Ubiquitin
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 1–76 | Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M Sodium acetate, 5% PEG 3000, 50 mM Zinc acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | Resolution 1.96 Å R-free 0.236 |
| 2 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain B； UniProt 1–76 | Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M Sodium acetate, 5% PEG 3000, 50 mM Zinc acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | Resolution 1.96 Å R-free 0.236 |
| 3 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain C； UniProt 1–76 | Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M Sodium acetate, 5% PEG 3000, 50 mM Zinc acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | Resolution 1.96 Å R-free 0.236 |
| 4 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain D； UniProt 1–76 | Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M Sodium acetate, 5% PEG 3000, 50 mM Zinc acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | Resolution 1.96 Å R-free 0.236 |
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 3HM3 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1C3T ROTAMER STRAIN AS A DETERMINANT OF PROTEIN STRUCTURAL SPECIFICITY Deposited 1999-07-28 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
87–162（76 aa）
|
Mutation：I3L,I13L,L15V,V17L,I23V,V26L,I61L,L67I | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 5.8；303 K；Ionic strength (raw mmCIF value) 50 mM；Pressure 1
NMR sample composition
2 MM 13C/15N 1D8 UBIQUITIN, 25 MM SODIUM PHOSPHATE, 25 MM SODIUM ACETATE (D3),
0.02% SODIUM AZIDE, PH 5.8
|
Resolution not provided |
| 1D3Z UBIQUITIN NMR STRUCTURE Deposited 1999-10-01 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
136–211（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；308 K；Ionic strength (raw mmCIF value) 20 mM；Pressure AMBIENT
NMR sample composition
UBIQUITIN HUMAN SEQUENCE
|
Resolution not provided |
| 1F9J STRUCTURE OF A NEW CRYSTAL FORM OF TETRAUBIQUITIN Deposited 2000-07-10 | 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
1–76（76 aa）
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；lithium sulfate, ammonium sulfate, sodium citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.70 Å R-free 0.292 |
| 1FXT STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTER COMPLEX Deposited 2000-09-26 | 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
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.5；30 K；Ionic strength (raw mmCIF value) 450mM NaCl；Pressure ambient
NMR sample composition
Yeast Ubc1 | 0.8 mM Ubc1 10uM E1 0.8 mM Ub
10mM ATP, 5 mM MgCl, 40 mM Hepes,
450 mM NaCl,, 1 mM EDTA in water
NMR sample composition
Human Ub | 0.8 mM Ubc1 10uM E1 0.8 mM Ub
10mM ATP, 5 mM MgCl, 40 mM Hepes,
450 mM NaCl,, 1 mM EDTA in water
|
Resolution not provided |
| 1G6J STRUCTURE OF RECOMBINANT HUMAN UBIQUITIN IN AOT REVERSE MICELLES Deposited 2000-11-06 | Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
293 K；Pressure ambient
NMR measurement conditions
293 K；Pressure 50
NMR sample composition
4 mg c13/n15 ubiquitin in 13.5 ul of buffer (50mM Sodium acetate, 250mM Sodium Chloride, pH 5.0) and 1 ml D12-pentane | 75mM bis(2-ethyl hexyl) sulfosuccinate in d-pentane
NMR sample composition
8 mg 13/n15 ubiquitin in 27 ul of buffer (50mM Sodium acetate, 250mM Sodium Chloride, pH 5.0) | 75mM bis(2-ethyl hexyl) sulfosuccinate in butane
NMR sample composition
4 mg n15 ubiquitin in 13.5 ul of buffer (50mM Sodium acetate, 250mM Sodium Chloride, pH 5.0) | 75mM bis(2-ethyl hexyl) sulfosuccinate in d-pentane
|
Resolution not provided |
| 1NBF Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde Deposited 2002-12-02 | 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
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；296 K；PEG3000, citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
|
Resolution 2.30 Å R-free 0.262 |
| 1NBF Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde Deposited 2002-12-02 | 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
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；296 K；PEG3000, citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
|
Resolution 2.30 Å R-free 0.262 |
| 1Q5W Ubiquitin Recognition by Npl4 Zinc-Fingers Deposited 2003-08-11 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 |
SOLUTION NMR
NMR measurement conditions
pH 5.5；291 K；Ionic strength (raw mmCIF value) 70mM；Pressure ambient
NMR measurement conditions
pH 5.5；291 K；Ionic strength (raw mmCIF value) 70mM；Pressure ambient
NMR measurement conditions
pH 5.5；291 K；Ionic strength (raw mmCIF value) 70mM；Pressure ambient
NMR measurement conditions
pH 5.5；291 K；Ionic strength (raw mmCIF value) 70mM；Pressure ambient
NMR sample composition
1mM Npl4 NZF U-15N,13C; 2mM unlabeled-Ubiquitin; 20mM phosphate buffer pH 5.5, 50mM NaCl; 90% H2O, 10% | 90% H2O/10% D2O
NMR sample composition
1mM Ubiquitin U-15N,13C; 2mM unlabeled-Npl4 NZF; 20mM phosphate buffer pH 5.5, 50mM NaCl; 90% H2O, 10% | 90% H2O/10% D2O
NMR sample composition
1mM Ubiquitin U-15N; 2mM unlabeled-Npl4 NZF; 20mM phosphate buffer pH 5.5, 50mM | 90% H2O/10% D2O
NMR sample composition
1mM Npl4 NZF U-15N; 2mM unlabeled-Ubiquitin; 20mM phosphate buffer pH 5.5, 50mM NaCl; 90% H2O, 10% | 90% H2O/10% D2O
|
Resolution not provided |
| 1S1Q TSG101(UEV) domain in complex with Ubiquitin Deposited 2004-01-07 | 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
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；1.4M Ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.240 |
| 1S1Q TSG101(UEV) domain in complex with Ubiquitin Deposited 2004-01-07 | 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
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 SO4 SULFATE ION × 2 ACY ACETIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；1.4M Ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.240 |
| 1SIF Crystal structure of a multiple hydrophobic core mutant of ubiquitin Deposited 2004-02-29 | 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
1–76（76 aa）
|
Mutation：M1L, I3L, V5I, I13F, L15V, V17M, V26L | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；288 K；31% Peg 4K, 0.05M citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K
|
Resolution 2.18 Å R-free 0.248 |
| 1TBE STRUCTURE OF TETRAUBIQUITIN SHOWS HOW MULTIUBIQUITIN CHAINS CAN BE FORMED Deposited 1993-10-14 | 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
1–76（76 aa）
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.40 Å |
| 1UBI SYNTHETIC STRUCTURAL AND BIOLOGICAL STUDIES OF THE UBIQUITIN SYSTEM. PART 1 Deposited 1994-02-03 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å |
| 1UBQ STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION Deposited 1987-01-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å |
