TP53-binding protein 1
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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 1488–1611 | Not recorded | WWQ (3S)-N-(4'-carbamoyl[1,1'-biphenyl]-3-yl)-1-[4-(4-methylpiperazin-1-yl)pyridine-2-carbonyl]piperidine-3-carboxamide × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2M Ammonium Formate | Resolution 1.60 Å R-free 0.262 |
| 2 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain B； UniProt 1488–1611 | Not recorded | WWQ (3S)-N-(4'-carbamoyl[1,1'-biphenyl]-3-yl)-1-[4-(4-methylpiperazin-1-yl)pyridine-2-carbonyl]piperidine-3-carboxamide × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2M Ammonium Formate | Resolution 1.60 Å R-free 0.262 |
| 3 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain C； UniProt 1488–1611 | Not recorded | WWQ (3S)-N-(4'-carbamoyl[1,1'-biphenyl]-3-yl)-1-[4-(4-methylpiperazin-1-yl)pyridine-2-carbonyl]piperidine-3-carboxamide × 1 UNX UNKNOWN LIGAND × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2M Ammonium Formate | Resolution 1.60 Å R-free 0.262 |
| 4 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain D； UniProt 1488–1611 | Not recorded | WWQ (3S)-N-(4'-carbamoyl[1,1'-biphenyl]-3-yl)-1-[4-(4-methylpiperazin-1-yl)pyridine-2-carbonyl]piperidine-3-carboxamide × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2M Ammonium Formate | Resolution 1.60 Å R-free 0.262 |
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 8SWJ | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1GZH Crystal structure of the BRCT domains of human 53BP1 bound to the p53 tumor supressor Deposited 2002-05-22 | Different construct 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
1724–1972（249 aa）
Fragment：BRCT TANDEM REPEAT, RESIDUES 1724-1972
|
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1724–1972（249 aa）
Fragment：BRCT TANDEM REPEAT, RESIDUES 1724-1972
|
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 |
| 1KZY Crystal Structure of the 53bp1 BRCT Region Complexed to Tumor Suppressor P53 Deposited 2002-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
1714–1972（259 aa）
Fragment：TANDEM-BRCT DOMAIN
Chain D
1714–1972（259 aa）
Fragment：TANDEM-BRCT 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 |
| 1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1485–1602（118 aa）
Fragment：residues 1485-1602
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.269 |
| 1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain J
1485–1602（118 aa）
Fragment：residues 1485-1602
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.269 |
| 1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1485–1602（118 aa）
Fragment：residues 1485-1602
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.269 |
| 1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1485–1602（118 aa）
Fragment：residues 1485-1602
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.269 |
| 1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1485–1602（118 aa）
Fragment：residues 1485-1602
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.269 |
| 1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
1485–1602（118 aa）
Fragment：residues 1485-1602
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.269 |
| 1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
1485–1602（118 aa）
Fragment：residues 1485-1602
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.269 |
| 1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain G
1485–1602（118 aa）
Fragment：residues 1485-1602
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.269 |
| 1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain H
1485–1602（118 aa）
Fragment：residues 1485-1602
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.269 |
| 1XNI Tandem Tudor Domain of 53BP1 Deposited 2004-10-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain I
1485–1602（118 aa）
Fragment：residues 1485-1602
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.269 |
| 2G3R Crystal Structure of 53BP1 tandem tudor domains at 1.2 A resolution Deposited 2006-02-20 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1484–1603（120 aa）
Fragment：Tandem tutor domains, residues 1484-1603 (SWS-Q12888)
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2% PEG 400, 0.1MHEPES/Na, 2M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.25 Å R-free 0.241 |
| 2G3R Crystal Structure of 53BP1 tandem tudor domains at 1.2 A resolution Deposited 2006-02-20 | 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 A
1484–1603（120 aa）
