain Mutant N235K Deposited 2013-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
94–312（219 aa）
Fragment：p53 Core Domain (UNP residues 94-312)
|
Mutation：N235K | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；2 microliter protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliter reservoir buffer(100 mM HEPES, 30 % (w/v) polyethylene glycol (PEG) 6000, pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.50 Å R-free 0.247 |
| 4LOE Human p53 Core Domain Mutant N239Y Deposited 2013-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：p53 Core Domain (UNP residues 94-312)
|
Mutation：N239Y | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.6；277 K；2 microliter protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliter reservoir buffer(200 mM lithium acetate, 20% (w/v) PEG 3350), VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.85 Å R-free 0.244 |
| 4LOE Human p53 Core Domain Mutant N239Y Deposited 2013-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：p53 Core Domain (UNP residues 94-312)
|
Mutation：N239Y | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.6；277 K；2 microliter protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliter reservoir buffer(200 mM lithium acetate, 20% (w/v) PEG 3350), VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.85 Å R-free 0.244 |
| 4LOE Human p53 Core Domain Mutant N239Y Deposited 2013-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
94–312（219 aa）
Fragment：p53 Core Domain (UNP residues 94-312)
|
Mutation：N239Y | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.6；277 K；2 microliter protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliter reservoir buffer(200 mM lithium acetate, 20% (w/v) PEG 3350), VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.85 Å R-free 0.244 |
| 4LOE Human p53 Core Domain Mutant N239Y Deposited 2013-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
94–312（219 aa）
Fragment：p53 Core Domain (UNP residues 94-312)
|
Mutation：N239Y | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.6；277 K；2 microliter protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliter reservoir buffer(200 mM lithium acetate, 20% (w/v) PEG 3350), VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.85 Å R-free 0.244 |
| 4LOF Human p53 Core Domain Mutant V157F/N235K/N239Y Deposited 2013-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：p53 Core Domain (UNP residues 94-312)
|
Mutation：V157F, N235K, N239Y | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.6；2 microliters protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliters reservoir buffer with 200 mM di-sodium hydrogen phosphate dehydrate (Na2HPO4), 20% (w/v) PEG 3350, VAPOR DIFFUSION
|
Resolution 2.00 Å R-free 0.256 |
| 4MZI Crystal structure of a human mutant p53 Deposited 2013-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–292（199 aa）
Fragment：UNP residues 94-292
|
Mutation：S121F, V122G | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；278 K；pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K
|
Resolution 1.25 Å R-free 0.201 |
| 4MZR Crystal structure of a polypeptide p53 mutant bound to DNA Deposited 2013-09-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
94–358（265 aa）
Fragment：UNP residues 94-358
Chain B
94–358（265 aa）
Fragment：UNP residues 94-358
Chain C
94–358（265 aa）
Fragment：UNP residues 94-358
Chain D
94–358（265 aa）
Fragment：UNP residues 94-358
|
Mutation：S121F, V122G Mutation：S121F, V122G Mutation：S121F, V122G Mutation：S121F, V122G | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；278 K；0.2M potassium sodium tartrate tetrahydrate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K
|
Resolution 2.90 Å R-free 0.281 |
| 4QO1 p53 DNA binding domain in complex with Nb139 Deposited 2014-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
92–312（221 aa）
Fragment：p53DBD, unp residues 92-312
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Crystals of the complex were obtained at 293K using the hanging-drop vapour diffusion method after mixing 1:l protein solution with 1:l reservoir solution equilibrated against 125 ul 0.2 M potassium formate 20% w/v PEG 3350 reservoir solution, pH 6.5, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.92 Å R-free 0.205 |
| 4RP6 Structure of the amyloid-forming segment LTIITLE from p53 (residues 252-258) Deposited 2014-10-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain Z
252–258（7 aa）
Fragment：UNP residues 252-258
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；reservoir contained 0.1 M Tris buffer pH 8.5 and 20% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.70 Å R-free 0.192 |
| 4RP7 Structure of the amyloid-forming segment TIITLE from p53 (residues 253-258) Deposited 2014-10-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain Z
253–258（6 aa）
Fragment：UNP residues 253-258
|
Not recorded | ZN ZINC ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；reservoir contained 0.01 M zinc
chloride, 0.1 M MES buffer pH 6, and 20% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.58 Å R-free 0.193 |
| 4XR8 Crystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.25 A resolution Deposited 2015-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
55–253（199 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 2 ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；7.5 % PEG 20K, 0.05 M MES pH 6.5
|
Resolution 2.25 Å R-free 0.246 |
| 4XR8 Crystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.25 A resolution Deposited 2015-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
55–253（199 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 2 ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；7.5 % PEG 20K, 0.05 M MES pH 6.5
|
Resolution 2.25 Å R-free 0.246 |
| 5A7B Structure of the p53 cancer Y220C bound to the stabilizing small molecule PhiKan5211 Deposited 2015-07-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 KMN 2-[[4-(diethylamino)piperidin-1-yl]methyl]-6-ethynyl-4-(3-phenoxyprop-1-ynyl)phenol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；CRYSTALLIZATION CONDITIONS: SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.40 Å R-free 0.192 |
| 5A7B Structure of the p53 cancer Y220C bound to the stabilizing small molecule PhiKan5211 Deposited 2015-07-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 KMN 2-[[4-(diethylamino)piperidin-1-yl]methyl]-6-ethynyl-4-(3-phenoxyprop-1-ynyl)phenol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；CRYSTALLIZATION CONDITIONS: SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.40 Å R-free 0.192 |
| 5AB9 Structure of the p53 cancer mutant Y220C with bound small molecule 7- ethyl-3-(piperidin-4-yl)-1H-indole Deposited 2015-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 92O 7-ethyl-3-(piperidin-4-yl)-1H-indole × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 40 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.36 Å R-free 0.166 |
| 5AB9 Structure of the p53 cancer mutant Y220C with bound small molecule 7- ethyl-3-(piperidin-4-yl)-1H-indole Deposited 2015-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 92O 7-ethyl-3-(piperidin-4-yl)-1H-indole × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 40 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.36 Å R-free 0.166 |
| 5ABA Structure of the p53 cancer mutant Y220C with bound small-molecule stabilizer PhiKan5149 Deposited 2015-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 UL7 1-{1-[(3-bromo-5-chloro-2-hydroxyphenyl)methyl piperidin-4-yl}piperidin-4-ol] × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.62 Å R-free 0.203 |
| 5ABA Structure of the p53 cancer mutant Y220C with bound small-molecule stabilizer PhiKan5149 Deposited 2015-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 UL7 1-{1-[(3-bromo-5-chloro-2-hydroxyphenyl)methyl piperidin-4-yl}piperidin-4-ol] × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.62 Å R-free 0.203 |
| 5AOI Structure of the p53 cancer mutant Y220C in complex with an indole- based small molecule Deposited 2015-09-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.78 Å R-free 0.206 |
| 5AOI Structure of the p53 cancer mutant Y220C in complex with an indole- based small molecule Deposited 2015-09-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 RZH 2-(5-BROMO-7-ETHYL-2-METHYL-1H-INDOLE-3-YL)ETHAN-1-AMIN × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.78 Å R-free 0.206 |
| 5AOJ Structure of the p53 cancer mutant Y220C in complex with 2-hydroxy-3, 5-diiodo-4-(1H-pyrrol-1-yl)benzoic acid Deposited 2015-09-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | Y0V 2-hydroxy-3,5-diiodo-4-(1H-pyrrol-1-yl)benzoic acid × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 23 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.47 Å R-free 0.178 |
| 5AOJ Structure of the p53 cancer mutant Y220C in complex with 2-hydroxy-3, 5-diiodo-4-(1H-pyrrol-1-yl)benzoic acid Deposited 2015-09-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | Y0V 2-hydroxy-3,5-diiodo-4-(1H-pyrrol-1-yl)benzoic acid × 1 ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 23 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.47 Å R-free 0.178 |
| 5AOK Structure of the p53 cancer mutant Y220C with bound small molecule PhiKan7099 Deposited 2015-09-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 GOL GLYCEROL × 1 GOH 5-[2-cyclopropyl-5-(1H-pyrrol-1-yl)-1,3-oxazol-4-yl]-1H-1,2,3,4-tetrazole × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 38 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.35 Å R-free 0.169 |
| 5AOK Structure of the p53 cancer mutant Y220C with bound small molecule PhiKan7099 Deposited 2015-09-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 GOL GLYCEROL × 1 GOH 5-[2-cyclopropyl-5-(1H-pyrrol-1-yl)-1,3-oxazol-4-yl]-1H-1,2,3,4-tetrazole × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 38 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.35 Å R-free 0.169 |
| 5AOL Structure of the p53 cancer mutant Y220C with bound 3-bromo-5-(trifluoromethyl)benzene-1,2-diamine Deposited 2015-09-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | UFV 3-BROMO-5-(TRIFLUOROMETHYL)BENZENE-1,2-DIAMINE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.50 Å R-free 0.169 |
| 5AOL Structure of the p53 cancer mutant Y220C with bound 3-bromo-5-(trifluoromethyl)benzene-1,2-diamine Deposited 2015-09-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.50 Å R-free 0.169 |
| 5AOM Structure of the p53 cancer mutant Y220C with bound small molecule PhiKan883 Deposited 2015-09-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | FY8 N-(5-chloranyl-2-oxidanyl-phenyl)piperidine-4-carboxamide × 2 GOL GLYCEROL × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: SATURATED SOLUTION OF COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.74 Å R-free 0.191 |
| 5AOM Structure of the p53 cancer mutant Y220C with bound small molecule PhiKan883 Deposited 2015-09-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | FY8 N-(5-chloranyl-2-oxidanyl-phenyl)piperidine-4-carboxamide × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: SATURATED SOLUTION OF COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.74 Å R-free 0.191 |
| 5BUA Lysine 120-acetylated P53 DNA binding domain in a complex with DNA. Deposited 2015-06-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
94–293（200 aa）
Fragment：P53 DNA binding domain, UNP residues 94-293
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.1；286 K；0.2M Ammonium fluoride; 20% PEG 3350
|
Resolution 1.81 Å R-free 0.213 |
| 5ECG Crystal structure of the BRCT domains of 53BP1 in complex with p53 and H2AX-pSer139 (gammaH2AX) Deposited 2015-10-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
95–312（218 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；200mM NaF, 100mM Bis-Tris Propane pH 6.5, 20% (w/v) PEG 3,350
|
Resolution 3.00 Å R-free 0.264 |
| 5ECG Crystal structure of the BRCT domains of 53BP1 in complex with p53 and H2AX-pSer139 (gammaH2AX) Deposited 2015-10-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
95–312（218 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；200mM NaF, 100mM Bis-Tris Propane pH 6.5, 20% (w/v) PEG 3,350
|
Resolution 3.00 Å R-free 0.264 |
| 5G4M Crystal structure of the p53 cancer mutant Y220C in complex with a monofluorinated derivative of the small molecule stabilizer Phikan083 Deposited 2016-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 O82 1-[9-(2-fluoroethyl)-9H-carbazol-3-yl]-N-methylmethanamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: SATURATED SOLUTION OF COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.38 Å R-free 0.170 |
| 5G4M Crystal structure of the p53 cancer mutant Y220C in complex with a monofluorinated derivative of the small molecule stabilizer Phikan083 Deposited 2016-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 O82 1-[9-(2-fluoroethyl)-9H-carbazol-3-yl]-N-methylmethanamine × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: SATURATED SOLUTION OF COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.38 Å R-free 0.170 |
| 5G4N Crystal structure of the p53 cancer mutant Y220C in complex with a difluorinated derivative of the small molecule stabilizer Phikan083 Deposited 2016-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 O83 1-[9-(2,2-difluoroethyl)-9H-carbazol-3-yl]-N-methylmethanamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: SATURATED SOLUTION OF COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL
|
Resolution 1.35 Å R-free 0.168 |
| 5G4N Crystal structure of the p53 cancer mutant Y220C in complex with a difluorinated derivative of the small molecule stabilizer Phikan083 Deposited 2016-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 O83 1-[9-(2,2-difluoroethyl)-9H-carbazol-3-yl]-N-methylmethanamine × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: SATURATED SOLUTION OF COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL
|
Resolution 1.35 Å R-free 0.168 |
| 5G4O Crystal structure of the p53 cancer mutant Y220C in complex with a trifluorinated derivative of the small molecule stabilizer Phikan083 Deposited 2016-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 O80 N,N-dimethyl-1-[9-(2,2,2-trifluoroethyl)-9H-carbazol-3-yl]methanamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: SATURATED SOLUTION OF COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.48 Å R-free 0.171 |