| 1XD3 Crystal structure of UCHL3-UbVME complex Deposited 2004-09-03 | 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
229–303（75 aa）
|
Not recorded | MG MAGNESIUM ION × 3 GVE METHYL 4-AMINOBUTANOATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.45 Å R-free 0.192 |
| 1XD3 Crystal structure of UCHL3-UbVME complex Deposited 2004-09-03 | 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
229–303（75 aa）
|
Not recorded | MG MAGNESIUM ION × 7 GVE METHYL 4-AMINOBUTANOATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.45 Å R-free 0.192 |
| 1YX5 Solution Structure of S5a UIM-1/Ubiquitin Complex Deposited 2005-02-19 | 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 B
1–76（76 aa）
Fragment：Sequence Database Residues 1-76
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1
NMR sample composition
0.5 mM S5a U-15N, 2H
2.0 mM ubiquitin unlabeled | 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O
NMR sample composition
0.5 mM S5a U-15N, 2H
2.0 mM ubiquitin U-13C | 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O
NMR sample composition
0.5 mM S5a U-13C
2.0 mM ubiquitin unlabeled | 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O
|
Resolution not provided |
| 1YX6 Solution Structure of S5a UIM-2/Ubiquitin Complex Deposited 2005-02-19 | 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 B
1–76（76 aa）
Fragment：Sequence Database Residues 1-76
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1
NMR sample composition
0.5 mM S5a U-15N, 2H; 2.0 mM ubiquitin unlabeled | 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O
NMR sample composition
0.5 mM S5a U-15N, 2H; 2.0 mM ubiquitin U-13C | 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O
NMR sample composition
0.5 mM S5a U-13C; 2.0 mM ubiquitin unlabeled | 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O
|
Resolution not provided |
| 2AYO Structure of USP14 bound to ubquitin aldehyde Deposited 2005-09-07 | 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
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；Tris, calsium chloride, PEG1000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
|
Resolution 3.50 Å R-free 0.330 |
| 2AYO Structure of USP14 bound to ubquitin aldehyde Deposited 2005-09-07 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；Tris, calsium chloride, PEG1000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
|
Resolution 3.50 Å R-free 0.330 |
| 2BGF NMR structure of Lys48-linked di-ubiquitin using chemical shift perturbation data together with RDCs and 15N-relaxation data Deposited 2004-12-22 | 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
1–76（76 aa）
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；298 K；Ionic strength (raw mmCIF value) 20；Pressure 1.0
NMR sample composition
90% WATER/10% D20
|
Resolution not provided |
| 2FUH Solution Structure of the UbcH5c/Ub Non-covalent Complex Deposited 2006-01-26 | 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 B
1–76（76 aa）
Fragment：Ubiquitin
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 150mM NaCl；Pressure ambient
NMR sample composition
1mM UbcH5c U-15N,13C
25mM sodium phosphate
150mM NaCl | 90% H20
10% D20
NMR sample composition
1mM Ubiquitin U-15N,13C
25mM sodium phosphate
150mM NaCl | 90% H20
10% D20
NMR sample composition
1mM UbcH5c U-15N,13C
1mM Ubiquitin
25mM sodium phosphate
150mM NaCl | 90% H20
10% D20
NMR sample composition
1mM Ubiquitin U-15N,13C
1mM UbcH5c
25mM sodium phosphate
150mM NaCl | 90% H20
10% D20
NMR sample composition
1mM UbcH5c U-15N,13C
1mM Ubiquitin
25mM sodium phosphate
150mM NaCl | 100% D20
NMR sample composition
1mM Ubiquitin U-15N,13C
1mM UbcH5c
25mM sodium phosphate
150mM NaCl | 100% D20
|
Resolution not provided |
| 2G45 Co-crystal structure of znf ubp domain from the deubiquitinating enzyme isopeptidase T (isot) in complex with ubiquitin Deposited 2006-02-21 | 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
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；300 K；16% polyethylene glycol 8000, 80 mM sodium cacodylate pH 6.5, 160 mM magenesium or calcium acetate, 20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 6.50
|
Resolution 1.99 Å R-free 0.268 |
| 2G45 Co-crystal structure of znf ubp domain from the deubiquitinating enzyme isopeptidase T (isot) in complex with ubiquitin Deposited 2006-02-21 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；300 K；16% polyethylene glycol 8000, 80 mM sodium cacodylate pH 6.5, 160 mM magenesium or calcium acetate, 20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 6.50
|
Resolution 1.99 Å R-free 0.268 |
| 2GBJ Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin. Deposited 2006-03-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.9；279.15 K；27-32% PEG 4000, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K
|
Resolution 1.35 Å R-free 0.226 |
| 2GBJ Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin. Deposited 2006-03-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.9；279.15 K；27-32% PEG 4000, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K
|
Resolution 1.35 Å R-free 0.226 |
| 2GBK Crystal Structure of the 9-10 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.9；293.15 K；27-32% PEG 6000, 4-12% Acetone, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 1.99 Å R-free 0.287 |
| 2GBK Crystal Structure of the 9-10 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.9；293.15 K；27-32% PEG 6000, 4-12% Acetone, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 1.99 Å R-free 0.287 |
| 2GBK Crystal Structure of the 9-10 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.9；293.15 K；27-32% PEG 6000, 4-12% Acetone, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 1.99 Å R-free 0.287 |
| 2GBK Crystal Structure of the 9-10 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.9；293.15 K；27-32% PEG 6000, 4-12% Acetone, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 1.99 Å R-free 0.287 |
| 2GBK Crystal Structure of the 9-10 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10 | 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 A
1–76（76 aa）
Chain C
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.9；293.15 K；27-32% PEG 6000, 4-12% Acetone, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 1.99 Å R-free 0.287 |
| 2GBK Crystal Structure of the 9-10 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
1–76（76 aa）
Chain D
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.9；293.15 K；27-32% PEG 6000, 4-12% Acetone, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 1.99 Å R-free 0.287 |
| 2GBM Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin Deposited 2006-03-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；293.15 K；25-30% PEG 4000, 50 mM Sodium Cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 5.50
|
Resolution 1.55 Å R-free 0.227 |