Fragment：Tandem tutor domains, residues 1484-1603 (SWS-Q12888)
|
Not recorded | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2% PEG 400, 0.1MHEPES/Na, 2M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.25 Å R-free 0.241 |
| 2IG0 Structure of 53BP1/methylated histone peptide complex Deposited 2006-09-22 | Different construct 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
1484–1603（120 aa）
Fragment：tandem tudor domains (resiudes 1484-1603)
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2% PEG 400, 0.1M HEPES/NA, 2M AMMONIUM SULFATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.251 |
| 2LVM Solution structure of human 53BP1 tandem Tudor domains in complex with a histone H4K20me2 peptide Deposited 2012-07-07 | Different construct 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
1484–1603（120 aa）
Fragment：UNP residues 1484-1603
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition
1.7 mM [U-100% 13C; U-100% 15N] protein_1, 8.5 mM protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1.7 mM [U-100% 13C; U-100% 15N] protein_1, 8.5 mM protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 100% D2O | 100% D2O
NMR sample composition
5 mM protein_1, 4 mM [U-100% 13C; U-100% 15N] protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
5 mM protein_1, 4 mM [U-100% 13C; U-100% 15N] protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 100% D2O | 100% 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 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
1484–1603（120 aa）
Fragment：Tudor-like region residues 1484-1603
|
Not recorded | 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 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
1484–1603（120 aa）
Fragment：Tudor-like region residues 1484-1603
|
Not recorded | 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 |
| 3LGF Crystal structure of the 53BP1 tandem tudor domain in complex with p53K370me2 Deposited 2010-01-20 | 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
1484–1603（120 aa）
Fragment：Tandem tudor domains (RESIUDES 1484-1603)
|
Not recorded | PGE TRIETHYLENE GLYCOL × 4 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M HEPES-Na pH 7.0, 2% PEG 400 and 2.4 M ammonium sulphate., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.50 Å R-free 0.232 |
| 3LGF Crystal structure of the 53BP1 tandem tudor domain in complex with p53K370me2 Deposited 2010-01-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1484–1603（120 aa）
Fragment：Tandem tudor domains (RESIUDES 1484-1603)
|
Not recorded | PGE TRIETHYLENE GLYCOL × 2 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M HEPES-Na pH 7.0, 2% PEG 400 and 2.4 M ammonium sulphate., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.50 Å R-free 0.232 |
| 3LGL Crystal structure of the 53BP1 tandem tudor domain in complex with p53K382me2 Deposited 2010-01-20 | Different construct 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
1484–1603（120 aa）
Fragment：TANDEM TUDOR DOMAINS (RESIUDES 1484-1603)
|
Not recorded | PGE TRIETHYLENE GLYCOL × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M HEPES-Na pH 7.0, 2% PEG 400 and 2.4 M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.60 Å R-free 0.251 |
| 3LH0 Crystal structure of the 53BP1 tandem tudor domain in complex with p53K372me2 Deposited 2010-01-21 | 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
1484–1603（120 aa）
Fragment：TANDEM TUDOR DOMAINS (RESIUDES 1484-1603)
|
Not recorded | PGE TRIETHYLENE GLYCOL × 4 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M HEPES-Na pH 7.0, 2% PEG 400 and 2.4 M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.90 Å R-free 0.232 |
| 3LH0 Crystal structure of the 53BP1 tandem tudor domain in complex with p53K372me2 Deposited 2010-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1484–1603（120 aa）
Fragment：TANDEM TUDOR DOMAINS (RESIUDES 1484-1603)
|
Not recorded | PGE TRIETHYLENE GLYCOL × 2 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M HEPES-Na pH 7.0, 2% PEG 400 and 2.4 M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.90 Å R-free 0.232 |
| 4CRI Crystal Structure of 53BP1 tandem tudor domains in complex with methylated K810 Rb peptide Deposited 2014-02-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1459–1634（176 aa）
Fragment：TANDEM TUDOR DOMAIN, RESIDUES 1459-1634
Chain B
1459–1634（176 aa）
Fragment：TANDEM TUDOR DOMAIN, RESIDUES 1459-1634
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；5%(W/V) PEG10K. 0.15M MAGNESIUM CHLORIDE, 0.1M TRIS PH 7.5