| 5G4O Crystal structure of the p53 cancer mutant Y220C in complex with a trifluorinated derivative of the small molecule stabilizer Phikan083 Deposited 2016-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-BINDING DOMAIN, RESIDUES 94-312
|
Mutation：YES | ZN ZINC ION × 1 O80 N,N-dimethyl-1-[9-(2,2,2-trifluoroethyl)-9H-carbazol-3-yl]methanamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: SATURATED SOLUTION OF COMPOUND IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.48 Å R-free 0.171 |
| 5HOU Solution Structure of p53TAD-TAZ1 Deposited 2016-01-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–61（61 aa）
Fragment：p53TAD, TAZ1 domain of CBP
|
Not recorded | ZN ZINC ION × 3 |
SOLUTION NMR
NMR measurement conditions
pH 6.8；308 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR measurement conditions
pH 6.4；308 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition
1.0 mM [U-15N] p53TAD - [NA] TAZ1 p53TAD-TAZ1 fusion protein, 20 mM TRIS, 50 mM sodium chloride, 2 mM DTT, 5 % [U-2H] D2O, 95% H2O, 5% D2O | 95% H2O/5% D2O
NMR sample composition
1.0 mM [U-15N][U-13C] p53TAD - [NA] TAZ1 p53TAD-TAZ1 fusion protein, 20 mM [U-2H] TRIS, 50 mM sodium chloride, 2 mM [U-2H] DTT, 99 % [U-2H] D2O, 99% D2O, 1% H2O | 99% D2O, 1% H2O
NMR sample composition
1.0 mM [NA] p53TAD - [U-15N] TAZ1 p53TAD-TAZ1 fusion protein, 20 mM TRIS, 50 mM sodium chloride, 2 mM DTT, 5 % [U-2H] D2O, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
1.0 mM [NA] p53TAD - [U-15N][U-13C] TAZ1 p53TAD-TAZ1 fusion protein, 20 mM [U-2H] TRIS, 50 mM sodium chloride, 2 mM [U-2H] DTT, 99 % [U-2H] D2O, 99% D2O, 1% H2O | 99% D2O, 1% H2O
NMR sample composition
1.0 mM [U-15N][U-13C] p53TAD - [NA] TAZ1 p53TAD-TAZ1 fusion protein, 20 mM TRIS, 50 mM sodium chloride, 2 mM DTT, 5 % [U-2H] D2O, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
1 mM [NA] p53TAD - [U-15N][U-13C] TAZ1 p53TAD-TAZ1 fusion protein, 20 mM TRIS, 50 mM sodium chloride, 2 mM DTT, 5 % [U-2H] D2O, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 5HP0 Solution Structure of TAZ2-p53AD2 Deposited 2016-01-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
37–61（25 aa）
Fragment：p53AD2, TAZ2 domain of CBP
|
Not recorded | ZN ZINC ION × 3 |
SOLUTION NMR
NMR measurement conditions
pH 6.8；305 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR measurement conditions
pH 6.4；305 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition
1 mM [U-13C; U-15N] TAZ2-p53AD2, 20 mM TRIS, 50 mM sodium chloride, 2 mM DTT, 10 % [U-2H] D2O, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1 mM [U-13C; U-15N] TAZ2-p53AD2, 20 mM [U-2H] TRIS, 50 mM sodium chloride, 2 mM [U-2H] DTT, 99 % [U-2H] D2O, 99% D2O, 1% H2O | 99% D2O, 1% H2O
NMR sample composition
1 mM [U-13C; U-15N] TAZ2-p53AD2, 20 mM TRIS, 50 mM sodium chloride, 2 mM DTT, 5 % [U-2H] D2O, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1 mM [U-13C] TAZ2, 1 mM p53AD2(38-61), 20 mM [U-2H] TRIS, 50 mM sodium chloride, 2 mM [U-2H] DTT, 5 % [U-2H] D2O, 99% D2O, 1% H2O | 99% D2O, 1% H2O
NMR sample composition
1 mM [U-13C] p53AD2, 1 mM TAZ2, 20 mM [U-2H] TRIS, 50 mM sodium chloride, 2 mM [U-2H] DTT, 99 % [U-2H] D2O, 99% D2O, 1% H2O | 99% D2O, 1% H2O
|
Resolution not provided |
| 5HPD Solution Structure of TAZ2-p53TAD Deposited 2016-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–61（60 aa）
Fragment：p53TAD, TAZ2 domain of CBP
|
Not recorded | ZN ZINC ION × 3 |
SOLUTION NMR
NMR measurement conditions
pH 6.8；305 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR measurement conditions
pH 6.4；305 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition
1.75 mM [U-13C; U-15N] TAZ2-p53TAD, 20 mM TRIS, 50 mM sodium chloride, 1 mM DTT, 10 % [U-2H] D2O, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1.75 mM [U-13C; U-15N] TAZ2-p53TAD, 20 mM [U-2H] TRIS, 50 mM sodium chloride, 1 mM [U-2H] DTT, 99 % [U-2H] D2O, 99% D2O, 1% H2O | 99% D2O, 1% H2O
NMR sample composition
1 mM [U-13C] TAZ2, 1 mM p53(13-37, 1 mM p53(38-61), 50 mM sodium chloride, 2 mM [U-2H] DTT, 99 % [U-2H] D2O, 20 mM [U-2H] TRIS, 99% D2O, 1% H2O | 99% D2O, 1% H2O
NMR sample composition
1 mM TAZ2, 1 mM [U-13C] p53(13-37), 1 mM [U-13C] p53(38-61), 20 mM [U-2H] TRIS, 50 mM sodium chloride, 2 mM [U-2H] DTT, 99 % [U-2H] D2O, 99% D2O, 1% H2O | 99% D2O, 1% H2O
NMR sample composition
1 mM TAZ2, 1 mM [U-15N] p53(13-61), 20 mM TRIS, 50 mM sodium chloride, 2 mM DTT, 10 % [U-2H] D2O, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1 mM [U-15N] TAZ2, 1 mM p53(13-61), 20 mM TRIS, 50 mM sodium chloride, 2 mM DTT, 10 % [U-2H] D2O, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1 mM TAZ2, 1 mM [U-13C] p53(13-61), 20 mM [U-2H] TRIS, 50 mM sodium chloride, 2 mM [U-2H] DTT, 99 % [U-2H] D2O, 99% D2O, 1% H2O | 99% D2O, 1% H2O
NMR sample composition
1 mM [U-13C] TAZ2, 1 mM p53(13-61), 20 mM [U-2H] TRIS, 50 mM sodium chloride, 2 mM [U-2H] DTT, 99 % [U-2H] D2O, 99% D2O, 1% H2O | 99% D2O, 1% H2O
|
Resolution not provided |
| 5LAP p53 cancer mutant Y220C with Cys182 alkylation Deposited 2016-06-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 6SM 5-chloranylpyrimidine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 mM Phikan11000 IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.42 Å R-free 0.193 |
| 5LAP p53 cancer mutant Y220C with Cys182 alkylation Deposited 2016-06-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 6SM 5-chloranylpyrimidine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 mM Phikan11000 IN 100 MM HEPES, PH 7.2, 10 MM SODIUM PHOSPHATE, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 20 % (V/V) GLYCEROL, 150 MM KCL.
|
Resolution 1.42 Å R-free 0.193 |
| 5LGY Lysine 120-acetylated P53 DNA binding domain in a complex with the BAX response element. Deposited 2016-07-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
94–291（198 aa）
Fragment：UNP residues 94-291
Chain B
94–291（198 aa）
Fragment：UNP residues 94-291
Chain C
94–291（198 aa）
Fragment：UNP residues 94-291
Chain D
94–291（198 aa）
Fragment：UNP residues 94-291
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.1；286 K；0.22 M Ammonium acetate, 10% w/v PEG 3350, tri-Sodium citrate pH 6.1
|
Resolution 2.92 Å R-free 0.277 |
| 5MCT New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-LHG1) Deposited 2016-11-10 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
94–293（200 aa）
Fragment：P53 DNA BINDING DOMAIN
Chain B
94–293（200 aa）
Fragment：P53 DNA BINDING DOMAIN
|
Not recorded | ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 12 FOR FORMYL GROUP × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7；292 K；0.1 M Ammonium citrate, 12% w/v Polyethylene glycol 3,350
|
Resolution 1.45 Å R-free 0.189 |
| 5MCU New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-LHG2) Deposited 2016-11-10 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
94–293（200 aa）
Fragment：P53 DNA BINDING DOMAIN
Chain B
94–293（200 aa）
Fragment：P53 DNA BINDING DOMAIN
|
Not recorded | ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7；292 K；0.05 M HEPES sodium salt, 12% w/v Polyethylene glycol 3,350
|
Resolution 1.70 Å R-free 0.201 |
| 5MCW New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-LWC2) Deposited 2016-11-10 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
94–293（200 aa）
Fragment：P53 DNA BINDING DOMAIN
Chain B
94–293（200 aa）
Fragment：P53 DNA BINDING DOMAIN
|
Not recorded | ZN ZINC ION × 4 FOR FORMYL GROUP × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 8.8；292 K；0.02 M Citric acid, 0.08 M BIS-TRIS propane, 18% w/v Polyethylene glycol 3,350
|
Resolution 1.90 Å R-free 0.235 |
| 5MF7 New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-GADD45) Deposited 2016-11-17 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
55–254（200 aa）
Fragment：P53 DNA BINDING DOMAIN
Chain B
55–254（200 aa）
Fragment：P53 DNA BINDING DOMAIN
|
Not recorded | ZN ZINC ION × 4 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 8；292 K；4% Tacsimate, 12% w/v Polyethylene glycol 3,350
|
Resolution 1.59 Å R-free 0.233 |
| 5MG7 New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-p53R2) Deposited 2016-11-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
94–293（200 aa）
Fragment：P53 DNA Binding Domain, UNP Residues 94-293
Chain B
94–293（200 aa）
Fragment：P53 DNA Binding Domain, UNP Residues 94-293
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7；292 K；0.07 M ammonium tartrate dibasic, 8.4% Polyethylene glycol 3,350
|
Resolution 1.45 Å R-free 0.202 |
| 5O1A p53 cancer mutant Y220C in complex with compound MB240 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9H5 [3,5-bis(iodanyl)-2-oxidanyl-4-pyrrol-1-yl-phenyl]-(4-methylpiperazin-1-yl)methanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.44 Å R-free 0.178 |
| 5O1A p53 cancer mutant Y220C in complex with compound MB240 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9H5 [3,5-bis(iodanyl)-2-oxidanyl-4-pyrrol-1-yl-phenyl]-(4-methylpiperazin-1-yl)methanone × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.44 Å R-free 0.178 |
| 5O1B p53 cancer mutant Y220C in complex with compound MB84 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9H2 6-(hydroxymethyl)-2,4-bis(iodanyl)-3-pyrrol-1-yl-phenol × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.43 Å R-free 0.174 |
| 5O1B p53 cancer mutant Y220C in complex with compound MB84 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9H2 6-(hydroxymethyl)-2,4-bis(iodanyl)-3-pyrrol-1-yl-phenol × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.43 Å R-free 0.174 |
| 5O1C p53 cancer mutant Y220C in complex with compound MB184 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9GZ 5-(4-fluorophenyl)-3-iodanyl-2-oxidanyl-4-pyrrol-1-yl-benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.32 Å R-free 0.172 |
| 5O1C p53 cancer mutant Y220C in complex with compound MB184 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9GZ 5-(4-fluorophenyl)-3-iodanyl-2-oxidanyl-4-pyrrol-1-yl-benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.32 Å R-free 0.172 |
| 5O1D p53 cancer mutant Y220C in complex with compound MB481 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9GW 3-iodanyl-2-oxidanyl-5-propoxy-4-pyrrol-1-yl-benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.36 Å R-free 0.164 |
| 5O1D p53 cancer mutant Y220C in complex with compound MB481 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9GW 3-iodanyl-2-oxidanyl-5-propoxy-4-pyrrol-1-yl-benzoic acid × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.36 Å R-free 0.164 |
| 5O1E p53 cancer mutant Y220C im complex with compound MB577 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9GT 3-iodanyl-2-oxidanyl-5-prop-2-enoxy-4-pyrrol-1-yl-benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.30 Å R-free 0.165 |
| 5O1E p53 cancer mutant Y220C im complex with compound MB577 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9GT 3-iodanyl-2-oxidanyl-5-prop-2-enoxy-4-pyrrol-1-yl-benzoic acid × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.30 Å R-free 0.165 |
| 5O1F p53 cancer mutant Y220C in complex with compound MB582 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9GQ 5-butoxy-3-iodanyl-2-oxidanyl-4-pyrrol-1-yl-benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.38 Å R-free 0.167 |
| 5O1F p53 cancer mutant Y220C in complex with compound MB582 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9GQ 5-butoxy-3-iodanyl-2-oxidanyl-4-pyrrol-1-yl-benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.38 Å R-free 0.167 |
| 5O1G p53 cancer mutant Y220C in complex with compound MB487 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9GK 3-iodanyl-2-oxidanyl-5-(2-phenylethoxy)-4-pyrrol-1-yl-benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.35 Å R-free 0.166 |
| 5O1G p53 cancer mutant Y220C in complex with compound MB487 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9GK 3-iodanyl-2-oxidanyl-5-(2-phenylethoxy)-4-pyrrol-1-yl-benzoic acid × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.35 Å R-free 0.166 |
| 5O1H p53 cancer mutant Y220C in complex with compound MB539 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9GN 3-iodanyl-2-oxidanyl-5-propylsulfanyl-4-pyrrol-1-yl-benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.32 Å R-free 0.160 |
| 5O1H p53 cancer mutant Y220C in complex with compound MB539 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9GN 3-iodanyl-2-oxidanyl-5-propylsulfanyl-4-pyrrol-1-yl-benzoic acid × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 30 mM compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.32 Å R-free 0.160 |
| 5O1I p53 cancer mutant Y220C in complex with compound MB710 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 9GH 2-(diethylamino)-6-iodanyl-5-oxidanyl-7-pyrrol-1-yl-1,3-benzothiazole-4-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.40 Å R-free 0.187 |
| 5O1I p53 cancer mutant Y220C in complex with compound MB710 Deposited 2017-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：UNP residues 94-312
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.40 Å R-free 0.187 |
| 5OL0 Structure of Leishmania infantum Silent Information Regulator 2 related protein 1 (LiSIR2rp1) in complex with acetylated p53 peptide Deposited 2017-07-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
372–389（18 aa）
Fragment：UNP residues 372-389
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；100mM Na Hepes pH7.5; 25% PEG2000 MME
|
Resolution 1.99 Å R-free 0.226 |
| 5OL0 Structure of Leishmania infantum Silent Information Regulator 2 related protein 1 (LiSIR2rp1) in complex with acetylated p53 peptide Deposited 2017-07-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
372–389（18 aa）
Fragment：UNP residues 372-389
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；100mM Na Hepes pH7.5; 25% PEG2000 MME
|
Resolution 1.99 Å R-free 0.226 |
| 5XZC Cryo-EM structure of p300-p53 protein complex Deposited 2017-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain B
92–356（265 aa）
Chain C
92–356（265 aa）
Chain D
92–356（265 aa）
Chain E
92–356（265 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 10.70 Å |
| 6FF9 Mutant R280K of human P53 Deposited 2018-01-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
58–250（193 aa）
|
Mutation：R280K | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；35% PEG 3350
|
Resolution 2.00 Å R-free 0.226 |
| 6FF9 Mutant R280K of human P53 Deposited 2018-01-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
58–250（193 aa）
|
Mutation：R280K | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；35% PEG 3350
|
Resolution 2.00 Å R-free 0.226 |
| 6FF9 Mutant R280K of human P53 Deposited 2018-01-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