| 2GBM Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin Deposited 2006-03-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Not recorded | ARS ARSENIC × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；293.15 K；25-30% PEG 4000, 50 mM Sodium Cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 5.50
|
Resolution 1.55 Å R-free 0.227 |
| 2GBM Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin Deposited 2006-03-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–76（76 aa）
|
Not recorded | ARS ARSENIC × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；293.15 K；25-30% PEG 4000, 50 mM Sodium Cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 5.50
|
Resolution 1.55 Å R-free 0.227 |
| 2GBM Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin Deposited 2006-03-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–76（76 aa）
|
Not recorded | ARS ARSENIC × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；293.15 K；25-30% PEG 4000, 50 mM Sodium Cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 5.50
|
Resolution 1.55 Å R-free 0.227 |
| 2GBN Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin Deposited 2006-03-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；279.15 K；25-30% PEG 4000, 50 mM Sodium Cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K
|
Resolution 1.60 Å R-free 0.265 |
| 2GBR Crystal Structure of the 35-36 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | CD CADMIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 3.9；293.15 K；24-30% PEG 4000, 50-80 mM Cadmium Chloride, 100 mM Sodium Acetate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 2.00 Å R-free 0.290 |
| 2GBR Crystal Structure of the 35-36 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Not recorded | CD CADMIUM ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 3.9；293.15 K；24-30% PEG 4000, 50-80 mM Cadmium Chloride, 100 mM Sodium Acetate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 2.00 Å R-free 0.290 |
| 2GBR Crystal Structure of the 35-36 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–76（76 aa）
|
Not recorded | CD CADMIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 3.9；293.15 K；24-30% PEG 4000, 50-80 mM Cadmium Chloride, 100 mM Sodium Acetate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 2.00 Å R-free 0.290 |
| 2GBR Crystal Structure of the 35-36 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
|
Not recorded | CD CADMIUM ION × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 3.9；293.15 K；24-30% PEG 4000, 50-80 mM Cadmium Chloride, 100 mM Sodium Acetate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 2.00 Å R-free 0.290 |
| 2GBR Crystal Structure of the 35-36 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10 | 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 A
1–76（76 aa）
Chain B
1–76（76 aa）
|
Not recorded | CD CADMIUM ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 3.9；293.15 K；24-30% PEG 4000, 50-80 mM Cadmium Chloride, 100 mM Sodium Acetate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 2.00 Å R-free 0.290 |
| 2HTH Structural basis for ubiquitin recognition by the human EAP45/ESCRT-II GLUE domain Deposited 2006-07-25 | 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
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；10% PEG8000; 10% Ethylene glycol; 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.70 Å R-free 0.289 |
| 2IBI Covalent Ubiquitin-USP2 Complex Deposited 2006-09-11 | 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
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 NEH ETHANAMINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 9；298 K；22% PEG1500, 0.1 M Bicine, 0.2 M
NaCl, 1 mM DTT, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 9.00
|
Resolution 2.20 Å R-free 0.259 |
| 2J7Q Crystal structure of the ubiquitin-specific protease encoded by murine cytomegalovirus tegument protein M48 in complex with a ubquitin-based suicide substrate Deposited 2006-10-16 | 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
1–75（75 aa）
Fragment：UBIQUITIN FUSED TO VINYLMETHYLESTER, UBVME, RESIDUES 1-75
|
Not recorded | MG MAGNESIUM ION × 2 GVE METHYL 4-AMINOBUTANOATE × 1 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；200 MM MAGNESIUM FORMATE, 14% PEG 3350, pH 7.50
|
Resolution 1.80 Å R-free 0.214 |
| 2J7Q Crystal structure of the ubiquitin-specific protease encoded by murine cytomegalovirus tegument protein M48 in complex with a ubquitin-based suicide substrate Deposited 2006-10-16 | 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
1–75（75 aa）
Fragment：UBIQUITIN FUSED TO VINYLMETHYLESTER, UBVME, RESIDUES 1-75
|
Not recorded | MG MAGNESIUM ION × 1 GVE METHYL 4-AMINOBUTANOATE × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；200 MM MAGNESIUM FORMATE, 14% PEG 3350, pH 7.50
|
Resolution 1.80 Å R-free 0.214 |
| 2JF5 crystal structure of Lys63-linked di-ubiquitin Deposited 2007-01-26 | 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
1–76（76 aa）
Chain B
1–76（76 aa）
|
Not recorded | CD CADMIUM ION × 2 MG MAGNESIUM ION × 1 CO COBALT (II) ION × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；12 % (W/V) PEG 3350, 5 MM NICKEL CHLORIDE, 5 MM COBALT CHLORIDE, 5 MM CADMIUM CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 0.1 M HEPES [PH 7.5]
|
Resolution 1.95 Å R-free 0.250 |
| 2JZZ Solid-State NMR Structure of Microcrystalline Ubiquitin Deposited 2008-01-22 | Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLID-STATE NMR
NMR measurement conditions
270 K；Pressure ambient
NMR sample composition
5.5 mg/mL [U-99% 13C; U-98% 15N] Ubiquitin, 20 mM ammonium acetate, 20 mM citric acid, 60 v/v 2-methyl-2,4-pentandiol, 0.05 % sodium azide, 100 % H2O | 100 % H2O
|
Resolution not provided |
| 2K6D CIN85 Sh3-C domain in complex with ubiquitin Deposited 2008-07-07 | 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 B
1–75（75 aa）
Fragment：ubiquitin
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.4；298 K；Ionic strength (raw mmCIF value) 0.150；Pressure ambient
NMR sample composition
0.1 mM CIN85, 0.1 mM [U-100% 15N] ubiquitin, 50 mM sodium phosphate, 2 mM DTT, 5 mM DSS, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.1 mM [U-100% 15N] CIN85, 0.1 mM ubiquitiny, 50 mM sodium phosphate, 2 mM DTT, 5 mM DSS, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1.0 mM [U-100% 13C; U-100% 15N] CIN85, 50 mM sodium phosphate, 2 mM DTT, 5 mM DSS, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2K8B Solution structure of PLAA family ubiquitin binding domain (PFUC) cis isomer in complex with ubiquitin Deposited 2008-09-04 | 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
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient
NMR sample composition
0.2 mM Ubiquitin, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