|
Resolution 2.35 Å R-free 0.230 |
| 4RG2 Tudor Domain of Tumor suppressor p53BP1 with small molecule ligand Deposited 2014-09-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1483–1606（124 aa）
Fragment：Tudor domain (UNP residues 1483-1606)
Chain B
1483–1606（124 aa）
Fragment：Tudor domain (UNP residues 1483-1606)
|
Not recorded | 3OO 3-bromo-N-[3-(tert-butylamino)propyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 3 UNX UNKNOWN LIGAND × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；19% PEG3350, 0.15 M DL-malic acid, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.50 Å R-free 0.220 |
| 4X34 Crystal structure of the 53BP1 tandem tudor domain in complex with p53K381acK382me2 Deposited 2014-11-27 | Different construct 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
1489–1608（120 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7.5；291 K；0.1 M sodium chloride and 4.0 M sodium formate
|
Resolution 1.80 Å R-free 0.218 |
| 4X34 Crystal structure of the 53BP1 tandem tudor domain in complex with p53K381acK382me2 Deposited 2014-11-27 | Different construct 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
1489–1608（120 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7.5；291 K；0.1 M sodium chloride and 4.0 M sodium formate
|
Resolution 1.80 Å R-free 0.218 |
| 5ECG Crystal structure of the BRCT domains of 53BP1 in complex with p53 and H2AX-pSer139 (gammaH2AX) Deposited 2015-10-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1713–1972（260 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
1713–1972（260 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 |
| 5J26 Crystal structure of a 53BP1 Tudor domain in complex with a ubiquitin variant Deposited 2016-03-29 | Different construct 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
1492–1608（117 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M Sodium Cacodylate pH 6.0, 0.2 M Sodium Acetate, 27% (w/v) PEG8000
|
Resolution 2.50 Å R-free 0.287 |
| 5Z78 Structure of TIRR/53BP1 complex Deposited 2018-01-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1484–1603（120 aa）
Fragment：UNP residues 1484-1603
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；Bis-Tris propane,PEG MME550
|
Resolution 1.76 Å R-free 0.222 |
| 5ZCJ Crystal structure of complex Deposited 2018-02-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1459–1634（176 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.7 M Ammonium tartrate, 0.1 M Sodium acetate pH 4.6
|
Resolution 2.00 Å R-free 0.219 |
| 6CO1 Structure of human TIRR in complex with 53BP1 Tudor domains Deposited 2018-03-10 | Different construct 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
1484–1603（120 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M MES, pH 5.5, 0.2 M calcium acetate, 7% isopropanol
|
Resolution 2.18 Å R-free 0.203 |
| 6CO1 Structure of human TIRR in complex with 53BP1 Tudor domains Deposited 2018-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
1484–1603（120 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M MES, pH 5.5, 0.2 M calcium acetate, 7% isopropanol
|
Resolution 2.18 Å R-free 0.203 |
| 6CO2 Structure of an engineered protein (NUDT16TI) in complex with 53BP1 Tudor domains Deposited 2018-03-10 | 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 C
1484–1603（120 aa）
Chain D
1484–1603（120 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M sodium citrate tribasic dehydrate, pH 5.6, 0.2 M ammonium acetate, 10% PEG 4,000
|
Resolution 2.49 Å R-free 0.270 |
| 6IU7 Crystal structure of importin-alpha1 bound to the 53BP1 nuclear localization signal (wild-type) Deposited 2018-11-27 | Different construct 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
1665–1686（22 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；sodium citrate, HEPES, DTT
|
Resolution 1.90 Å R-free 0.185 |
| 6IUA Crystal structure of importin-alpha1 bound to the 53BP1 nuclear localization signal (S1678D) Deposited 2018-11-27 | 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
1665–1686（22 aa）
|
Mutation：S1678D | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；sodium citrate, HEPES, DTT
|
Resolution 1.70 Å R-free 0.179 |
| 6MXX Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC2991 Deposited 2018-10-31 | 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
1484–1603（120 aa）
Chain B
1484–1603（120 aa）
|
Not recorded | PO4 PHOSPHATE ION × 3 K6P N-[3-(tert-butylamino)propyl]-3-iodobenzamide × 1 FMT FORMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1 M sodium formate; 0.1 M Bis-Tris propane, pH 7.0