58–250（193 aa）
|
Mutation：R280K | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；35% PEG 3350
|
Resolution 2.00 Å R-free 0.226 |
| 6FF9 Mutant R280K of human P53 Deposited 2018-01-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
58–250（193 aa）
|
Mutation：R280K | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；35% PEG 3350
|
Resolution 2.00 Å R-free 0.226 |
| 6FJ5 New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-AGG-HG) Deposited 2018-01-20 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
94–293（200 aa）
Fragment：P53 DNA BINDING DOMAIN, UNP residues 94-293
Chain B
94–293（200 aa）
Fragment：P53 DNA BINDING DOMAIN, UNP residues 94-293
Chain C
94–293（200 aa）
Fragment：P53 DNA BINDING DOMAIN, UNP residues 94-293
Chain D
94–293（200 aa）
Fragment：P53 DNA BINDING DOMAIN, UNP residues 94-293
|
Not recorded | ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7；292 K；0.1 M Sodium formate pH 7.0, 12% w/v Polyethylene glycol 3,350
|
Resolution 2.05 Å R-free 0.244 |
| 6GGA p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9284 Deposited 2018-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | EY2 (7-bromanyl-9-ethyl-carbazol-3-yl)methyl-methyl-azanium × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.55 Å R-free 0.200 |
| 6GGA p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9284 Deposited 2018-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | EY2 (7-bromanyl-9-ethyl-carbazol-3-yl)methyl-methyl-azanium × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.55 Å R-free 0.200 |
| 6GGB p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9318 Deposited 2018-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 EXQ [9-ethyl-7-(4-methylthiophen-2-yl)carbazol-3-yl]methyl-methyl-azanium × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.32 Å R-free 0.161 |
| 6GGB p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9318 Deposited 2018-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 EXQ [9-ethyl-7-(4-methylthiophen-2-yl)carbazol-3-yl]methyl-methyl-azanium × 1 GOL GLYCEROL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.32 Å R-free 0.161 |
| 6GGC p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9320 Deposited 2018-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 EXN [9-ethyl-7-(furan-2-yl)carbazol-3-yl]methyl-methyl-azanium × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.24 Å R-free 0.166 |
| 6GGC p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9320 Deposited 2018-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 EXN [9-ethyl-7-(furan-2-yl)carbazol-3-yl]methyl-methyl-azanium × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.24 Å R-free 0.166 |
| 6GGD p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9324 Deposited 2018-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Mutation：M133L, V203A, Y220C, N239Y, N268D, | ZN ZINC ION × 1 EYB [9-ethyl-7-(1,2-oxazol-4-yl)carbazol-3-yl]methyl-methyl-azanium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.40 Å R-free 0.170 |
| 6GGD p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9324 Deposited 2018-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Mutation：M133L, V203A, Y220C, N239Y, N268D, | ZN ZINC ION × 1 EYB [9-ethyl-7-(1,2-oxazol-4-yl)carbazol-3-yl]methyl-methyl-azanium × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.40 Å R-free 0.170 |
| 6GGE p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9327 Deposited 2018-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Mutation：M133L, V203A, Y220S,N239Y, N268D | ZN ZINC ION × 1 EYE [9-ethyl-7-(5-methylthiophen-2-yl)carbazol-3-yl]methyl-methyl-azanium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.25 Å R-free 0.171 |
| 6GGE p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9327 Deposited 2018-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Mutation：M133L, V203A, Y220S,N239Y, N268D | ZN ZINC ION × 1 EYE [9-ethyl-7-(5-methylthiophen-2-yl)carbazol-3-yl]methyl-methyl-azanium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.25 Å R-free 0.171 |
| 6GGF Structure of the p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9328 Deposited 2018-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 EXQ [9-ethyl-7-(4-methylthiophen-2-yl)carbazol-3-yl]methyl-methyl-azanium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm NaCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm NaCl.
|
Resolution 1.32 Å R-free 0.171 |
| 6GGF Structure of the p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9328 Deposited 2018-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 EXQ [9-ethyl-7-(4-methylthiophen-2-yl)carbazol-3-yl]methyl-methyl-azanium × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm NaCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm NaCl.
|
Resolution 1.32 Å R-free 0.171 |
| 6LHD Crystal structure of p53/BCL-xL fusion complex Deposited 2019-12-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
57–253（197 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；0.2M sodium malonate pH 7.0, 20%(w/v) polyethylene glycol 3,350
|
Resolution 2.50 Å R-free 0.260 |
| 6LHD Crystal structure of p53/BCL-xL fusion complex Deposited 2019-12-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
57–253（197 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；0.2M sodium malonate pH 7.0, 20%(w/v) polyethylene glycol 3,350
|
Resolution 2.50 Å R-free 0.260 |
| 6RJZ Fragment AZ-015 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-04-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 4 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 K6B 7-(6-azanylpyridin-2-yl)-1-benzothiophene-2-carboximidamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.58 Å R-free 0.218 |
| 6RK8 Fragment AZ-014 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 4 CL CHLORIDE ION × 2 K6N 7-(3-azanyl-4-methyl-pyrazol-1-yl)-1-benzothiophene-2-carboximidamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.60 Å R-free 0.229 |
| 6RKI Fragment AZ-023 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 4 CL CHLORIDE ION × 2 K6T 5-[(3-aminophenyl)amino]-4-phenyl-thiophene-2-carboximidamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.88 Å R-free 0.206 |
| 6RKK Fragment AZ-021 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 4 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 K6W 4-phenyl-5-(phenylmethyl)thiophene-2-carboximidamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.88 Å R-free 0.272 |
| 6RKM Fragment AZ-022 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 2 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 K6Z 4-phenyl-5-phenylazanyl-thiophene-2-carboximidamide × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.88 Å R-free 0.230 |
| 6RL3 Fragment AZ-003 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 4 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 K48 5-azanyl-4-phenyl-thiophene-2-carboximidamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.30 Å R-free 0.192 |
| 6RL4 Fragment AZ-025 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 4 CL CHLORIDE ION × 2 K7N 5-[1-(2-azanylethyl)imidazol-4-yl]-4-phenyl-thiophene-2-carboximidamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.60 Å R-free 0.180 |
| 6RL6 Fragment AZ-024 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 2 CL CHLORIDE ION × 2 K7Q ~{N}-(2-azanylethyl)-2-carbamimidoyl-7-methoxy-1-benzothiophene-4-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.60 Å R-free 0.183 |
| 6RM5 Fragment AZ-016 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-05-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 6 CL CHLORIDE ION × 2 K8W 7-(6-azanyl-5-methyl-pyridin-2-yl)-1-benzothiophene-2-carboximidamide × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.88 Å R-free 0.207 |
| 6RM7 Fragment AZ-026 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-05-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 4 CL CHLORIDE ION × 2 K92 5-[3-(2-azanylethyl)imidazol-4-yl]-4-phenyl-thiophene-2-carboximidamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.60 Å R-free 0.169 |
| 6RWH Fragment AZ-007 binding at a primary and secondary binding site of the the p53pT387/14-3-3 sigma complex Deposited 2019-06-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | KLB 5-(1~{H}-imidazol-5-yl)-4-phenyl-thiophene-2-carboximidamide × 4 CA CALCIUM ION × 2 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.68 Å R-free 0.227 |
| 6RWI Fragment AZ-002 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-06-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | KLE 5-phenylthiophene-2-carboximidamide × 2 CA CALCIUM ION × 2 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.65 Å R-free 0.204 |
| 6RWS Fragment AZ-009 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-06-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | KLZ 4-chloranyl-6-(sulfanylmethyl)-1-benzothiophene-2-carboximidamide × 2 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.53 Å R-free 0.200 |
| 6RWU Fragment AZ-010 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-06-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | KM8 ~{N}-[3-(5-carbamimidoylthiophen-3-yl)phenyl]propanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.46 Å R-free 0.221 |
| 6RX2 Fragment AZ-005 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-06-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 6 CA CALCIUM ION × 2 KM2 7-[[(2~{S})-1-azanylpropan-2-yl]amino]-1-benzothiophene-2-carboximidamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.82 Å R-free 0.220 |
| 6RZ3 Crystal structure of a complex between the DNA-binding domain of p53 and the carboxyl-terminal conserved region of iASPP Deposited 2019-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
62–292（231 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；18% (w/v) polyethylene glycol 3350, 0.18 M tri-sodium citrate
|
Resolution 4.23 Å R-free 0.292 |
| 6S39 Fragment AZ-018 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-06-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | K5Z 5-(3-azanylpropyl)-4-phenyl-thiophene-2-carboximidamide × 2 CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.88 Å R-free 0.388 |
| 6S9Q Fragment AZ-004 binding at a primary and secondary site in a p53pT387/14-3-3 complex Deposited 2019-07-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | L1T 4-methyl-5-phenyl-thiophene-2-carboximidamide × 6 CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
|
Resolution 1.69 Å R-free 0.226 |
| 6SHZ p53 cancer mutant Y220C Deposited 2019-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–311（218 aa）
Fragment：DNA-binding domain
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT.
|
Resolution 1.24 Å R-free 0.172 |
| 6SHZ p53 cancer mutant Y220C Deposited 2019-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–311（218 aa）
Fragment：DNA-binding domain
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT.
|
Resolution 1.24 Å R-free 0.172 |
| 6SI0 p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9323 Deposited 2019-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-binding domain
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 LEK 1-[9-ethyl-7-(1,3-thiazol-4-yl)carbazol-3-yl]-~{N}-methyl-methanamine × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of PK9323 in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.53 Å R-free 0.171 |
| 6SI0 p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9323 Deposited 2019-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-binding domain
|
Mutation：M133L, V203A, Y220C, N239Y, N268D | ZN ZINC ION × 1 LEK 1-[9-ethyl-7-(1,3-thiazol-4-yl)carbazol-3-yl]-~{N}-methyl-methanamine × 1 GOL GLYCEROL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of PK9323 in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.53 Å R-free 0.171 |
| 6SI1 p53 cancer mutant Y220H Deposited 2019-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-binding domain
|
Mutation：M133L, V203A, Y220H, N239Y, N268D | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT.
|
Resolution 1.44 Å R-free 0.178 |
| 6SI1 p53 cancer mutant Y220H Deposited 2019-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-binding domain
|
Mutation：M133L, V203A, Y220H, N239Y, N268D | ZN ZINC ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT.
|
Resolution 1.44 Å R-free 0.178 |
| 6SI2 p53 cancer mutant Y220S Deposited 2019-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-binding domain
|
Mutation：M133L, V203A, Y220S, N239Y, N268D | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT.
|
Resolution 1.50 Å R-free 0.178 |
| 6SI2 p53 cancer mutant Y220S Deposited 2019-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-binding domain
|
Mutation：M133L, V203A, Y220S, N239Y, N268D | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT.
|
Resolution 1.50 Å R-free 0.178 |
| 6SI3 p53 cancer mutant Y220S in complex with small-molecule stabilizer PK9301 Deposited 2019-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-binding domain
|
Mutation：M133L, V203A, Y220S, N239Y, N268D | ZN ZINC ION × 1 LEB 1-[7-bromanyl-9-[2,2,2-tris(fluoranyl)ethyl]carbazol-3-yl]-~{N}-methyl-methanamine × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of PK9301 in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.40 Å R-free 0.176 |
| 6SI3 p53 cancer mutant Y220S in complex with small-molecule stabilizer PK9301 Deposited 2019-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-binding domain
|
Mutation：M133L, V203A, Y220S, N239Y, N268D | ZN ZINC ION × 1 LEB 1-[7-bromanyl-9-[2,2,2-tris(fluoranyl)ethyl]carbazol-3-yl]-~{N}-methyl-methanamine × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of PK9301 in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl.
|
Resolution 1.40 Å R-free 0.176 |
| 6SI4 p53 cancer mutant Y220S in complex with small-molecule stabilizer PK9323 Deposited 2019-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-binding domain
|
Mutation：M133L, V203A, Y220S, N239Y, N268D | ZN ZINC ION × 1 LEK 1-[9-ethyl-7-(1,3-thiazol-4-yl)carbazol-3-yl]-~{N}-methyl-methanamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT, 2 mM PK9323.
|
Resolution 1.80 Å R-free 0.225 |
| 6SI4 p53 cancer mutant Y220S in complex with small-molecule stabilizer PK9323 Deposited 2019-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-binding domain
|
Mutation：M133L, V203A, Y220S, N239Y, N268D | ZN ZINC ION × 1 LEK 1-[9-ethyl-7-(1,3-thiazol-4-yl)carbazol-3-yl]-~{N}-methyl-methanamine × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT, 2 mM PK9323.