0.2 mM PFUC_cis, 90% H2O, 10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2K8C Solution structure of PLAA family ubiquitin binding domain (PFUC) trans isomer in complex with ubiquitin Deposited 2008-09-04 | 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
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient
NMR sample composition
0.2 mM [U-100% 15N] Ubiquitin, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
0.2 mM [U-100% 15N] PFUC_trans, 90% H2O, 10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2KDF NMR structure of minor S5a (196-306):K48 linked diubiquitin species Deposited 2009-01-06 | 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 × 3 PDB declaration: trimeric |
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 20 mM NaPO4; 100 mM NaCl；Pressure ambient
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 20 mM NaPO4; 50 mM NaCl；Pressure ambient
NMR sample composition
0.4 mM [U-100% 15N; U-50% 2H] S5a (196-306)-1, 1.2 mM K48 linked diubiquitin-2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.5 mM [U-100% 13C] S5a (196-306)-3, 1.5 mM K48 linked diubiquitin-4, 100% D2O | 100% D2O
NMR sample composition
0.5 mM [U-100% 13C of the proximal Ub; natural abundance of the distal subunit] K48 linked diubiquitin-5, 1.0 mM S5a (196-306)-6, 100% D2O | 100% D2O
NMR sample composition
0.5 mM [U-100% 13C of the distal subunit; natural abundance of the proximal Ub] K48 linked diubiquitin-7, 1.0 mM S5a (196-306)-8, 100% D2O | 100% D2O
NMR sample composition
0.4 mM [U-100% 13C] S5a (196-306)-9, 1.2 mM [U-100% 2H of the proximal Ub; natural abundance of the distal subunit] K48 linked diubiquitin-10, 100% D2O | 100% D2O
|
Resolution not provided |
| 2KHW Solution Structure of the human Polymerase iota UBM2-Ubiquitin Complex Deposited 2009-04-13 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition
1 mM [U-100% 15N] entity_1-1, 4 mM entity_2-2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
3 mM [U-100% 15N] entity_1-3, 3 mM [U-100% 15N] entity_2-4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
3 mM [U-100% 13C; U-100% 15N] entity_1-5, 3 mM [U-100% 13C; U-100% 15N] entity_2-6, 100% D2O | 100% D2O
NMR sample composition
1 mM [U-100% 13C; U-100% 15N] entity_1-7, 4 mM entity_2-8, 100% D2O | 100% D2O
|
Resolution not provided |
| 2KJH NMR based structural model of the UBCH8-UBIQUITIN complex Deposited 2009-05-28 | 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
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.4；298 K；Ionic strength (raw mmCIF value) 250；Pressure ambient
NMR sample composition
0.35 mM [U-100% 13C; U-100% 15N] UbcH8-1, 0.35 mM Ubiquitin-2, 20 mM sodium phosphate-3, 1 mM EDTA-4, 250 mM sodium chloride-5, 50 mM Arginine-6, 50 mM Glutamic Acid-7, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.35 mM UbcH8-8, 0.35 mM [U-100% 13C; U-100% 15N] Ubiquitin-9, 20 mM sodium phosphate-10, 1 mM EDTA-11, 250 mM sodium chloride-12, 50 mM Arginine-13, 50 mM Glutamic Acid-14, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.35 mM [U-100% 15N; U-99% 2H] UbcH8-15, 0.35 mM Ubiquitin-16, 20 mM sodium phosphate-17, 1 mM EDTA-18, 250 mM sodium chloride-19, 50 mM Arginine-20, 50 mM Glutamic Acid-21, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.35 mM UbcH8-22, 0.35 mM [U-100% 15N; U-99% 2H] Ubiquitin-23, 20 mM sodium phosphate-24, 1 mM EDTA-25, 250 mM sodium chloride-26, 50 mM Arginine-27, 50 mM Glutamic Acid-28, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2KLG PERE NMR structure of ubiquitin Deposited 2009-07-02 | Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；303 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition
50mM potassium phosphate-1, 3mM sodium azide-2, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2KN5 A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family Deposited 2009-08-14 | Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；308 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition
0.9 mM [U-100% 13C; U-100% 15N] human ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.6-0.9 mM [U-100% 13C; U-100% 15N] human ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2KOX NMR residual dipolar couplings identify long range correlated motions in the backbone of the protein ubiquitin Deposited 2009-10-02 | Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
Pressure ambient
NMR sample composition
[U-100% 13C; U-100% 15N] Ubiquitin-1, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2KTF Solution NMR structure of human polymerase iota UBM2 in complex with ubiquitin Deposited 2010-02-01 | 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
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；301 K；Ionic strength (raw mmCIF value) 0.08；Pressure ambient
NMR sample composition
1 mM [U-100% 13C; U-100% 15N] protein, 3.5 mM peptide, 20 mM sodium phosphate, 30 mM sodium chloride, 0.001 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
2.5 mM protein, 0.5 mM [U-100% 13C; U-100% 15N] peptide, 20 mM sodium phosphate, 30 mM sodium chloride, 0.001 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2KWU Solution Structure of UBM2 of murine Polymerase iota in Complex with Ubiquitin Deposited 2010-04-19 | 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
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6；288 K；Ionic strength (raw mmCIF value) 0.189；Pressure ambient
NMR sample composition
1-2 mM [U-99% 15N] DNA polymerase iota UBM2, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
1-2 mM [U-95% 13C; U-99% 15N] DNA polymerase iota UBM2, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
4-8 mM DNA polymerase iota UBM2, 1-2 mM [U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
4-8 mM DNA polymerase iota UBM2, 1-2 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
1.7 mM DNA polymerase iota UBM2, 6.8 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 2KWV Solution Structure of UBM1 of murine Polymerase iota in Complex with Ubiquitin Deposited 2010-04-20 | 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
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6；288 K；Ionic strength (raw mmCIF value) 0.189；Pressure ambient
NMR sample composition
1-2 mM [U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
1-2 mM [U-95% 13C; U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
1.0 mM DNA polymerase iota UBM1, 4 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 2L0F Solution NMR structure of human polymerase iota UBM2 (P692A mutant) in complex with ubiquitin Deposited 2010-07-01 | 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
1–76（76 aa）
|
Mutation：P692A | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 0.18；Pressure ambient
NMR sample composition
1 mM [U-100% 13C; U-100% 15N] UBM2, 3 mM ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
5 mM UBM2, 1.5 mM [U-100% 13C; U-100% 15N] ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1 mM [U-100% 13C; U-100% 15N] UBM2, 3 mM ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 100% D2O | 100% D2O