|
Resolution 2.30 Å R-free 0.232 |
| 6MXX Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC2991 Deposited 2018-10-31 | Different construct Different mutation/modification 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
1484–1603（120 aa）
Chain D
1484–1603（120 aa）
|
Not recorded | PO4 PHOSPHATE ION × 6 K6P N-[3-(tert-butylamino)propyl]-3-iodobenzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1 M sodium formate; 0.1 M Bis-Tris propane, pH 7.0
|
Resolution 2.30 Å R-free 0.232 |
| 6MXX Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC2991 Deposited 2018-10-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain E
1484–1603（120 aa）
Chain F
1484–1603（120 aa）
|
Not recorded | PO4 PHOSPHATE ION × 4 K6P N-[3-(tert-butylamino)propyl]-3-iodobenzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1 M sodium formate; 0.1 M Bis-Tris propane, pH 7.0
|
Resolution 2.30 Å R-free 0.232 |
| 6MXX Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC2991 Deposited 2018-10-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain G
1484–1603（120 aa）
Chain H
1484–1603（120 aa）
|
Not recorded | PO4 PHOSPHATE ION × 4 K6P N-[3-(tert-butylamino)propyl]-3-iodobenzamide × 1 FMT FORMIC ACID × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1 M sodium formate; 0.1 M Bis-Tris propane, pH 7.0
|
Resolution 2.30 Å R-free 0.232 |
| 6MXX Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC2991 Deposited 2018-10-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain I
1484–1603（120 aa）
Chain J
1484–1603（120 aa）
|
Not recorded | PO4 PHOSPHATE ION × 4 K6P N-[3-(tert-butylamino)propyl]-3-iodobenzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1 M sodium formate; 0.1 M Bis-Tris propane, pH 7.0
|
Resolution 2.30 Å R-free 0.232 |
| 6MXY Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC3351 Deposited 2018-10-31 | 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
1484–1603（120 aa）
Chain B
1484–1603（120 aa）
|
Not recorded | PO4 PHOSPHATE ION × 5 K6M N-[3-(tert-butylamino)propyl]-3-(trifluoromethyl)benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；0.1 M sodium citrate tribasic, pH 5.6; 1M ammonium phosphate monobasic
|
Resolution 1.62 Å R-free 0.213 |
| 6MXZ Structure of 53BP1 Tudor domains in complex with small molecule UNC3474 Deposited 2018-10-31 | 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
1484–1603（120 aa）
Chain B
1484–1603（120 aa）
|
Not recorded | K6S N-[3-(tert-butylamino)propyl]-3-(propan-2-yl)benzamide × 1 FMT FORMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；2 M sodium formate; 0.1 M bis-tris propane, pH 7.0
|
Resolution 2.50 Å R-free 0.223 |
| 6MXZ Structure of 53BP1 Tudor domains in complex with small molecule UNC3474 Deposited 2018-10-31 | Different construct Different mutation/modification 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
1484–1603（120 aa）
Chain D
1484–1603（120 aa）
|
Not recorded | K6S N-[3-(tert-butylamino)propyl]-3-(propan-2-yl)benzamide × 1 FMT FORMIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；2 M sodium formate; 0.1 M bis-tris propane, pH 7.0
|
Resolution 2.50 Å R-free 0.223 |
| 6MXZ Structure of 53BP1 Tudor domains in complex with small molecule UNC3474 Deposited 2018-10-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain E
1484–1603（120 aa）
Chain F
1484–1603（120 aa）
|
Not recorded | K6S N-[3-(tert-butylamino)propyl]-3-(propan-2-yl)benzamide × 1 FMT FORMIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；2 M sodium formate; 0.1 M bis-tris propane, pH 7.0
|
Resolution 2.50 Å R-free 0.223 |
| 6MXZ Structure of 53BP1 Tudor domains in complex with small molecule UNC3474 Deposited 2018-10-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain G
1484–1603（120 aa）
Chain H
1484–1603（120 aa）
|
Not recorded | K6S N-[3-(tert-butylamino)propyl]-3-(propan-2-yl)benzamide × 1 FMT FORMIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；2 M sodium formate; 0.1 M bis-tris propane, pH 7.0
|
Resolution 2.50 Å R-free 0.223 |
| 6MXZ Structure of 53BP1 Tudor domains in complex with small molecule UNC3474 Deposited 2018-10-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain I
1484–1603（120 aa）
Chain J
1484–1603（120 aa）
|
Not recorded | K6S N-[3-(tert-butylamino)propyl]-3-(propan-2-yl)benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；2 M sodium formate; 0.1 M bis-tris propane, pH 7.0
|
Resolution 2.50 Å R-free 0.223 |