|
Resolution 1.80 Å R-free 0.225 |
| 6SIN Fragment AZ-020 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-08-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | K65 ~{N}-[2-(5-carbamimidoylthiophen-3-yl)phenyl]prop-2-enamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT
|
Resolution 1.64 Å R-free 0.211 |
| 6SIO Fragment AZ-017 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-08-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 4 CL CHLORIDE ION × 2 LFQ 5-methyl-4-phenyl-thiophene-2-carboximidamide × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT
|
Resolution 1.60 Å R-free 0.195 |
| 6SIP Fragment AZ-011 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-08-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 4 CL CHLORIDE ION × 2 LFB 7-methoxy-1-benzothiophene-2-carboximidamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT
|
Resolution 1.60 Å R-free 0.196 |
| 6SIQ Fragment AZ-012 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-08-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CL CHLORIDE ION × 2 LF5 4-chloranyl-7-propan-2-yloxy-1-benzothiophene-2-carboximidamide × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT
|
Resolution 1.60 Å R-free 0.217 |
| 6SL6 p53 charged core Deposited 2019-08-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
89–311（223 aa）
|
Mutation：A138G, L252K, T256R, R267L, N268D | GOL GLYCEROL × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M Ammonium citrate tribasic pH 7.0, 20% w/v Polyethylene glycol 3,350
|
Resolution 1.67 Å R-free 0.180 |
| 6SLV Fragment AZ-013 binding at the p53pT387/14-3-3 sigma interface Deposited 2019-08-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
382–393（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 6 CL CHLORIDE ION × 2 LJW 4-(methylamino)-7-propan-2-yloxy-1-benzothiophene-2-carboximidamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT
|
Resolution 1.90 Å R-free 0.218 |
| 6T58 Structure determination of the transactivation domain of p53 in complex with S100A4 using annexin A2 as a crystallization chaperone Deposited 2019-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–56（40 aa）
|
Mutation：A280E,A280E,A280E,A280E | GOL GLYCEROL × 2 CA CALCIUM ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.12 M Alcohols
0.1 M Sodium HEPES; MOPS (acid) pH7.5
20% v/v Ethylene glycol; 10 % w/v PEG 8000
Morpheus D6
|
Resolution 3.10 Å R-free 0.272 |
| 6T58 Structure determination of the transactivation domain of p53 in complex with S100A4 using annexin A2 as a crystallization chaperone Deposited 2019-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
17–56（40 aa）
|
Mutation：A280E,A280E,A280E,A280E | GOL GLYCEROL × 2 CA CALCIUM ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.12 M Alcohols
0.1 M Sodium HEPES; MOPS (acid) pH7.5
20% v/v Ethylene glycol; 10 % w/v PEG 8000
Morpheus D6
|
Resolution 3.10 Å R-free 0.272 |
| 6VR1 Complex of HLA-A2, a class I MHC, with a p53 peptide Deposited 2020-02-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain P
168–176（9 aa）
Fragment：residues 168-176
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；296 K；15% PEG 8000, 0.1 M Tris-HCl, 0.2 M magnesium chloride
|
Resolution 2.37 Å R-free 0.274 |
| 6VR1 Complex of HLA-A2, a class I MHC, with a p53 peptide Deposited 2020-02-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain Q
168–176（9 aa）
Fragment：residues 168-176
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；296 K；15% PEG 8000, 0.1 M Tris-HCl, 0.2 M magnesium chloride
|
Resolution 2.37 Å R-free 0.274 |
| 6VR5 Complex of HLA-A2, a class I MHC, with a p53 peptide Deposited 2020-02-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain P
168–176（9 aa）
Fragment：residues 168-176
|
Mutation：R175H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；295 K；15% PEG 8000, 0.1 M Tris-HCl, 0.2 M magnesium chloride
|
Resolution 2.38 Å R-free 0.280 |
| 6VR5 Complex of HLA-A2, a class I MHC, with a p53 peptide Deposited 2020-02-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain Q
168–176（9 aa）
Fragment：residues 168-176
|
Mutation：R175H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；295 K；15% PEG 8000, 0.1 M Tris-HCl, 0.2 M magnesium chloride
|
Resolution 2.38 Å R-free 0.280 |
| 6VRM T cell receptor-p53-HLA-A2 complex Deposited 2020-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain P
168–176（9 aa）
|
Mutation：R175H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；295 K；20% (w/v) polyacrylic acid 5100, 0.1 M HEPES, 20 mM MgCl2
|
Resolution 2.61 Å R-free 0.275 |
| 6VRN T cell receptor-p53-HLA-A2 complex Deposited 2020-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain P
168–176（9 aa）
|
Mutation：R175H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.7；295 K；20% (w/v) PEG 3350, 0.2 M ammonium tartrate dibasic
|
Resolution 2.46 Å R-free 0.259 |
| 6W51 Structure of the antibody fragment H2 in complex with HLA-A*02:01/p53R175H Deposited 2020-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
168–176（9 aa）
|
Mutation：R175H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；0.2 M Ammonium chloride, 20% w/v PEG 3350
|
Resolution 3.53 Å R-free 0.283 |
| 6W51 Structure of the antibody fragment H2 in complex with HLA-A*02:01/p53R175H Deposited 2020-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain F
168–176（9 aa）
|
Mutation：R175H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；0.2 M Ammonium chloride, 20% w/v PEG 3350
|
Resolution 3.53 Å R-free 0.283 |
| 6W51 Structure of the antibody fragment H2 in complex with HLA-A*02:01/p53R175H Deposited 2020-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain I
168–176（9 aa）
|
Mutation：R175H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；0.2 M Ammonium chloride, 20% w/v PEG 3350
|
Resolution 3.53 Å R-free 0.283 |
| 6W51 Structure of the antibody fragment H2 in complex with HLA-A*02:01/p53R175H Deposited 2020-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain L
168–176（9 aa）
|
Mutation：R175H | PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；0.2 M Ammonium chloride, 20% w/v PEG 3350
|
Resolution 3.53 Å R-free 0.283 |
| 6XRE Structure of the p53/RNA polymerase II assembly Deposited 2020-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain M
1–393（393 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE；The assembled p53/Pol II co-complex was applied directly on the grid for 10 sec followed by
5.5 sec of blotting. The sample grid was then washed with 3.5% trehalose in 0.1 M KCl/HEM buffer (20 mM HEPES, 0.2 mM EDTA, 2 mM MgCl2 at pH 7.9) for 10 sec, blotted for 5.5 sec, and finally frozen in liquid ethane.
|
Resolution 4.60 Å |
| 6ZNC Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human wild-type p53DBD bound to DNA and MQ: wt-DNA-MQ (I) Deposited 2020-07-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
94–293（200 aa）
Fragment：p53 human DNA binding domain
|
Not recorded | ZN ZINC ION × 2 QNN (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 6 QN8 (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；292 K；Protein/DNA ratio 1:2.4, TRIS pH=8.5 100mM, 2.0% Tacsimate(tm) pH=8.0, 16% w/v PEG 3350
|
Resolution 1.64 Å R-free 0.190 |
| 7B46 Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human wild-type p53DBD bound to DNA and MQ: wt-DNA-MQ (P1) Deposited 2020-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: octameric |
Chain A
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain B
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain C
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain D
94–293（200 aa）
Fragment：p53 human DNA binding domain
|
Mutation：' Mutation：' Mutation：' Mutation：' | ZN ZINC ION × 4 QN8 (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 7 ACT ACETATE ION × 1 QNN (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；292 K；Protein/DNA ratio 1:2.4, 0.1M DL-Malic acid pH=7.0, 19% w/v PEG 3350
|
Resolution 2.02 Å R-free 0.203 |
| 7B47 Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273H mutant bound to MQ: R273H-MQ (I) Deposited 2020-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain B
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain C
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain D
94–293（200 aa）
Fragment：p53 human DNA binding domain
|
Mutation：R273H Mutation：R273H Mutation：R273H Mutation：R273H | ZN ZINC ION × 4 QN8 (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 6 QNN (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.1；292 K；0.1M Li Acetate, 16% w/v PEG 3350
|
Resolution 1.80 Å R-free 0.202 |
| 7B48 Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273H mutant bound to MQ: R273H-MQ (II) Deposited 2020-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain B
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain C
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain D
94–293（200 aa）
Fragment：p53 human DNA binding domain
|
Mutation：R273H Mutation：R273H Mutation：R273H Mutation：R273H | ZN ZINC ION × 4 QNN (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 2 EDO 1,2-ETHANEDIOL × 6 ACT ACETATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.1；292 K；0.2M Li Acetate, 2.0% w/v Agarose, 20% w/v PEG 3350
|
Resolution 2.05 Å R-free 0.228 |
| 7B49 Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273H mutant bound to DNA and MQ: R273H-DNA-MQ Deposited 2020-12-02 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain B
94–293（200 aa）
Fragment：p53 human DNA binding domain
|
Mutation：R273H Mutation：R273H | ZN ZINC ION × 4 QN8 (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 4 QNN (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 4 FMT FORMIC ACID × 48 ACT ACETATE ION × 4 EDO 1,2-ETHANEDIOL × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.1；292 K；Protein/DNA ratio 1:1.4, 0.075M Sodium formate, 7.5% w/v PEG 3350
|
Resolution 1.42 Å R-free 0.229 |
| 7B4A Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273H mutant bound to DNA: R273H-DNA Deposited 2020-12-02 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexamer |
Chain A
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain B
94–293（200 aa）
Fragment：p53 human DNA binding domain
|
Mutation：R273H Mutation：R273H | ZN ZINC ION × 4 FMT FORMIC ACID × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.1；292 K；Protein/DNA ratio 1:1.4, 0.075M Sodium formate, 7.5% w/v PEG 3350
|
Resolution 1.90 Å R-free 0.254 |
| 7B4B Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273C mutant bound to MQ: R273C-MQ (I) Deposited 2020-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetramer |
Chain A
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain B
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain C
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain D
94–293（200 aa）
Fragment：p53 human DNA binding domain
|
Mutation：R273C Mutation：R273C Mutation：R273C Mutation：R273C | ZN ZINC ION × 4 QN8 (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 4 QNN (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 6 EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.1；292 K；PROTEIN/DNA RATIO 1:2.4, 0.2M Sodium Fluoride, 20% w/v PEG 3350
|
Resolution 1.76 Å R-free 0.218 |
| 7B4C Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273C mutant bound to MQ: R273C-MQ (II) Deposited 2020-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetramer |
Chain A
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain B
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain C
94–293（200 aa）
Fragment：p53 human DNA binding domain
Chain D
94–293（200 aa）
Fragment：p53 human DNA binding domain
|
Mutation：R273C Mutation：R273C Mutation：R273C Mutation：R273C | ZN ZINC ION × 4 QNN (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 6 EDO 1,2-ETHANEDIOL × 4 QN8 (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 1 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.1；292 K；0.2M Sodium Fluoride, 20% w/v PEG 3350
|
Resolution 1.71 Å R-free 0.182 |
| 7B4D Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273C/S240R double mutant bound to DNA and MQ: R273C/S240R-DNA-MQ Deposited 2020-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetramer |
Chain A
94–293（200 aa）
Fragment：p53 human DNA binding domain
|
Mutation：R273C S240R | ZN ZINC ION × 2 QNN (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 6 QN8 (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 2 FMT FORMIC ACID × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.1；292 K；Protein/DNA ratio 1:2.4, 0.2M Sodium formate, 20% w/v PEG 3350
|
Resolution 1.85 Å R-free 0.204 |
| 7B4E Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R282W mutant bound to DNA and MQ: R282W-DNA-MQ Deposited 2020-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetramer |
Chain A
94–293（200 aa）
Fragment：p53 human DNA binding domain
|
Mutation：R282W | ZN ZINC ION × 2 QN8 (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 6 QNN (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 2 PG4 TETRAETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.1；292 K；Protein/DNA ratio 1:1.5, 0.1M Sodium Acetate, 20% w/v PEG 3350
|
Resolution 1.58 Å R-free 0.201 |
| 7B4F Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R282W mutant bound to DNA: R282W-MQ (I) Deposited 2020-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetramer |
Chain A
94–293（200 aa）
Fragment：p53 human DNA binding domain
|
Mutation：R282W | ZN ZINC ION × 2 FMT FORMIC ACID × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；292 K；Protein/DNA ratio 1:1.5, 0.03M Citric acid, 0.07M BIS-TRIS propane pH=7.6, 20% w/v PEG 3350
|
Resolution 1.78 Å R-free 0.195 |
| 7B4G Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R282W mutant bound to DNA: R282W-MQ (II) Deposited 2020-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
94–293（200 aa）
Fragment：p53 human DNA binding domain
|
Mutation：R282W | ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 8 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；292 K；Protein/DNA ratio 1:1.5, 0.2M Sodium Acetate, 20% w/v PEG 3350
|
Resolution 1.86 Å R-free 0.205 |
| 7B4H Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human wild-type p53DBD bound to DNA and MQ: wt-DNA-MQ (III) Deposited 2020-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
94–293（200 aa）
Fragment：p53 human DNA binding domain
|
Not recorded | ZN ZINC ION × 2 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 2 QN8 (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 4 QNN (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 2 FMT FORMIC ACID × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；292 K；Protein/DNA ratio 1:2.4, 0.1M TRIS pH=8.5, 2% Tacsimate(TM) pH=8.0, 16% w/v PEG 3350