NMR sample composition
5 mM UBM2, 1.5 mM [U-100% 13C; U-100% 15N] ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 100% D2O | 100% D2O
|
Resolution not provided |
| 2L0T Solution structure of the complex of ubiquitin and the VHS domain of Stam2 Deposited 2010-07-15 | 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
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；288 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition
250 uM [U-99% 15N] Ubiquitin protein, 250 uM [U-99% 15N] VHS domain of Stam2, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2NR2 The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteins Deposited 2006-11-01 | Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 2O6V Crystal structure and solution NMR studies of Lys48-linked tetraubiquitin at neutral pH Deposited 2006-12-08 | 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
1–76（76 aa）
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
Chain D
1–76（76 aa）
|
Mutation：K63R Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；2M ammonium sulfate, 4% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.20 Å R-free 0.262 |
| 2O6V Crystal structure and solution NMR studies of Lys48-linked tetraubiquitin at neutral pH Deposited 2006-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain E
1–76（76 aa）
Chain F
1–76（76 aa）
Chain G
1–76（76 aa）
Chain H
1–76（76 aa）
|
Mutation：K63R 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；298 K；2M ammonium sulfate, 4% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.20 Å R-free 0.262 |
| 2O6V Crystal structure and solution NMR studies of Lys48-linked tetraubiquitin at neutral pH Deposited 2006-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
Chain D
1–76（76 aa）
|
Mutation：K63R Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；2M ammonium sulfate, 4% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.20 Å R-free 0.262 |
| 2OJR Structure of ubiquitin solved by SAD using the Lanthanide-Binding Tag Deposited 2007-01-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | TB TERBIUM(III) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；298 K；0.1M HEPES pH 7.5, 3.7 M NaCl, 33% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50
|
Resolution 2.60 Å R-free 0.254 |
| 2PE9 NMR Based Structure of the Open Conformation of LYS48-Linked Di-UBiquitin Using Experimental Global Rotational Diffusion Tensor from NMR Relaxation Measurements Deposited 2007-04-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM；Pressure AMBIENT
NMR sample composition
DI-UBIQUITIN, 90% WATER/10% D20
|
Resolution not provided |
| 2PEA NMR Based Structure of the Closed Conformation of LYS48-Linked Di-Ubiquitin Using Experimental Global Rotational Diffusion Tensor from NMR Relaxation Measurements Deposited 2007-04-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM；Pressure AMBIENT
NMR sample composition
DI-UBIQUITIN, 90% WATER/10% D20
|
Resolution not provided |
| 2W9N crystal structure of linear di-ubiquitin Deposited 2009-01-27 | 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
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 4 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；22% PEG 3350 AND 200 MM ZNOAC, pH 7
|
Resolution 2.25 Å R-free 0.276 |
| 2WDT Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME Deposited 2009-03-26 | 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 D
1–75（75 aa）
Fragment：RESIDUES 1-75
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；100 MM BIS-TRIS PH 5.5, 200 MM NACL, 25 % PEG 3350
|
Resolution 2.30 Å R-free 0.235 |
| 2WDT Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME Deposited 2009-03-26 | 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 B
1–75（75 aa）
Fragment：RESIDUES 1-75
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；100 MM BIS-TRIS PH 5.5, 200 MM NACL, 25 % PEG 3350
|
Resolution 2.30 Å R-free 0.235 |
| 2XEW Crystal structure of K11-linked diubiquitin Deposited 2010-05-18 | 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
1–76（76 aa）
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
Chain D
1–76（76 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 3.5；3M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE PH3.5
|
Resolution 2.20 Å R-free 0.252 |
| 2XEW Crystal structure of K11-linked diubiquitin Deposited 2010-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain E
1–76（76 aa）
Chain F
1–76（76 aa）
Chain G
1–76（76 aa）
Chain H
1–76（76 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 3 FLC CITRATE ANION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 3.5；3M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE PH3.5
|
Resolution 2.20 Å R-free 0.252 |
| 2XEW Crystal structure of K11-linked diubiquitin Deposited 2010-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain I
1–76（76 aa）
Chain J
1–76（76 aa）
Chain K
1–76（76 aa）
Chain L
1–76（76 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 3.5；3M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE PH3.5
|
Resolution 2.20 Å R-free 0.252 |
| 2XK5 Crystal structure of K6-linked diubiquitin Deposited 2010-07-07 | 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
1–76（76 aa）
Chain B
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；19-20 % PEG 3350, 0.2 M ZINC ACETATE, pH 7
|
Resolution 3.00 Å R-free 0.248 |
| 2Z59 Complex Structures of Mouse Rpn13 (22-130aa) and ubiquitin Deposited 2007-07-01 | 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
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；298 K；Pressure ambient
NMR sample composition
0.6mM MmRpn13 U-15N, 13C; U-70% 2H; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
0.6mM MmRpn13 U-15N; U-50% 2H; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
0.6mM MmRpn13 U-15N, 13C; U-70% 2H; 0.6mM ubiquitin; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
0.4mM MmRpn13 U-15N; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
0.4mM ubiquitin U-15N; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
0.4mM MmRpn13 U-13C; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 100% D2O | 100% D2O
|
Resolution not provided |
| 2ZCB Crystal Structure of ubiquitin P37A/P38A Deposited 2007-11-08 | 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
1–76（76 aa）
|
Mutation：P37A, P38A | ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.3；293 K；0.2M Zinc Acetate dehydrate, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.60 Å R-free 0.224 |
| 2ZCB Crystal Structure of ubiquitin P37A/P38A Deposited 2007-11-08 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Mutation：P37A, P38A | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.3；293 K；0.2M Zinc Acetate dehydrate, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.60 Å R-free 0.224 |