| 6MY0 Structure of 53BP1 Tandem Tudor domains with E1549P and D1550N mutations Deposited 2018-10-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1484–1603（120 aa）
|
Mutation：E1549P, D1550N | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；1.5 M sodium/potassium phosphate, pH 6.0
|
Resolution 2.20 Å R-free 0.233 |
| 6MY0 Structure of 53BP1 Tandem Tudor domains with E1549P and D1550N mutations Deposited 2018-10-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1484–1603（120 aa）
|
Mutation：E1549P, D1550N | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；1.5 M sodium/potassium phosphate, pH 6.0
|
Resolution 2.20 Å R-free 0.233 |
| 6VA5 Tudor Domain of Tumor suppressor p53BP1 with MFP-4184 Deposited 2019-12-16 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1488–1611（124 aa）
|
Not recorded | QSS 2-(4-methylpiperazin-1-yl)aniline × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 4 UNX UNKNOWN LIGAND × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；2M ammonium sulfate, 0.1 M HEPES pH 7.5, 2% PEG 400
|
Resolution 1.28 Å R-free 0.185 |
| 6VIP TUDOR DOMAIN OF TUMOR SUPPRESSOR P53BP1 WITH MFP-6008 Deposited 2020-01-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1488–1611（124 aa）
|
Not recorded | QXY {4-[(3,5-dimethyl-1H-pyrazol-1-yl)methyl]phenyl}(4-ethylpiperazin-1-yl)methanone × 1 UNX UNKNOWN LIGAND × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；2M ammonium sulfate, 0.1 M HEPES pH 7.5, 2% PEG 400
|
Resolution 1.36 Å R-free 0.211 |
| 6VIP TUDOR DOMAIN OF TUMOR SUPPRESSOR P53BP1 WITH MFP-6008 Deposited 2020-01-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1488–1611（124 aa）
|
Not recorded | QXY {4-[(3,5-dimethyl-1H-pyrazol-1-yl)methyl]phenyl}(4-ethylpiperazin-1-yl)methanone × 1 UNX UNKNOWN LIGAND × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；2M ammonium sulfate, 0.1 M HEPES pH 7.5, 2% PEG 400
|
Resolution 1.36 Å R-free 0.211 |
| 7LIN X-ray structure of SPOP MATH domain (D140G) in complex with a 53BP1 peptide Deposited 2021-01-27 | Different construct 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
1636–1650（15 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；SPOP MATH was at 24 mg/ml and 1:5 protein:53BP1 peptide molar ratio.
Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml. Reservoir solution: 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 0.2 M (NH4)2SO4, 1 M Li2SO4
|
Resolution 1.44 Å R-free 0.186 |
| 7LIO X-ray structure of SPOP MATH domain (S119D) in complex with a 53BP1 peptide Deposited 2021-01-27 | Different construct 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
1636–1650（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；SPOP MATH (S119D) was at a concentration of 20 mg/ml with a 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml of 2 M (NH4)2SO4.
|
Resolution 3.01 Å R-free 0.277 |
| 7LIO X-ray structure of SPOP MATH domain (S119D) in complex with a 53BP1 peptide Deposited 2021-01-27 | Different construct 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
1636–1650（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；SPOP MATH (S119D) was at a concentration of 20 mg/ml with a 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml of 2 M (NH4)2SO4.
|
Resolution 3.01 Å R-free 0.277 |
| 8EOM TUDOR DOMAIN OF TUMOR SUPPRESSOR P53BP1 WITH MFP-5973 Deposited 2022-10-03 | 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
1488–1611（124 aa）
Chain B
1488–1611（124 aa）
|
Not recorded | WNQ 4-(4-methylpiperazine-1-sulfonyl)benzamide × 2 UNX UNKNOWN LIGAND × 3 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；2M ammonium sulfate, 0.1 M HEPES pH 7.5, 2% PEG 400
|
Resolution 1.70 Å R-free 0.244 |
| 8F0W Tudor Domain of Tumor suppressor p53BP1 with MFP-5956 Deposited 2022-11-04 | 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
1488–1611（124 aa）
Chain B
1488–1611（124 aa）
|
Not recorded | X9N 1-[4-(4-ethylpiperazin-1-yl)-3-fluorophenyl]butan-1-one × 2 UNX UNKNOWN LIGAND × 35 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；2M ammonium sulfate, 0.1 M HEPES pH 7.5, 2% PEG 400
|
Resolution 1.52 Å R-free 0.234 |
| 8HKW Crystal structure of importin-alpha3 bound to the 53BP1 nuclear localization signal Deposited 2022-11-28 | 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 C
1665–1686（22 aa）
Chain D
1665–1686（22 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Mother liquor contained PEG3350 and lithium nitrate. Crystal was grown in the presence of a synthetic peptide (amino acid sequence: GTSFSGRKIKTAVRRRK) that corresponds to human Nup153 residues 1459-1475).