|
Resolution 1.39 Å R-free 0.200 |
| 7B4N Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human wild-type p53DBD bound to DNA and MQ: wt-DNA-MQ (II) Deposited 2020-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
94–293（200 aa）
Fragment：p53 human DNA binding domain
|
Not recorded | ZN ZINC ION × 2 QN8 (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 4 QNN (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one × 2 FMT FORMIC ACID × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；292 K；Protein/DNA ratio 1:2.4, 0.1M TRIS pH=8.5, 2% Tacsimate(TM) pH=8.0, 16% w/v PEG 3350
|
Resolution 1.32 Å R-free 0.166 |
| 7BWN Crystal Structure of a Designed Protein Heterocatenane Deposited 2020-04-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain L
326–356（31 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Bis-Tris, (NH4)2SO4
|
Resolution 2.40 Å R-free 0.239 |
| 7BWN Crystal Structure of a Designed Protein Heterocatenane Deposited 2020-04-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
326–356（31 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Bis-Tris, (NH4)2SO4
|
Resolution 2.40 Å R-free 0.239 |
| 7BWN Crystal Structure of a Designed Protein Heterocatenane Deposited 2020-04-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
326–356（31 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Bis-Tris, (NH4)2SO4
|
Resolution 2.40 Å R-free 0.239 |
| 7BWN Crystal Structure of a Designed Protein Heterocatenane Deposited 2020-04-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
326–356（31 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Bis-Tris, (NH4)2SO4
|
Resolution 2.40 Å R-free 0.239 |
| 7BWN Crystal Structure of a Designed Protein Heterocatenane Deposited 2020-04-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain I
326–356（31 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Bis-Tris, (NH4)2SO4
|
Resolution 2.40 Å R-free 0.239 |
| 7BWN Crystal Structure of a Designed Protein Heterocatenane Deposited 2020-04-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain K
326–356（31 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Bis-Tris, (NH4)2SO4
|
Resolution 2.40 Å R-free 0.239 |
| 7BWN Crystal Structure of a Designed Protein Heterocatenane Deposited 2020-04-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain N
326–356（31 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Bis-Tris, (NH4)2SO4
|
Resolution 2.40 Å R-free 0.239 |
| 7BWN Crystal Structure of a Designed Protein Heterocatenane Deposited 2020-04-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
326–356（31 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Bis-Tris, (NH4)2SO4
|
Resolution 2.40 Å R-free 0.239 |
| 7DHY Arsenic-bound p53 DNA-binding domain mutant G245S Deposited 2020-11-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
|
Mutation：G245S | ARS ARSENIC × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Tris (pH 8.0-8.5), 20% (w/v) PEG 8000, 0.2 M Li2SO4, 2 mM EDTA, and 2 mM As2O3
|
Resolution 2.15 Å R-free 0.219 |
| 7DHY Arsenic-bound p53 DNA-binding domain mutant G245S Deposited 2020-11-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–293（200 aa）
|
Mutation：G245S | ARS ARSENIC × 1 ZN ZINC ION × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Tris (pH 8.0-8.5), 20% (w/v) PEG 8000, 0.2 M Li2SO4, 2 mM EDTA, and 2 mM As2O3
|
Resolution 2.15 Å R-free 0.219 |
| 7DHY Arsenic-bound p53 DNA-binding domain mutant G245S Deposited 2020-11-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
94–293（200 aa）
|
Mutation：G245S | ARS ARSENIC × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Tris (pH 8.0-8.5), 20% (w/v) PEG 8000, 0.2 M Li2SO4, 2 mM EDTA, and 2 mM As2O3
|
Resolution 2.15 Å R-free 0.219 |
| 7DHY Arsenic-bound p53 DNA-binding domain mutant G245S Deposited 2020-11-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
94–293（200 aa）
|
Mutation：G245S | ARS ARSENIC × 1 ZN ZINC ION × 1 GOL GLYCEROL × 3 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Tris (pH 8.0-8.5), 20% (w/v) PEG 8000, 0.2 M Li2SO4, 2 mM EDTA, and 2 mM As2O3
|
Resolution 2.15 Å R-free 0.219 |
| 7DHZ Arsenic-bound p53 DNA-binding domain mutant R249S Deposited 2020-11-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
|
Mutation：R249S | GOL GLYCEROL × 1 ARS ARSENIC × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1 M Bis-Tris (pH 7) and 22% PEG5000-MME
|
Resolution 1.74 Å R-free 0.257 |
| 7DHZ Arsenic-bound p53 DNA-binding domain mutant R249S Deposited 2020-11-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–293（200 aa）
|
Mutation：R249S | GOL GLYCEROL × 2 ARS ARSENIC × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1 M Bis-Tris (pH 7) and 22% PEG5000-MME
|
Resolution 1.74 Å R-free 0.257 |
| 7DVD The crystal structure of p53 DNA binding domain and PUMA complex Deposited 2021-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
92–290（199 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.1 M Tris (pH 7.0)
20% (w/w) PEG-200 MME
|
Resolution 2.59 Å R-free 0.318 |
| 7DVD The crystal structure of p53 DNA binding domain and PUMA complex Deposited 2021-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
92–290（199 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.1 M Tris (pH 7.0)
20% (w/w) PEG-200 MME
|
Resolution 2.59 Å R-free 0.318 |
| 7DVD The crystal structure of p53 DNA binding domain and PUMA complex Deposited 2021-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
92–290（199 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.1 M Tris (pH 7.0)
20% (w/w) PEG-200 MME
|
Resolution 2.59 Å R-free 0.318 |
| 7DVD The crystal structure of p53 DNA binding domain and PUMA complex Deposited 2021-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
92–290（199 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.1 M Tris (pH 7.0)
20% (w/w) PEG-200 MME
|
Resolution 2.59 Å R-free 0.318 |
| 7EAX Crystal complex of p53-V272M and antimony ion Deposited 2021-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
96–289（194 aa）
|
Mutation：V272M | ZN ZINC ION × 1 SB ANTIMONY (III) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M Tris pH 8.5, 10% w/v PEG3350 and 0.2M Magnesium chloride
|
Resolution 2.55 Å R-free 0.235 |
| 7EAX Crystal complex of p53-V272M and antimony ion Deposited 2021-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
96–289（194 aa）
|
Mutation：V272M | ZN ZINC ION × 1 SB ANTIMONY (III) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M Tris pH 8.5, 10% w/v PEG3350 and 0.2M Magnesium chloride
|
Resolution 2.55 Å R-free 0.235 |
| 7EAX Crystal complex of p53-V272M and antimony ion Deposited 2021-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
96–289（194 aa）
|
Mutation：V272M | ZN ZINC ION × 1 SB ANTIMONY (III) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M Tris pH 8.5, 10% w/v PEG3350 and 0.2M Magnesium chloride
|
Resolution 2.55 Å R-free 0.235 |
| 7EAX Crystal complex of p53-V272M and antimony ion Deposited 2021-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
96–289（194 aa）
|
Mutation：V272M | ZN ZINC ION × 1 SB ANTIMONY (III) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M Tris pH 8.5, 10% w/v PEG3350 and 0.2M Magnesium chloride
|
Resolution 2.55 Å R-free 0.235 |
| 7EDS Human p53 core domain with germline hot spot mutation M133T in complex with the natural PIG3 p53-response element and Arsenic Deposited 2021-03-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
94–293（200 aa）
|
Mutation：M133T | ARS ARSENIC × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Tris pH 8.5-9, 17-19% PEG20000, 0.1 M MgCl2, 2 mM EDTA, 2 mM As2O3
|
Resolution 1.77 Å R-free 0.227 |
| 7EEU Human p53 core domain with hot spot mutation R282W in complex with the natural CDKN1A(p21) p53-response element and Arsenic Deposited 2021-03-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
94–293（200 aa）
Chain B
94–293（200 aa）
Chain C
94–293（200 aa）
Chain D
94–293（200 aa）
|
Mutation：R282W Mutation：R282W Mutation：R282W Mutation：R282W | ARS ARSENIC × 4 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Sodium acetate, 0.1 M HEPES pH 8.0, 10% w/v PEG 4000, 2mM EDTA and 2mM As2O3
|
Resolution 2.90 Å R-free 0.264 |
| 7EEU Human p53 core domain with hot spot mutation R282W in complex with the natural CDKN1A(p21) p53-response element and Arsenic Deposited 2021-03-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain E
94–293（200 aa）
Chain F
94–293（200 aa）
Chain G
94–293（200 aa）
Chain H
94–293（200 aa）
|
Mutation：R282W Mutation：R282W Mutation：R282W Mutation：R282W | ARS ARSENIC × 4 ZN ZINC ION × 4 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Sodium acetate, 0.1 M HEPES pH 8.0, 10% w/v PEG 4000, 2mM EDTA and 2mM As2O3
|
Resolution 2.90 Å R-free 0.264 |
| 7EL4 The crystal structure of p53p peptide fragment in complex with the N-terminal domain of MdmX Deposited 2021-04-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
23–29（7 aa）
|
Not recorded | O4B 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE × 2 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.16；291 K；0.1 M MES pH 6.5, 2 M MgSO4
|
Resolution 2.11 Å R-free 0.225 |
| 7NMI Transactivation domain of p53 in complex with S100P, using annexin A2 as crystallization chaperone Deposited 2021-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–56（40 aa）
|
Not recorded | GOL GLYCEROL × 1 CA CALCIUM ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Morpheus screen (MD) H6
0.1 M Amino acids, 0.1 M Buffer System 2, pH 7.5, 30 % v/v Precipitant Mix 2
|
Resolution 2.10 Å R-free 0.228 |
| 7RM4 Neoantigen p53R175H-specific TCR 6-11 binds to p53R175H-HLA-A2 Deposited 2021-07-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
168–176（9 aa）
|
Mutation：R175H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% (w/v) PEG 3350, 0.1 M Bis-Tris propane (pH 8.5), and 0.2 M Potassium thiocyanate
|
Resolution 3.33 Å R-free 0.295 |
| 7RM4 Neoantigen p53R175H-specific TCR 6-11 binds to p53R175H-HLA-A2 Deposited 2021-07-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain H
168–176（9 aa）
|
Mutation：R175H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% (w/v) PEG 3350, 0.1 M Bis-Tris propane (pH 8.5), and 0.2 M Potassium thiocyanate
|
Resolution 3.33 Å R-free 0.295 |
| 7RM4 Neoantigen p53R175H-specific TCR 6-11 binds to p53R175H-HLA-A2 Deposited 2021-07-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain M
168–176（9 aa）
|
Mutation：R175H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% (w/v) PEG 3350, 0.1 M Bis-Tris propane (pH 8.5), and 0.2 M Potassium thiocyanate
|
Resolution 3.33 Å R-free 0.295 |
| 7RM4 Neoantigen p53R175H-specific TCR 6-11 binds to p53R175H-HLA-A2 Deposited 2021-07-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
168–176（9 aa）
|
Mutation：R175H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% (w/v) PEG 3350, 0.1 M Bis-Tris propane (pH 8.5), and 0.2 M Potassium thiocyanate
|
Resolution 3.33 Å R-free 0.295 |
| 7V97 Arsenic-bound p53 DNA-binding domain mutant V272M Deposited 2021-08-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–293（200 aa）
|
Not recorded | ARS ARSENIC × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；0.1 M Tris pH 8.2, 0.2 M Magnesium chloride, 16% w/v PEG 8000
|
Resolution 2.02 Å R-free 0.251 |
| 7V97 Arsenic-bound p53 DNA-binding domain mutant V272M Deposited 2021-08-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–293（200 aa）
|
Not recorded | ARS ARSENIC × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；0.1 M Tris pH 8.2, 0.2 M Magnesium chloride, 16% w/v PEG 8000
|
Resolution 2.02 Å R-free 0.251 |
| 7V97 Arsenic-bound p53 DNA-binding domain mutant V272M Deposited 2021-08-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
94–293（200 aa）
|
Not recorded | ARS ARSENIC × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；0.1 M Tris pH 8.2, 0.2 M Magnesium chloride, 16% w/v PEG 8000
|
Resolution 2.02 Å R-free 0.251 |
| 7V97 Arsenic-bound p53 DNA-binding domain mutant V272M Deposited 2021-08-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
94–293（200 aa）
|
Not recorded | ARS ARSENIC × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；0.1 M Tris pH 8.2, 0.2 M Magnesium chloride, 16% w/v PEG 8000
|
Resolution 2.02 Å R-free 0.251 |
| 7XZX Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain Deposited 2022-06-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain K
94–293（200 aa）
Chain L
94–293（200 aa）
Chain M
94–293（200 aa）
Chain N
94–293（200 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.53 Å |
| 7XZZ Cryo-EM structure of the nucleosome in complex with p53 Deposited 2022-06-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain K
1–393（393 aa）
Chain L
1–393（393 aa）
Chain M
1–393（393 aa）
Chain N
1–393（393 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.07 Å |
| 7YGI Crystal structure of p53 DBD domain in complex with azurin Deposited 2022-07-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
92–289（198 aa）
Chain B
92–289（198 aa）
|
Not recorded | NA SODIUM ION × 2 ZN ZINC ION × 2 K POTASSIUM ION × 2 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；298 K；0.05M Na2HPO4+19.5% PEG3350
|
Resolution 2.10 Å R-free 0.270 |
| 8A31 p53 cancer mutant Y220C in complex with iodophenol-based small-molecule stabilizer JC694 Deposited 2022-06-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-binding domain
|
Not recorded | KV0 4-(3-fluoranylpyrrol-1-yl)-3,5-bis(iodanyl)-2-oxidanyl-benzoic acid × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 5.7 mg/ml protein in 25 mM sodium phosphate, pH 7.2, 150 mm NaCl, 0.5 mM TCEP. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 20 mM compound in 100 mm HEPES, pH 7.2, 10 mM sodium phosphate, pH 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm NaCl.
|
Resolution 1.46 Å R-free 0.191 |
| 8A31 p53 cancer mutant Y220C in complex with iodophenol-based small-molecule stabilizer JC694 Deposited 2022-06-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-binding domain
|
Not recorded | KV0 4-(3-fluoranylpyrrol-1-yl)-3,5-bis(iodanyl)-2-oxidanyl-benzoic acid × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 5.7 mg/ml protein in 25 mM sodium phosphate, pH 7.2, 150 mm NaCl, 0.5 mM TCEP. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 20 mM compound in 100 mm HEPES, pH 7.2, 10 mM sodium phosphate, pH 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm NaCl.