| 2ZCB Crystal Structure of ubiquitin P37A/P38A Deposited 2007-11-08 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–76（76 aa）
|
Mutation：P37A, P38A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.3；293 K；0.2M Zinc Acetate dehydrate, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.60 Å R-free 0.224 |
| 2ZCB Crystal Structure of ubiquitin P37A/P38A Deposited 2007-11-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
|
Mutation：P37A, P38A Mutation：P37A, P38A Mutation：P37A, P38A | ZN ZINC ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.3；293 K；0.2M Zinc Acetate dehydrate, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.60 Å R-free 0.224 |
| 3A33 UbcH5b~Ubiquitin Conjugate Deposited 2009-06-08 | 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
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；2.0M NaCl, 0.1M Potassium acetate, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.20 Å R-free 0.280 |
| 3BY4 Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin Deposited 2008-01-15 | 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
1–75（75 aa）
|
Not recorded | 3CN 3-AMINOPROPANE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；Bis-Tris, Magnesium Chloride, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.55 Å R-free 0.211 |
| 3C0R Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin Deposited 2008-01-21 | 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 D
1–75（75 aa）
|
Not recorded | 3CN 3-AMINOPROPANE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
hanging drop；pH 6.5；277 K；MES, ammonium acetate, PEG3350, pH 6.5, hanging drop, temperature 277K
|
Resolution 2.31 Å R-free 0.243 |
| 3C0R Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin Deposited 2008-01-21 | 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 B
1–75（75 aa）
|
Not recorded | 3CN 3-AMINOPROPANE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
hanging drop；pH 6.5；277 K；MES, ammonium acetate, PEG3350, pH 6.5, hanging drop, temperature 277K
|
Resolution 2.31 Å R-free 0.243 |
| 3DVG Crystal structure of K63-specific fab Apu.3A8 bound to K63-linked di-ubiquitin Deposited 2008-07-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain X
1–76（76 aa）
Chain Y
1–76（76 aa）
|
Mutation：D77 Mutation：K63R | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.3；291 K；protein: 17.0 mg/mL in 20 mM Tris-HCl pH 7.3, 150 mM NaCl
well solution: 0.1M Tris-HCl pH 8.0, 1.6M LiS04 , VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.60 Å R-free 0.261 |
| 3DVN Crystal structure of K63-specific fab Apu2.16 bound to K63-linked di-ubiquitin Deposited 2008-07-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain X
1–76（76 aa）
Chain Y
1–76（76 aa）
|
Mutation：D77 Mutation：K63R | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.3；291 K；protein: 12.7 mg/mL in 10 mM Tris-HCl pH 8.0, 75 mM NaCl
well: 0.2M Na Cl, 0.1 M Tris pH 8.2, 0.1 M citrate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.70 Å R-free 0.268 |
| 3DVN Crystal structure of K63-specific fab Apu2.16 bound to K63-linked di-ubiquitin Deposited 2008-07-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain U
1–76（76 aa）
Chain V
1–76（76 aa）
|
Mutation：D77 Mutation：K63R | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.3；291 K；protein: 12.7 mg/mL in 10 mM Tris-HCl pH 8.0, 75 mM NaCl
well: 0.2M Na Cl, 0.1 M Tris pH 8.2, 0.1 M citrate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.70 Å R-free 0.268 |
| 3EEC X-ray structure of human ubiquitin Cd(II) adduct Deposited 2008-09-04 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | CD CADMIUM ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 200mM cadmium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.00 Å R-free 0.300 |
| 3EEC X-ray structure of human ubiquitin Cd(II) adduct Deposited 2008-09-04 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Not recorded | CD CADMIUM ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 200mM cadmium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.00 Å R-free 0.300 |
| 3EEC X-ray structure of human ubiquitin Cd(II) adduct Deposited 2008-09-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–76（76 aa）
|
Not recorded | CD CADMIUM ION × 18 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 200mM cadmium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.00 Å R-free 0.300 |
| 3EEC X-ray structure of human ubiquitin Cd(II) adduct Deposited 2008-09-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain B
1–76（76 aa）
|
Not recorded | CD CADMIUM ION × 18 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 200mM cadmium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.00 Å R-free 0.300 |
| 3EFU X-ray structure of human ubiquitin-Hg(II) adduct Deposited 2008-09-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | HG MERCURY (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% PEG 1450, 50mM HEPES, 2.92mM mercurium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.84 Å R-free 0.293 |
| 3EHV X-ray structure of human ubiquitin Zn(II) adduct Deposited 2008-09-15 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 25mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.81 Å R-free 0.271 |
| 3EHV X-ray structure of human ubiquitin Zn(II) adduct Deposited 2008-09-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 25mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.81 Å R-free 0.271 |
| 3EHV X-ray structure of human ubiquitin Zn(II) adduct Deposited 2008-09-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 25mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.81 Å R-free 0.271 |
| 3H7P Crystal structure of K63-linked di-ubiquitin Deposited 2009-04-28 | 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
1–76（76 aa）
Chain B
1–76（76 aa）
|
Mutation：K63R | CD CADMIUM ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH UNDER OIL；pH 5.2；291 K；0.2 M Cadmium sulfate, 5% w/v PEG 8000 and 0.1 M Imidazole-Cl pH 6.5, Al's oil, MICROBATCH UNDER OIL, temperature 291K
|
Resolution 1.90 Å R-free 0.236 |
| 3H7S Crystal structures of K63-linked di- and tri-ubiquitin reveal a highly extended chain architecture Deposited 2009-04-28 | 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
1–76（76 aa）
Chain B
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH UNDER OIL；pH 5.2；291 K；0.2 M Zinc acetate, 6% w/v PEG 8000 and 0.1 M Imidazole-Cl pH 6.5, Al's oil, MICROBATCH UNDER OIL, temperature 291K
|
Resolution 2.30 Å R-free 0.253 |
| 3H7S Crystal structures of K63-linked di- and tri-ubiquitin reveal a highly extended chain architecture Deposited 2009-04-28 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH UNDER OIL；pH 5.2；291 K；0.2 M Zinc acetate, 6% w/v PEG 8000 and 0.1 M Imidazole-Cl pH 6.5, Al's oil, MICROBATCH UNDER OIL, temperature 291K
|
Resolution 2.30 Å R-free 0.253 |