|
Resolution 1.90 Å R-free 0.221 |
| 8U4U Crystal structure of 53BP1 tandem Tudor domain homodimer engineered with two disulfide bridges Deposited 2023-09-11 | 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
1484–1603（120 aa）
Chain B
1484–1603（120 aa）
|
Mutation：E1549C, E1567C Mutation：E1549C, E1567C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Crystals of the protein (15 mg/mL) were obtained by the hanging drop vapor diffusion method, mixing 1 microliter of the sample in 50 mM Tris-HCl, pH 7.0, 100 mM NaCl and 1 microliter of the reservoir solution (0.1 M Bis-Tris, pH 6.5) at 293 K. The crystals were cryoprotected with 25% (w/v) xylitol
|
Resolution 3.79 Å R-free 0.300 |
| 8U4U Crystal structure of 53BP1 tandem Tudor domain homodimer engineered with two disulfide bridges Deposited 2023-09-11 | Different construct Different mutation/modification 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
1484–1603（120 aa）
Chain D
1484–1603（120 aa）
|
Mutation：E1549C, E1567C Mutation：E1549C, E1567C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Crystals of the protein (15 mg/mL) were obtained by the hanging drop vapor diffusion method, mixing 1 microliter of the sample in 50 mM Tris-HCl, pH 7.0, 100 mM NaCl and 1 microliter of the reservoir solution (0.1 M Bis-Tris, pH 6.5) at 293 K. The crystals were cryoprotected with 25% (w/v) xylitol
|
Resolution 3.79 Å R-free 0.300 |
| 8U4U Crystal structure of 53BP1 tandem Tudor domain homodimer engineered with two disulfide bridges Deposited 2023-09-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain E
1484–1603（120 aa）
Chain F
1484–1603（120 aa）
|
Mutation：E1549C, E1567C Mutation：E1549C, E1567C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Crystals of the protein (15 mg/mL) were obtained by the hanging drop vapor diffusion method, mixing 1 microliter of the sample in 50 mM Tris-HCl, pH 7.0, 100 mM NaCl and 1 microliter of the reservoir solution (0.1 M Bis-Tris, pH 6.5) at 293 K. The crystals were cryoprotected with 25% (w/v) xylitol
|
Resolution 3.79 Å R-free 0.300 |
| 8U4U Crystal structure of 53BP1 tandem Tudor domain homodimer engineered with two disulfide bridges Deposited 2023-09-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain G
1484–1603（120 aa）
Chain H
1484–1603（120 aa）
|
Mutation：E1549C, E1567C Mutation：E1549C, E1567C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Crystals of the protein (15 mg/mL) were obtained by the hanging drop vapor diffusion method, mixing 1 microliter of the sample in 50 mM Tris-HCl, pH 7.0, 100 mM NaCl and 1 microliter of the reservoir solution (0.1 M Bis-Tris, pH 6.5) at 293 K. The crystals were cryoprotected with 25% (w/v) xylitol
|
Resolution 3.79 Å R-free 0.300 |
| 8U4U Crystal structure of 53BP1 tandem Tudor domain homodimer engineered with two disulfide bridges Deposited 2023-09-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain I
1484–1603（120 aa）
Chain J
1484–1603（120 aa）
|
Mutation：E1549C, E1567C Mutation：E1549C, E1567C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Crystals of the protein (15 mg/mL) were obtained by the hanging drop vapor diffusion method, mixing 1 microliter of the sample in 50 mM Tris-HCl, pH 7.0, 100 mM NaCl and 1 microliter of the reservoir solution (0.1 M Bis-Tris, pH 6.5) at 293 K. The crystals were cryoprotected with 25% (w/v) xylitol
|
Resolution 3.79 Å R-free 0.300 |
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| UniProt name | TP53B_HUMAN |
| Isoform | Q12888-3 |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 2–125； UniProt 1488–1611 Author chain B； PDBConstruct 2–125； UniProt 1488–1611 Author chain C； PDBConstruct 2–125； UniProt 1488–1611 Author chain D； PDBConstruct 2–125； UniProt 1488–1611 |