|
Resolution 1.46 Å R-free 0.191 |
| 8A32 p53 cancer mutant Y220C in complex with iodophenol-based small-molecule stabilizer JC769 Deposited 2022-06-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-binding domain
|
Not recorded | KVA 4-[3,4-bis(fluoranyl)pyrrol-1-yl]-3,5-bis(iodanyl)-2-oxidanyl-benzoic acid × 1 EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 5.7 mg/ml protein in 25 mM sodium phosphate, pH 7.2, 150 mm NaCl, 0.5 mM TCEP. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 20 mM compound in 100 mm HEPES, pH 7.2, 10 mM sodium phosphate, pH 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm NaCl.
|
Resolution 1.47 Å R-free 0.193 |
| 8A32 p53 cancer mutant Y220C in complex with iodophenol-based small-molecule stabilizer JC769 Deposited 2022-06-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-binding domain
|
Not recorded | KVA 4-[3,4-bis(fluoranyl)pyrrol-1-yl]-3,5-bis(iodanyl)-2-oxidanyl-benzoic acid × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 5.7 mg/ml protein in 25 mM sodium phosphate, pH 7.2, 150 mm NaCl, 0.5 mM TCEP. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: 20 mM compound in 100 mm HEPES, pH 7.2, 10 mM sodium phosphate, pH 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm NaCl.
|
Resolution 1.47 Å R-free 0.193 |
| 8A92 p53-Y220C Core Domain in Complex with a Bromo-trifluoro-pyrazole-amine Deposited 2022-06-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Mutation：Y220C,M133L,V203A,N239Y,N268D | LE9 4-bromanyl-5-(trifluoromethyl)-1H-pyrazol-3-amine × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.15；293 K；100 mM HEPES (pH = 7.15), 19 % PEG4000 and
10 mM DTT
|
Resolution 1.37 Å R-free 0.183 |
| 8A92 p53-Y220C Core Domain in Complex with a Bromo-trifluoro-pyrazole-amine Deposited 2022-06-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Mutation：Y220C,M133L,V203A,N239Y,N268D | LE9 4-bromanyl-5-(trifluoromethyl)-1H-pyrazol-3-amine × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.15；293 K；100 mM HEPES (pH = 7.15), 19 % PEG4000 and
10 mM DTT
|
Resolution 1.37 Å R-free 0.183 |
| 8CG7 Structure of p53 cancer mutant Y220C with arylation at Cys182 and Cys277 Deposited 2023-02-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 A1IH3 5-iodanyl-2-methylsulfonyl-pyrimidine × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml in 25 mM phosphate buffer, pH 7.2, 0.5 mM TCEP. Crystallization buffer: 19% polyethylene glycol 4000, 100 mM Hepes, pH 7.0. For covalent modification, crystals were soaked for 4 hours in crystallization buffer complemented with 20% glycerol and 30 mM compound before flash freezing in liquid nitrogen.
|
Resolution 1.53 Å R-free 0.187 |
| 8CG7 Structure of p53 cancer mutant Y220C with arylation at Cys182 and Cys277 Deposited 2023-02-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 A1IH3 5-iodanyl-2-methylsulfonyl-pyrimidine × 2 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml in 25 mM phosphate buffer, pH 7.2, 0.5 mM TCEP. Crystallization buffer: 19% polyethylene glycol 4000, 100 mM Hepes, pH 7.0. For covalent modification, crystals were soaked for 4 hours in crystallization buffer complemented with 20% glycerol and 30 mM compound before flash freezing in liquid nitrogen.
|
Resolution 1.53 Å R-free 0.187 |
| 8DC4 Crystal structure of p53 Y220C covalently bound to carbazole KG3 Deposited 2022-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Mutation：Y220C | ZN ZINC ION × 1 R3R 9-propanoyl-9H-carbazole-3-carbaldehyde, bound form × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM HEPES, 2.2M MgSO4
|
Resolution 2.40 Å R-free 0.231 |
| 8DC4 Crystal structure of p53 Y220C covalently bound to carbazole KG3 Deposited 2022-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Mutation：Y220C | ZN ZINC ION × 1 R3R 9-propanoyl-9H-carbazole-3-carbaldehyde, bound form × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM HEPES, 2.2M MgSO4
|
Resolution 2.40 Å R-free 0.231 |
| 8DC4 Crystal structure of p53 Y220C covalently bound to carbazole KG3 Deposited 2022-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
94–312（219 aa）
|
Mutation：Y220C | ZN ZINC ION × 1 R3R 9-propanoyl-9H-carbazole-3-carbaldehyde, bound form × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM HEPES, 2.2M MgSO4
|
Resolution 2.40 Å R-free 0.231 |
| 8DC4 Crystal structure of p53 Y220C covalently bound to carbazole KG3 Deposited 2022-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
94–312（219 aa）
|
Mutation：Y220C | ZN ZINC ION × 1 R3R 9-propanoyl-9H-carbazole-3-carbaldehyde, bound form × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM HEPES, 2.2M MgSO4
|
Resolution 2.40 Å R-free 0.231 |
| 8DC6 Crystal structure of p53 Y220C covalently bound to indole KG6 Deposited 2022-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Mutation：Y220C | ZN ZINC ION × 1 SO4 SULFATE ION × 5 R4F 1-(2-methylprop-2-enoyl)-1H-indole-3-carbaldehyde, bound form × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM HEPES, 2.2M MgSO4
|
Resolution 1.60 Å R-free 0.202 |
| 8DC6 Crystal structure of p53 Y220C covalently bound to indole KG6 Deposited 2022-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Mutation：Y220C | ZN ZINC ION × 1 SO4 SULFATE ION × 3 R4F 1-(2-methylprop-2-enoyl)-1H-indole-3-carbaldehyde, bound form × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM HEPES, 2.2M MgSO4
|
Resolution 1.60 Å R-free 0.202 |
| 8DC6 Crystal structure of p53 Y220C covalently bound to indole KG6 Deposited 2022-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
94–312（219 aa）
|
Mutation：Y220C | ZN ZINC ION × 1 SO4 SULFATE ION × 2 R4F 1-(2-methylprop-2-enoyl)-1H-indole-3-carbaldehyde, bound form × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM HEPES, 2.2M MgSO4
|
Resolution 1.60 Å R-free 0.202 |
| 8DC6 Crystal structure of p53 Y220C covalently bound to indole KG6 Deposited 2022-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
94–312（219 aa）
|
Mutation：Y220C | ZN ZINC ION × 1 SO4 SULFATE ION × 3 R4F 1-(2-methylprop-2-enoyl)-1H-indole-3-carbaldehyde, bound form × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM HEPES, 2.2M MgSO4
|
Resolution 1.60 Å R-free 0.202 |
| 8DC7 Crystal structure of p53 Y220C covalently bound to indole KG10 Deposited 2022-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | SO4 SULFATE ION × 3 ZN ZINC ION × 1 MG MAGNESIUM ION × 2 R4R 4-[4-(4-methylpiperazin-1-yl)phenyl]-1-(2-methylprop-2-enoyl)-1H-indole-3-carbaldehyde, bound form × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM HEPES, 2.2M MgSO4
|
Resolution 1.99 Å R-free 0.193 |
| 8DC8 Crystal structure of p53 Y220C covalently bound to azaindole KG13 Deposited 2022-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | R50 2-methyl-1-[(4P)-3-methyl-4-(2-methyl-1,2,3,4-tetrahydroisoquinolin-6-yl)-1H-pyrrolo[2,3-c]pyridin-1-yl]prop-2-en-1-one, bound form × 1 SO4 SULFATE ION × 2 ZN ZINC ION × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM HEPES, 2.2M MgSO4
|
Resolution 1.72 Å R-free 0.204 |
| 8E7A Crystal structure of the p53 (Y107H) core domain orthorhombic P form Deposited 2022-08-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：S94-T312
|
Mutation：Y107H | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；30 % (w/v) PEG 2000 MME, 100 mM potassium thiocyanate
|
Resolution 1.30 Å R-free 0.174 |
| 8E7B Crystal structure of the p53 (Y107H) core domain monoclinic P form Deposited 2022-08-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：S94-T312
|
Mutation：Y107H | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；28 % (w/v) PEG 2000 MME, 100 mM Bis-Tris
|
Resolution 2.50 Å R-free 0.279 |
| 8E7B Crystal structure of the p53 (Y107H) core domain monoclinic P form Deposited 2022-08-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：S94-T312
|
Mutation：Y107H | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；28 % (w/v) PEG 2000 MME, 100 mM Bis-Tris
|
Resolution 2.50 Å R-free 0.279 |
| 8GCR HPV16 E6-E6AP-p53 complex Deposited 2023-03-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.38 Å |
| 8HLL Crystal structure of p53/BCL2 fusion complex (complex 1) Deposited 2022-11-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
95–290（196 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；PEG 8K 8%-13%, 0.1M HEPES, 0.8% ethylene glycol
|
Resolution 2.62 Å R-free 0.280 |
| 8HLM Crystal structure of p53/BCL2 fusion complex (complex 2) Deposited 2022-11-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
95–290（196 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；0.1 M Imidazole, PEG8K 15-21%
|
Resolution 2.52 Å R-free 0.290 |
| 8HLN Crystal structure of p53/BCL2 fusion complex(complex3) Deposited 2022-11-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
95–290（196 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；0.1 M HEPES, PEG8000 8%-13%, 0.8% ethylene glycol
|
Resolution 2.35 Å R-free 0.253 |
| 8J8N Structure of p53 DNA-binding domain and ZNF568 KRAB domain complex Deposited 2023-05-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
92–292（201 aa）
Fragment：DNA binding domain
Chain B
92–292（201 aa）
Fragment：DNA binding domain
Chain C
92–292（201 aa）
Fragment：DNA binding domain
Chain D
92–292（201 aa）
Fragment：DNA binding domain
|
Not recorded | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 9.02 Å |
| 8OXM ATM(Q2971A) activated by oxidative stress in complex with Mg AMP-PNP and p53 peptide Deposited 2023-05-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
11–22（12 aa）
Chain F
11–22（12 aa）
|
Not recorded | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8OXO ATM(Q2971A) dimeric C-terminal region activated by oxidative stress in complex with Mg AMP-PNP and p53 peptide Deposited 2023-05-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
11–22（12 aa）
Chain F
11–22（12 aa）
|
Not recorded | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8QWK Structure of p53 cancer mutant Y126C Deposited 2023-10-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 5.5-6.0 mg/ml in 25 mM HEPES (pH 7.5), 300 mM NaCl, 0.5 mM TCEP.
Reservoir buffer: 0.7 M sodium citrate and 0.1 M bis-tris-propane (pH 7.0).
|
Resolution 1.69 Å R-free 0.218 |
| 8QWL Structure of p53 cancer mutant Y163C Deposited 2023-10-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3 MLI MALONATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 5.5-6.0 mg/ml in 25 mM HEPES (pH 7.5), 200 mM NaCl, 0.5 mM TCEP.
Reservoir buffer: 24% PEG 3350 (w/v), 10% ethylene glycol (v/v), 0.2 M sodium malonate (pH 7.0).
|
Resolution 1.65 Å R-free 0.189 |
| 8QWM Structure of p53 cancer mutant Y205C Deposited 2023-10-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 TLA L(+)-TARTARIC ACID × 1 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 5.5-6.0 mg/ml in 25 mM HEPES (pH 7.5), 200 mM NaCl, 0.5 mM TCEP
Reservoir buffer: 18% PEG 3350 (w/v), 15% ethylene glycol (v/v), 0.2 M Na/K tartrate.
|
Resolution 1.54 Å R-free 0.221 |
| 8QWM Structure of p53 cancer mutant Y205C Deposited 2023-10-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 TLA L(+)-TARTARIC ACID × 1 EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 5.5-6.0 mg/ml in 25 mM HEPES (pH 7.5), 200 mM NaCl, 0.5 mM TCEP
Reservoir buffer: 18% PEG 3350 (w/v), 15% ethylene glycol (v/v), 0.2 M Na/K tartrate.
|
Resolution 1.54 Å R-free 0.221 |
| 8QWN Structure of p53 cancer mutant Y220C (hexagonal crystal form) Deposited 2023-10-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 5.5-6.0 mg/ml in 25 mM HEPES (pH 7.5), 200 mM NaCl, 0.5 mM TCEP
Reservoir buffer: 20% w/v PEG 8000 (w/v), 0.1 M Tris pH 8.5, 0.2 M magnesium chloride hexahydrate.
|
Resolution 1.44 Å R-free 0.209 |
| 8QWO Structure of p53 cancer mutant Y234C Deposited 2023-10-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 5.5-6.0 mg/ml in 25 mM phosphate (pH 7.5), 150 mM NaCl, 0.5 mM TCEP
Reservoir buffer: 19% PEG 4000 (w/v), 0.1 M HEPES (pH 7.0), 5 mM DTT.
|
Resolution 1.38 Å R-free 0.178 |
| 8QWO Structure of p53 cancer mutant Y234C Deposited 2023-10-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 5.5-6.0 mg/ml in 25 mM phosphate (pH 7.5), 150 mM NaCl, 0.5 mM TCEP
Reservoir buffer: 19% PEG 4000 (w/v), 0.1 M HEPES (pH 7.0), 5 mM DTT.
|
Resolution 1.38 Å R-free 0.178 |
| 8QWP Structure of p53 cancer mutant Y236C Deposited 2023-10-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 TLA L(+)-TARTARIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 5.5-6.0 mg/ml in 25 mM HEPES (pH 7.5), 200 mM NaCl, 0.5 mM TCEP.
Reservoir buffer: 19% PEG 3350 (w/v), 5% ethylene glycol (v/v), 0.2 M Na/K tartrate.
|
Resolution 2.10 Å R-free 0.268 |
| 8QWP Structure of p53 cancer mutant Y236C Deposited 2023-10-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 TLA L(+)-TARTARIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 5.5-6.0 mg/ml in 25 mM HEPES (pH 7.5), 200 mM NaCl, 0.5 mM TCEP.