| 3H7S Crystal structures of K63-linked di- and tri-ubiquitin reveal a highly extended chain architecture Deposited 2009-04-28 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH UNDER OIL；pH 5.2；291 K；0.2 M Zinc acetate, 6% w/v PEG 8000 and 0.1 M Imidazole-Cl pH 6.5, Al's oil, MICROBATCH UNDER OIL, temperature 291K
|
Resolution 2.30 Å R-free 0.253 |
| 3I3T Crystal structure of covalent ubiquitin-USP21 complex Deposited 2009-06-30 | 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
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 NEH ETHANAMINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；13% PEG 3350, 0.1 M Bis-Tris, 0.1 M Ammonium sulfate, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.59 Å R-free 0.218 |
| 3I3T Crystal structure of covalent ubiquitin-USP21 complex Deposited 2009-06-30 | 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
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 NEH ETHANAMINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；13% PEG 3350, 0.1 M Bis-Tris, 0.1 M Ammonium sulfate, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.59 Å R-free 0.218 |
| 3I3T Crystal structure of covalent ubiquitin-USP21 complex Deposited 2009-06-30 | Different construct 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
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 NEH ETHANAMINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；13% PEG 3350, 0.1 M Bis-Tris, 0.1 M Ammonium sulfate, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.59 Å R-free 0.218 |
| 3I3T Crystal structure of covalent ubiquitin-USP21 complex Deposited 2009-06-30 | Different construct 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
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 NEH ETHANAMINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；13% PEG 3350, 0.1 M Bis-Tris, 0.1 M Ammonium sulfate, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.59 Å R-free 0.218 |
| 3IFW Crystal structure of the S18Y variant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester. Deposited 2009-07-26 | 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
1–75（75 aa）
|
Not recorded | GVE METHYL 4-AMINOBUTANOATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；2.4 M ammonium sulfate, 0.1M BICINE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.40 Å R-free 0.256 |
| 3IHP Covalent Ubiquitin-Usp5 Complex Deposited 2009-07-30 | 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
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 NEH ETHANAMINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；298 K；Crystals of the covalent ubiquitin complex of Usp5 were grown at 298 K using the hanging drop method by mixing equal volumes of protein solution (25 mg/ml) and Crystallization Buffer (1.45 M ammonium sulfate, 0.1 M bis-Tris, pH 6.5, 0.2 M sodium acetate, 5% ethyleneglycol and 1 mM dithiothreitol). The crystals were cryoprotected by immersion in Paratone N in paraffin oil 30% (v/v) and placed in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.80 Å R-free 0.276 |
| 3IHP Covalent Ubiquitin-Usp5 Complex Deposited 2009-07-30 | 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
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 NEH ETHANAMINE × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；298 K；Crystals of the covalent ubiquitin complex of Usp5 were grown at 298 K using the hanging drop method by mixing equal volumes of protein solution (25 mg/ml) and Crystallization Buffer (1.45 M ammonium sulfate, 0.1 M bis-Tris, pH 6.5, 0.2 M sodium acetate, 5% ethyleneglycol and 1 mM dithiothreitol). The crystals were cryoprotected by immersion in Paratone N in paraffin oil 30% (v/v) and placed in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.80 Å R-free 0.276 |
| 3JSV Crystal structure of mouse NEMO CoZi in complex with Lys63-linked di-ubiquitin Deposited 2009-09-11 | 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
1–76（76 aa）
Chain B
1–76（76 aa）
|
Mutation：K63R Mutation：X77D | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.294 |
| 3JVZ E2~Ubiquitin-HECT Deposited 2009-09-17 | 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 X
1–76（76 aa）
|
Mutation：Ubiquitin G76 ester linked to UbcH5B S85 | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, pH 5.1-5.2, 2.4-2.5 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.30 Å R-free 0.267 |
| 3JVZ E2~Ubiquitin-HECT Deposited 2009-09-17 | 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 Y
1–76（76 aa）
|
Mutation：Ubiquitin G76 ester linked to UbcH5B S85 | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, pH 5.1-5.2, 2.4-2.5 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.30 Å R-free 0.267 |
| 3JW0 E2~Ubiquitin-HECT Deposited 2009-09-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain X
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, 2.4M sodium chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.10 Å R-free 0.287 |
| 3JW0 E2~Ubiquitin-HECT Deposited 2009-09-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain Y
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, 2.4M sodium chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.10 Å R-free 0.287 |
| 3K9P The crystal structure of E2-25K and ubiquitin complex Deposited 2009-10-16 | 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
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100mM HEPES-NaOH (pH 7.5), 25% (w/v) PEG 3350, 50mM Sodium Fluoride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.296 |
| 3K9P The crystal structure of E2-25K and ubiquitin complex Deposited 2009-10-16 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100mM HEPES-NaOH (pH 7.5), 25% (w/v) PEG 3350, 50mM Sodium Fluoride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.296 |
| 3KVF Crystal structure of the I93M mutant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester Deposited 2009-11-30 | 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
1–75（75 aa）
|
Not recorded | GVE METHYL 4-AMINOBUTANOATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.1M BICINE, 2.4M Ammonium Sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.80 Å R-free 0.284 |
| 3KW5 Crystal structure of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester Deposited 2009-11-30 | 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
1–75（75 aa）
|
Not recorded | GVE METHYL 4-AMINOBUTANOATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.1M BICINE, 2.4M Ammonium Sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.83 Å R-free 0.286 |
| 3LDZ Crystal structure of human STAM1 VHS domain in complex with ubiquitin Deposited 2010-01-13 | 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 E
1–73（73 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2M Na thiocyanate, 20% PEG3350, 0.1M imidazole pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.60 Å R-free 0.234 |