Reservoir buffer: 19% PEG 3350 (w/v), 5% ethylene glycol (v/v), 0.2 M Na/K tartrate.
|
Resolution 2.10 Å R-free 0.268 |
| 8R1F Monomeric E6AP-E6-p53 ternary complex Deposited 2023-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–393（393 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.67 Å |
| 8R1G Dimeric ternary structure of E6AP-E6-p53 Deposited 2023-11-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain C
1–393（393 aa）
Chain F
1–393（393 aa）
|
Not recorded | ZN ZINC ION × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.99 Å |
| 8RBA p53-Y220C Core Domain Covalently Bound to 2,5,6-trifluoropyridine-3-carbonitrile Soaked at 5 mM Deposited 2023-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Mutation：M133L, V203A, N239Y, N268D, Y220C | YLW 2,5-bis(fluoranyl)pyridine-3-carbonitrile × 1 PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 7 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
|
Resolution 1.57 Å R-free 0.183 |
| 8RBA p53-Y220C Core Domain Covalently Bound to 2,5,6-trifluoropyridine-3-carbonitrile Soaked at 5 mM Deposited 2023-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Mutation：M133L, V203A, N239Y, N268D, Y220C | YLW 2,5-bis(fluoranyl)pyridine-3-carbonitrile × 1 PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 5 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 ZN ZINC ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
|
Resolution 1.57 Å R-free 0.183 |
| 8RBB p53-Y220C Core Domain Covalently Bound to 2,5,6-trifluoropyridine-3-carbonitrile Soaked at 40 mM Deposited 2023-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | YLW 2,5-bis(fluoranyl)pyridine-3-carbonitrile × 5 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
|
Resolution 1.69 Å R-free 0.207 |
| 8RBB p53-Y220C Core Domain Covalently Bound to 2,5,6-trifluoropyridine-3-carbonitrile Soaked at 40 mM Deposited 2023-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Not recorded | YLW 2,5-bis(fluoranyl)pyridine-3-carbonitrile × 4 EDO 1,2-ETHANEDIOL × 3 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
|
Resolution 1.69 Å R-free 0.207 |
| 8RBC p53-Y220C Core Domain Covalently Bound to 3-amino-5-chloropyrazine-2,6-dicarbonitrile Soaked at 5 mM Deposited 2023-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | YM0 3-azanylpyrazine-2,6-dicarbonitrile × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
|
Resolution 2.06 Å R-free 0.260 |
| 8RBC p53-Y220C Core Domain Covalently Bound to 3-amino-5-chloropyrazine-2,6-dicarbonitrile Soaked at 5 mM Deposited 2023-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Not recorded | YM0 3-azanylpyrazine-2,6-dicarbonitrile × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
|
Resolution 2.06 Å R-free 0.260 |
| 8RCI Human p53 DNA-binding domain bound to DARPin C10 Deposited 2023-12-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
94–294（201 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 4 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 2.5 mg/ml of p53 DBD-DARPin C10 complex (1:1 ratio) in 50 mM Tris, pH 8, 150 mM NaCl, 0.5 mM TCEP
Crystallization buffer: 25 % w/v PEG 3350
|
Resolution 1.50 Å R-free 0.197 |
| 8UQR Crystal structure of the human p53 tetramerization domain Deposited 2023-10-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
326–356（31 aa）
Chain B
326–356（31 aa）
Chain C
326–356（31 aa）
Chain D
326–356（31 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；296 K；15% PEG 1500
|
Resolution 1.22 Å R-free 0.177 |
| 8WD2 The Crystal Structure of p53 from Biortus. Deposited 2023-09-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Mutation：M133L,V203A,Y220C,N239Y,N268D | PO4 PHOSPHATE ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.04M Potassium phosphate monobasic, 16% w/v PEG 8000, 20% v/v Glycerol
|
Resolution 1.85 Å R-free 0.208 |
| 8WD2 The Crystal Structure of p53 from Biortus. Deposited 2023-09-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Mutation：M133L,V203A,Y220C,N239Y,N268D | PO4 PHOSPHATE ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.04M Potassium phosphate monobasic, 16% w/v PEG 8000, 20% v/v Glycerol
|
Resolution 1.85 Å R-free 0.208 |
| 8XCB Cocrystal structure of p53 in complex of B20 Deposited 2023-12-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
94–293（200 aa）
Chain B
94–293（200 aa）
|
Not recorded | ZN ZINC ION × 2 GOL GLYCEROL × 1 A1LUZ 2-[2,4-bis(oxidanylidene)-1,3-thiazolidin-5-ylidene]ethanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Tris pH 8.5, 10% w/v PEG3350 and 0.2M Magnesium chloride
|
Resolution 1.83 Å R-free 0.245 |
| 8XCB Cocrystal structure of p53 in complex of B20 Deposited 2023-12-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
94–293（200 aa）
Chain D
94–293（200 aa）
|
Not recorded | ZN ZINC ION × 2 GOL GLYCEROL × 2 A1LUZ 2-[2,4-bis(oxidanylidene)-1,3-thiazolidin-5-ylidene]ethanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Tris pH 8.5, 10% w/v PEG3350 and 0.2M Magnesium chloride
|
Resolution 1.83 Å R-free 0.245 |
| 8XCE cocrystal structure of p53 in complex of B23 Deposited 2023-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
94–293（200 aa）
Chain B
94–293（200 aa）
Chain C
94–293（200 aa）
Chain D
94–293（200 aa）
|
Not recorded | ZN ZINC ION × 4 A1LU0 2-[(2~{Z})-2-(3-ethynylphenyl)imino-4-oxidanylidene-1,3-thiazolidin-5-ylidene]ethanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M Tris pH 8.5, 10% w/v PEG3350 and 0.2M Magnesium chloride
|
Resolution 2.00 Å R-free 0.223 |
| 8XP5 The Crystal Structure of p53/BCL-xL fusion complex from Biortus. Deposited 2024-01-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
95–292（198 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.05M MgCl2, 0.1M MES pH6.5, 5% PEG 4000, 10% 2-Propanol, 30% w/v D-Sorbito
|
Resolution 2.55 Å R-free 0.328 |
| 8XP5 The Crystal Structure of p53/BCL-xL fusion complex from Biortus. Deposited 2024-01-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
95–292（198 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.05M MgCl2, 0.1M MES pH6.5, 5% PEG 4000, 10% 2-Propanol, 30% w/v D-Sorbito
|
Resolution 2.55 Å R-free 0.328 |
| 9BR3 Crystal structure of p53 Y220C mutant in complex with PC-10709 Deposited 2024-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Mutation：Y220C | A1ARO 2-{3-[4-(methanesulfonyl)-2-methoxyanilino]prop-1-yn-1-yl}-N-(1-methylpiperidin-4-yl)-1-(2,2,2-trifluoroethyl)-1H-indol-4-amine × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；p53, CID 3799, at 6.93mg/ml; Optimization screen PMV1-opt1 e3: 16% PEG 8000, 20% glycerol, 20mM K2HPO4; protein + 1mM BSI 107743; cryo: direct; crystal tracking ID 285723e3, puck tai0-7
|
Resolution 1.90 Å R-free 0.191 |
| 9BR3 Crystal structure of p53 Y220C mutant in complex with PC-10709 Deposited 2024-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Mutation：Y220C | A1ARO 2-{3-[4-(methanesulfonyl)-2-methoxyanilino]prop-1-yn-1-yl}-N-(1-methylpiperidin-4-yl)-1-(2,2,2-trifluoroethyl)-1H-indol-4-amine × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；p53, CID 3799, at 6.93mg/ml; Optimization screen PMV1-opt1 e3: 16% PEG 8000, 20% glycerol, 20mM K2HPO4; protein + 1mM BSI 107743; cryo: direct; crystal tracking ID 285723e3, puck tai0-7
|
Resolution 1.90 Å R-free 0.191 |
| 9BR4 Crystal structure of p53 Y220C mutant in complex with PC-9859 Deposited 2024-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：p53
|
Not recorded | A1ARZ 2-methyl-2-{5-[(3-{4-[(1-methylpiperidin-4-yl)amino]-1-(2,2,2-trifluoroethyl)-1H-indol-2-yl}prop-2-yn-1-yl)amino]pyridin-2-yl}propanenitrile × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；p53, at 6.93mg/ml; Optimization screen PMV1-opt1 e2: 18% PEG 8000, 20% glycerol, 20mM K2HPO4; protein + 1mM compound PC-8959; cryo: direct; crystal tracking ID 272674 e2, puck mqj6-10
|
Resolution 1.70 Å R-free 0.175 |
| 9BR4 Crystal structure of p53 Y220C mutant in complex with PC-9859 Deposited 2024-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：p53
|
Not recorded | A1ARZ 2-methyl-2-{5-[(3-{4-[(1-methylpiperidin-4-yl)amino]-1-(2,2,2-trifluoroethyl)-1H-indol-2-yl}prop-2-yn-1-yl)amino]pyridin-2-yl}propanenitrile × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；p53, at 6.93mg/ml; Optimization screen PMV1-opt1 e2: 18% PEG 8000, 20% glycerol, 20mM K2HPO4; protein + 1mM compound PC-8959; cryo: direct; crystal tracking ID 272674 e2, puck mqj6-10
|
Resolution 1.70 Å R-free 0.175 |
| 9C5S Disulfide-linked, antiparallel p53-derived peptide dimer (CV1) Deposited 2024-06-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
17–30（14 aa）
Chain B
17–30（14 aa）
Chain C
17–30（14 aa）
Chain D
17–30（14 aa）
|
Mutation：p53-derived Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：p53-derived Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：p53-derived Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：p53-derived Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 20% v/v glycerol, 10% w/v PEG4000, 100 mM imidazole/MES monohydrate buffer, pH 6.5
|
Resolution 1.01 Å R-free 0.202 |
| 9CHT Human E3 ligase E6AP in complex with HPV16-E6 and p53 Deposited 2024-07-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–312（312 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.54 Å |
| 9FZB Human p53 DNA-binding domain bound to DARPin C10-H82R Deposited 2024-07-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
94–294（201 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 2.6 mg/ml p53 DBD-DARPin C10-H82R complex in
50 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM TCEP.
Reservoir solution: 0.1 M Bis-Tris propane, pH 7.5, 0.02 M sodium potassium phosphate, pH 7.5, 20% (w/v) PEG 3350, 10% (v/v) ethylene glycol.
Drop volume ratio: 2:1
|
Resolution 1.44 Å R-free 0.184 |
| 9G5H p53-Y220C Core Domain Covalently Bound to 2-chloro-5-cyanopyrazine Soaked at 5 mM Deposited 2024-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Mutation：Y220C, M133L, V203A, N239Y, N268D | A1IIO 5-chloranylpyrazine-2-carbonitrile × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 6 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
|
Resolution 1.65 Å R-free 0.206 |
| 9G5H p53-Y220C Core Domain Covalently Bound to 2-chloro-5-cyanopyrazine Soaked at 5 mM Deposited 2024-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Mutation：Y220C, M133L, V203A, N239Y, N268D | A1IIO 5-chloranylpyrazine-2-carbonitrile × 3 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
|
Resolution 1.65 Å R-free 0.206 |
| 9G6T p53-Y220C Core Domain Covalently Bound to 5-Chloro-6-methylpyrazine-2-carbonitrile Soaked at 5 mM Deposited 2024-07-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
94–312（219 aa）
Chain B
94–312（219 aa）
|
Mutation：Y220C, M133L, V203A, N239Y, N268D Mutation：Y220C, M133L, V203A, N239Y, N268D | A1II4 5-chloranyl-6-methyl-pyrazine-2-carbonitrile × 5 EDO 1,2-ETHANEDIOL × 6 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 PEG DI(HYDROXYETHYL)ETHER × 3 GOL GLYCEROL × 3 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
|
Resolution 1.56 Å R-free 0.199 |
| 9G6U p53-Y220C Core Domain Covalently Bound to 3,5-Dichloro-6-Ethylpyrazine-2-carbonitirle Soaked at 5 mM Deposited 2024-07-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Mutation：Y220C, M133L, V203A, N239Y, N268D | A1II1 3,5-bis(chloranyl)-6-ethyl-pyrazine-2-carbonitrile × 2 PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 6 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
|
Resolution 1.64 Å R-free 0.229 |
| 9G6U p53-Y220C Core Domain Covalently Bound to 3,5-Dichloro-6-Ethylpyrazine-2-carbonitirle Soaked at 5 mM Deposited 2024-07-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Mutation：Y220C, M133L, V203A, N239Y, N268D | A1II1 3,5-bis(chloranyl)-6-ethyl-pyrazine-2-carbonitrile × 3 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 3 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ZN ZINC ION × 1 GOL GLYCEROL × 3 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
|
Resolution 1.64 Å R-free 0.229 |
| 9R04 p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample) Deposited 2025-04-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain K
1–393（393 aa）
Chain L
1–393（393 aa）
Chain M
1–393（393 aa）
Chain N
1–393（393 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 9R2M p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, composite map) Deposited 2025-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain K
1–393（393 aa）
Chain L
1–393（393 aa）
Chain M
1–393（393 aa）
Chain N
1–393（393 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9R2P p53 bound to nucleosome at position SHL+5.9 (crosslinked sample) Deposited 2025-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain K
1–393（393 aa）
Chain L
1–393（393 aa）
Chain M
1–393（393 aa）
Chain N
1–393（393 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.18 Å |
| 9R2Q p53 bound to nucleosome at position SHL-5.7 (non-crosslinked sample) Deposited 2025-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain K
1–393（393 aa）
Chain L
1–393（393 aa）
Chain M
1–393（393 aa）
Chain N
1–393（393 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9S9L Crystal structure of p53 cancer mutant Y220C in complex with rezatapopt precursor Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 A1JMS ~{N}-[3-[1-ethyl-5-(methylaminomethyl)indol-2-yl]prop-2-ynyl]aniline × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mm sodium phosphate, pH 7.2, 150 mM KCl, 5 mM DTT. Reservoir buffer: 100 mM Hepes, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mM DTT. Soaking buffer: 19 mM compound in 100 mM Hepes, ph 7.2, 10 mM sodium phosphate, pH 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mM KCl.
|
Resolution 1.38 Å R-free 0.174 |
| 9S9L Crystal structure of p53 cancer mutant Y220C in complex with rezatapopt precursor Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 A1JMS ~{N}-[3-[1-ethyl-5-(methylaminomethyl)indol-2-yl]prop-2-ynyl]aniline × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mm sodium phosphate, pH 7.2, 150 mM KCl, 5 mM DTT. Reservoir buffer: 100 mM Hepes, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mM DTT. Soaking buffer: 19 mM compound in 100 mM Hepes, ph 7.2, 10 mM sodium phosphate, pH 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mM KCl.
|
Resolution 1.38 Å R-free 0.174 |
| 9S9M Crystal structure of p53 cancer mutant Y220C in complex with rezatapopt analog 7 Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | A1JMO 2-[3-[(4-dimethylphosphorylphenyl)amino]prop-1-ynyl]-~{N}-(1-methylpiperidin-4-yl)-1-[2,2,2-tris(fluoranyl)ethyl]indol-4-amine × 1 EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；mM Hepes, pH 7.0, 19% (w/v) polyethylene glycol 4000. Soaking buffer: 19 mM compound in 100 mM Hepes, pH 7.2, 10 mM sodium phosphate, pH 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mM KCl.
|
Resolution 1.83 Å R-free 0.226 |
| 9S9M Crystal structure of p53 cancer mutant Y220C in complex with rezatapopt analog 7 Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Not recorded | A1JMO 2-[3-[(4-dimethylphosphorylphenyl)amino]prop-1-ynyl]-~{N}-(1-methylpiperidin-4-yl)-1-[2,2,2-tris(fluoranyl)ethyl]indol-4-amine × 1 EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；mM Hepes, pH 7.0, 19% (w/v) polyethylene glycol 4000. Soaking buffer: 19 mM compound in 100 mM Hepes, pH 7.2, 10 mM sodium phosphate, pH 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mM KCl.
|
Resolution 1.83 Å R-free 0.226 |
| 9S9N Crystal structure of p53 cancer mutant Y220C in complex with rezatapopt analog 8 Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | A1JMP 1-~{tert}-butyl-~{N}-[[3-[4-[[(3~{S},4~{R})-3-fluoranyl-1-methyl-piperidin-4-yl]amino]-1-[2,2,2-tris(fluoranyl)ethyl]indol-2-yl]-1,2,4-oxadiazol-5-yl]methyl]pyrazole-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 5 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM Hepes, pH 7.5, 150 mM NaCl, 0.5 mM TCEP. Reservoir buffer: 100 mM Hepes, pH 7.0, 19% (w/v) polyethylene glycol 4000. Soaking buffer: 17 mM compound in 100 mM Hepes, pH 7.2, 10 mM sodium phosphate, pH 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mM KCl.
|
Resolution 1.72 Å R-free 0.207 |
| 9S9N Crystal structure of p53 cancer mutant Y220C in complex with rezatapopt analog 8 Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Not recorded | A1JMP 1-~{tert}-butyl-~{N}-[[3-[4-[[(3~{S},4~{R})-3-fluoranyl-1-methyl-piperidin-4-yl]amino]-1-[2,2,2-tris(fluoranyl)ethyl]indol-2-yl]-1,2,4-oxadiazol-5-yl]methyl]pyrazole-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM Hepes, pH 7.5, 150 mM NaCl, 0.5 mM TCEP. Reservoir buffer: 100 mM Hepes, pH 7.0, 19% (w/v) polyethylene glycol 4000. Soaking buffer: 17 mM compound in 100 mM Hepes, pH 7.2, 10 mM sodium phosphate, pH 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mM KCl.
|
Resolution 1.72 Å R-free 0.207 |
| 9S9O Crystal structure of p53 cancer mutant Y220C in complex with rezatapopt Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 A1JMR 4-[3-[4-[[(3~{S},4~{R})-3-fluoranyl-1-methyl-piperidin-4-yl]amino]-1-[2,2,2-tris(fluoranyl)ethyl]indol-2-yl]prop-2-ynylamino]-3-methoxy-~{N}-methyl-benzamide × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM Hepes, pH 7.5, 150 mM NaCl, 0.5 mM TCEP. Reservoir buffer: 100 mM Hepes, pH 7.0, 19% (w/v) polyethylene glycol 4000. Soaking buffer: 18 mM compound in 100 mM Hepes, pH 7.2, 10 mM sodium phosphate, pH 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mM KCl
|
Resolution 1.49 Å R-free 0.186 |
| 9S9O Crystal structure of p53 cancer mutant Y220C in complex with rezatapopt Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 A1JMR 4-[3-[4-[[(3~{S},4~{R})-3-fluoranyl-1-methyl-piperidin-4-yl]amino]-1-[2,2,2-tris(fluoranyl)ethyl]indol-2-yl]prop-2-ynylamino]-3-methoxy-~{N}-methyl-benzamide × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml protein in 25 mM Hepes, pH 7.5, 150 mM NaCl, 0.5 mM TCEP. Reservoir buffer: 100 mM Hepes, pH 7.0, 19% (w/v) polyethylene glycol 4000. Soaking buffer: 18 mM compound in 100 mM Hepes, pH 7.2, 10 mM sodium phosphate, pH 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mM KCl
|
Resolution 1.49 Å R-free 0.186 |
| 9S9P Crystal structure of p53 cancer mutant Y220S in complex with rezatapopt Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
Fragment：DNA-binding domain
|
Not recorded | ZN ZINC ION × 1 A1JMR 4-[3-[4-[[(3~{S},4~{R})-3-fluoranyl-1-methyl-piperidin-4-yl]amino]-1-[2,2,2-tris(fluoranyl)ethyl]indol-2-yl]prop-2-ynylamino]-3-methoxy-~{N}-methyl-benzamide × 1 EDO 1,2-ETHANEDIOL × 6 NO3 NITRATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml in 25 mM Hepes, pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 1 mM Rezatapopt, 2% DMSO. Reservoir buffer: 0.2 M ammonium nitrate, 20% PEG 3350 (protein:buffer 2:1). Cryo: reservoir buffer supplemented with 23% ethylene glycol.
|
Resolution 1.40 Å R-free 0.188 |
| 9S9P Crystal structure of p53 cancer mutant Y220S in complex with rezatapopt Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
Fragment：DNA-binding domain
|
Not recorded | ZN ZINC ION × 1 A1JMR 4-[3-[4-[[(3~{S},4~{R})-3-fluoranyl-1-methyl-piperidin-4-yl]amino]-1-[2,2,2-tris(fluoranyl)ethyl]indol-2-yl]prop-2-ynylamino]-3-methoxy-~{N}-methyl-benzamide × 1 EDO 1,2-ETHANEDIOL × 10 NO3 NITRATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml in 25 mM Hepes, pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 1 mM Rezatapopt, 2% DMSO. Reservoir buffer: 0.2 M ammonium nitrate, 20% PEG 3350 (protein:buffer 2:1). Cryo: reservoir buffer supplemented with 23% ethylene glycol.
|
Resolution 1.40 Å R-free 0.188 |
| 9S9Q Crystal structure of p53 cancer mutant Y220N in complex with rezatapopt Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 A1JMR 4-[3-[4-[[(3~{S},4~{R})-3-fluoranyl-1-methyl-piperidin-4-yl]amino]-1-[2,2,2-tris(fluoranyl)ethyl]indol-2-yl]prop-2-ynylamino]-3-methoxy-~{N}-methyl-benzamide × 1 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml in 25 mM Hepes, pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 1 mM Rezatapopt, 2% DMSO. Reservoir buffer: 10% PEG 8000, 8% ethylene glycol, 0.1 M HEPES pH 7.5 (protein:buffer 1:1). Cryo: reservoir buffer supplemented with 23% ethylene glycol.
|
Resolution 1.87 Å R-free 0.243 |
| 9S9Q Crystal structure of p53 cancer mutant Y220N in complex with rezatapopt Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 A1JMR 4-[3-[4-[[(3~{S},4~{R})-3-fluoranyl-1-methyl-piperidin-4-yl]amino]-1-[2,2,2-tris(fluoranyl)ethyl]indol-2-yl]prop-2-ynylamino]-3-methoxy-~{N}-methyl-benzamide × 1 EDO 1,2-ETHANEDIOL × 5 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 6 mg/ml in 25 mM Hepes, pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 1 mM Rezatapopt, 2% DMSO. Reservoir buffer: 10% PEG 8000, 8% ethylene glycol, 0.1 M HEPES pH 7.5 (protein:buffer 1:1). Cryo: reservoir buffer supplemented with 23% ethylene glycol.
|
Resolution 1.87 Å R-free 0.243 |
| 9S9R Crystal structure of p53 cancer mutant Y220N Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；22.5% (w/v) BMW PEG smear broad, 0.1 M potassium sodium tartrate, 10% (w/v) ethylene glycol, 0.1 M sodium cacodylate, pH 5.3-5.8
|
Resolution 1.70 Å R-free 0.229 |
| 9S9R Crystal structure of p53 cancer mutant Y220N Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；22.5% (w/v) BMW PEG smear broad, 0.1 M potassium sodium tartrate, 10% (w/v) ethylene glycol, 0.1 M sodium cacodylate, pH 5.3-5.8
|
Resolution 1.70 Å R-free 0.229 |
| 9SPM p53 cancer mutant V143A in complex with DARPin C10 Deposited 2025-09-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
94–294（201 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 7 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 0.75 mg/ml p53-DARPin complex in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP. Reservoir buffer: 20% PEG smear broad, 0.1 M HEPES pH 7.5, 0.2 M ammonium nitrate. Drop volume ratio 1:1.
|
Resolution 1.71 Å R-free 0.218 |
| 9SPN p53 cancer mutant V157F in complex with DARPin C10 Deposited 2025-09-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
94–294（201 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 0.6 mg/ml DARPin-p53 complex in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP. Reservoir solution: 20% PEG3350, 10% ethylene glycol, 0.2 M sodium/potassium phosphate. Drop volume ratio 2:1.
|
Resolution 1.93 Å R-free 0.223 |
| 9SPO p53 cancer mutant Y220C in complex with DARPin C10 Deposited 2025-09-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
94–294（201 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 9 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 2.3 mg/ml DARPin-p53 complex in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP. Reservoir solution: 20% PEG3350, 10% ethylene glycol, 0.1 M bis-tris-propane pH 8.5, 0.2 M sodium formate. Drop volume ratio 2:1.
|
Resolution 1.48 Å R-free 0.182 |
| 9SPP p53 cancer mutant Y234C in complex with DARPin C10 Deposited 2025-09-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
94–294（201 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 8 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 1.5 mg/ml p53-DARPin complex in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP. Reservoir buffer: 15% PEG3350, 0.1 M magnesium formate. Drop volume ratio 2:1.
|
Resolution 1.47 Å R-free 0.192 |
| 9SPQ p53 cancer mutant V272M in complex with DARPin C10 Deposited 2025-09-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
94–294（201 aa）
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 0.9 mg/ml p53-DARPin complex in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP. Reservoir buffer: 2.4 M sodium malonate. Drop volume ratio 2:1.
|
Resolution 2.20 Å R-free 0.222 |
| 9SPR p53 cancer mutant R282W in complex with DARPin C10 Deposited 2025-09-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
94–294（201 aa）
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein concentration: 1.8 mg/ml in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP. Reservoir buffer: 25% PEG3350, 0.1M HEPES pH 7.5, 0.2M lithium sulfate. Drop volume ratio 1:1.
|
Resolution 1.66 Å R-free 0.201 |
| 9SPS p53 cancer mutant E285K in complex with DARPin C10-H82R Deposited 2025-09-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
94–294（201 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein concentration p53-DARPin complex: 0.54 mg/ml in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP. Reservoir buffer: 25% PEG3350, 0.2 M lithium sulfate monohydrate, 0.1 M Tris pH 8.5. Drop ratio protein vs reservoir buffer: 2:1.
|
Resolution 1.42 Å R-free 0.177 |
| 9SUK p53-R282W Core Domain Covalently Bound to a Vinyl-Sulfone Fragment Deposited 2025-09-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Mutation：M133L, V203A, N239Y, N268D, R282W | EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 PEG DI(HYDROXYETHYL)ETHER × 3 A1JQW 3-bromanyl-1-benzothiophene 1,1-dioxide × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
|
Resolution 1.56 Å R-free 0.206 |
| 9SUK p53-R282W Core Domain Covalently Bound to a Vinyl-Sulfone Fragment Deposited 2025-09-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Mutation：M133L, V203A, N239Y, N268D, R282W | EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1 A1JQW 3-bromanyl-1-benzothiophene 1,1-dioxide × 1 EDO 1,2-ETHANEDIOL × 4 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
|
Resolution 1.56 Å R-free 0.206 |
| 9SZZ p53-Y220C Core Domain Covalently Bound to a Vinyl-Sulfone Fragment Deposited 2025-10-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
94–312（219 aa）
|
Not recorded | A1JQW 3-bromanyl-1-benzothiophene 1,1-dioxide × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 ZN ZINC ION × 1 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
|
Resolution 1.70 Å R-free 0.213 |
| 9SZZ p53-Y220C Core Domain Covalently Bound to a Vinyl-Sulfone Fragment Deposited 2025-10-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
94–312（219 aa）
|
Not recorded | A1JQW 3-bromanyl-1-benzothiophene 1,1-dioxide × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT
|
Resolution 1.70 Å R-free 0.213 |
291 other PDB entries and 462 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | P53_HUMAN |
| Isoform | P04637-6 |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–200； UniProt 55–254 Author chain B； PDBConstruct 1–200； UniProt 55–254 |