| 3LDZ Crystal structure of human STAM1 VHS domain in complex with ubiquitin Deposited 2010-01-13 | Different construct 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
1–73（73 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2M Na thiocyanate, 20% PEG3350, 0.1M imidazole pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.60 Å R-free 0.234 |
| 3LDZ Crystal structure of human STAM1 VHS domain in complex with ubiquitin Deposited 2010-01-13 | Different construct 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
1–73（73 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2M Na thiocyanate, 20% PEG3350, 0.1M imidazole pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.60 Å R-free 0.234 |
| 3MHS Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde Deposited 2010-04-08 | 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 D
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Hepes pH 6.5,
10% (w/v) PEG 8000,
20% (v/v) Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.89 Å R-free 0.208 |
| 3MTN Usp21 in complex with a ubiquitin-based, USP21-specific inhibitor Deposited 2010-04-30 | 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
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 3 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.3；291 K；11% PEG 4000, 0.1 M SODIUM CITRATE, 0.1 M AMMONIUM ACETATE, 5 MM TCEP, PH 5.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
|
Resolution 2.70 Å R-free 0.273 |
| 3MTN Usp21 in complex with a ubiquitin-based, USP21-specific inhibitor Deposited 2010-04-30 | 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
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.3；291 K；11% PEG 4000, 0.1 M SODIUM CITRATE, 0.1 M AMMONIUM ACETATE, 5 MM TCEP, PH 5.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
|
Resolution 2.70 Å R-free 0.273 |
| 3N30 Crystal Structure of cubic Zn3-hUb (human ubiquitin) adduct Deposited 2010-05-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25 mg/ml milliQ water protein solution, 25% (w/v) PEG 1450, 50 mM HEPES, 200 mM Zn acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.00 Å R-free 0.318 |
| 3N30 Crystal Structure of cubic Zn3-hUb (human ubiquitin) adduct Deposited 2010-05-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25 mg/ml milliQ water protein solution, 25% (w/v) PEG 1450, 50 mM HEPES, 200 mM Zn acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.00 Å R-free 0.318 |
| 3N32 The crystal structure of human Ubiquitin adduct with Zeise's salt Deposited 2010-05-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | PT PLATINUM (II) ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；30% PEG 1450, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.79 Å R-free 0.258 |
| 3N3K The catalytic domain of USP8 in complex with a USP8 specific inhibitor Deposited 2010-05-20 | Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–76（76 aa）
|
Mutation：Q2R, F4V, T9M, K11R, T14I, Q62H, K63N, E64H, T66A, H68Y, V70L, R72K | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；24% PEG3350, 0.1 M BIS-TRIS, 0.2 M AMMONIUM ACETATE, 1 MM DTT, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.60 Å R-free 0.242 |
| 3NHE High Resolution Structure (1.26A) of USP2a in Complex with Ubiquitin Deposited 2010-06-14 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；5% PEG4000, 0.1M Hepes, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.26 Å R-free 0.189 |
| 3NOB Structure of K11-linked di-ubiquitin Deposited 2010-06-25 | 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
1–76（76 aa）
Chain B
1–76（76 aa）
|
Not recorded | SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；292 K；25 mg/mL protein in 50 mM Tris 7.5 and 75 mM NaCl were grown in 0.2 M ammonium sulfate, 20% PEG3350. Seeds from this were further microseeded into 0.17 M Ammonium sulfate, 15% glycerol, 20% PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.19 Å R-free 0.281 |
| 3NOB Structure of K11-linked di-ubiquitin Deposited 2010-06-25 | 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
1–76（76 aa）
Chain D
1–76（76 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；292 K；25 mg/mL protein in 50 mM Tris 7.5 and 75 mM NaCl were grown in 0.2 M ammonium sulfate, 20% PEG3350. Seeds from this were further microseeded into 0.17 M Ammonium sulfate, 15% glycerol, 20% PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.19 Å R-free 0.281 |
| 3NOB Structure of K11-linked di-ubiquitin Deposited 2010-06-25 | 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
1–76（76 aa）
Chain F
1–76（76 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；292 K；25 mg/mL protein in 50 mM Tris 7.5 and 75 mM NaCl were grown in 0.2 M ammonium sulfate, 20% PEG3350. Seeds from this were further microseeded into 0.17 M Ammonium sulfate, 15% glycerol, 20% PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.19 Å R-free 0.281 |
| 3NOB Structure of K11-linked di-ubiquitin Deposited 2010-06-25 | 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
1–76（76 aa）
Chain H
1–76（76 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；292 K；25 mg/mL protein in 50 mM Tris 7.5 and 75 mM NaCl were grown in 0.2 M ammonium sulfate, 20% PEG3350. Seeds from this were further microseeded into 0.17 M Ammonium sulfate, 15% glycerol, 20% PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.19 Å R-free 0.281 |
| 3NS8 Crystal structure of an open conformation of Lys48-linked diubiquitin at pH 7.5 Deposited 2010-07-01 | 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
1–76（76 aa）
Chain B
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；HEPES, PEG 8000, Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.71 Å R-free 0.237 |
| 3NS8 Crystal structure of an open conformation of Lys48-linked diubiquitin at pH 7.5 Deposited 2010-07-01 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；HEPES, PEG 8000, Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.71 Å R-free 0.237 |
| 3NS8 Crystal structure of an open conformation of Lys48-linked diubiquitin at pH 7.5 Deposited 2010-07-01 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；HEPES, PEG 8000, Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.71 Å R-free 0.237 |
| 3PHD Crystal structure of human HDAC6 in complex with ubiquitin Deposited 2010-11-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain E
1–76（76 aa）
Chain F
1–76（76 aa）
Chain G
1–76（76 aa）
Chain H
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.6；297 K；15% PEG 3350, 0.1M Ammonium Sulphate, 0.1M Bis-Tris, pH 5.6, temperature 297K
|
Resolution 3.00 Å R-free 0.265 |
83 other PDB entries and 135 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | UBIQ_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–76； UniProt 1–76 Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain C； PDBConstruct 1–76； UniProt 1–76 Author chain D； PDBConstruct 1–76； UniProt 1–76 |
