Ubiquitin carboxyl-terminal hydrolase 7
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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain A； UniProt 560–890 Chain B； UniProt 560–890 | Fragment：UNP residues 560-890 | Peptide from E3 ubiquitin-protein ligase RNF169 × 2 （Q8NCN4） | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；0.2M sodium chloride, 6% w/v PEG 8000, 0.1M Sodium cacodylate, pH 5.8 | Resolution 3.11 Å R-free 0.268 |
| 2 | Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain C； UniProt 560–890 Chain D； UniProt 560–890 | Fragment：UNP residues 560-890 | Peptide from E3 ubiquitin-protein ligase RNF169 × 2 （Q8NCN4） | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；0.2M sodium chloride, 6% w/v PEG 8000, 0.1M Sodium cacodylate, pH 5.8 | Resolution 3.11 Å R-free 0.268 |
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 5GG4 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 12ZJ Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980) Deposited 2026-04-24 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
62–205（144 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.63 Å R-free 0.217 |
| 12ZJ Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980) Deposited 2026-04-24 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
62–205（144 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.63 Å R-free 0.217 |
| 12ZJ Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980) Deposited 2026-04-24 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
62–205（144 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.63 Å R-free 0.217 |
| 1NB8 Structure of the catalytic domain of USP7 (HAUSP) Deposited 2002-12-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
208–560（353 aa）
Fragment：HAUSP core domain
|
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 7；295 K；PEG 1000, Tris, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.30 Å R-free 0.279 |
| 1NB8 Structure of the catalytic domain of USP7 (HAUSP) Deposited 2002-12-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
208–560（353 aa）
Fragment：HAUSP core domain
|
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 7；295 K；PEG 1000, Tris, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.30 Å R-free 0.279 |
| 1NBF Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde Deposited 2002-12-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
208–560（353 aa）
Fragment：hausp core domain
|
Not recorded | 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 construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
208–560（353 aa）
Fragment：hausp core domain
|
Not recorded | 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 construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
208–560（353 aa）
Fragment：hausp core domain
|
Not recorded | 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 |
| 1YY6 The Crystal Structure of the N-terminal domain of HAUSP/USP7 complexed with an EBNA1 peptide Deposited 2005-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
54–204（151 aa）
|
Not recorded | NA SODIUM ION × 21 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30 % PEG 4000, 0.1 M Tris pH 8.5, 0.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.70 Å R-free 0.230 |
| 1YZE Crystal structure of the N-terminal domain of USP7/HAUSP. Deposited 2005-02-28 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
54–205（152 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；USP7/HAUSP (30 mg/ml) 35 % MPD, 0.2 M MgOAc and 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.00 Å R-free 0.367 |
| 1YZE Crystal structure of the N-terminal domain of USP7/HAUSP. Deposited 2005-02-28 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
54–205（152 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；USP7/HAUSP (30 mg/ml) 35 % MPD, 0.2 M MgOAc and 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.00 Å R-free 0.367 |
| 1YZE Crystal structure of the N-terminal domain of USP7/HAUSP. Deposited 2005-02-28 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
54–205（152 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；USP7/HAUSP (30 mg/ml) 35 % MPD, 0.2 M MgOAc and 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.00 Å R-free 0.367 |
| 2F1W Crystal structure of the TRAF-like domain of HAUSP/USP7 Deposited 2005-11-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
53–206（154 aa）
Fragment：N-terminal fragment (Residues : 53-206)
|
Not recorded | CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；285 K；240 mM CaCl2, 6.5% PEG4000, 20 mM ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
|
Resolution 1.65 Å R-free 0.212 |
| 2F1X Crystal structure of the TRAF-like domain of HAUSP/USP7 bound to a p53 peptide Deposited 2005-11-15 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
53–200（148 aa）
Fragment：p53 peptide fusion with HAUSP N terminal
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG2000 monomethylether, calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.263 |
| 2F1X Crystal structure of the TRAF-like domain of HAUSP/USP7 bound to a p53 peptide Deposited 2005-11-15 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
53–200（148 aa）
Fragment：p53 peptide fusion with HAUSP N terminal
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG2000 monomethylether, calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.263 |
| 2F1Y Crystal structure of the TRAF-like domain of HAUSP/USP7 bound to a MDM2 peptide Deposited 2005-11-15 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
53–198（146 aa）
Fragment：HAUSP N-terminal domain with MDM2 peptide fused to its C-terminal
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；26% PEG4000, 300 mM calcium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.237 |
| 2F1Z Crystal structure of HAUSP Deposited 2005-11-15 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
43–560（518 aa）
Fragment：residues: 43-560
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；0.8% PEG10000, 50 mM 1,6-hexanediol, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.20 Å R-free 0.316 |
| 2F1Z Crystal structure of HAUSP Deposited 2005-11-15 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
43–560（518 aa）
Fragment：residues: 43-560
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；0.8% PEG10000, 50 mM 1,6-hexanediol, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.20 Å R-free 0.316 |
| 2FOJ The Crystal Structure of the N-terminal domain of HAUSP/USP7 complexed with p53 peptide 364-367 Deposited 2006-01-13 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
54–205（152 aa）
Fragment：MATH domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30% PEG4K,
0.1 M Tris pH 8.5
0.2 M Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.60 Å R-free 0.262 |
| 2FOO The Crystal Structure of the N-terminal domain of HAUSP/USP7 complexed with p53 peptide 359-362 Deposited 2006-01-13 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
54–205（152 aa）
Fragment：MATH domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30% PEG4K, 0.1 M Tris, 0.2 M Lithium Sulfate , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.246 |
| 2FOP The Crystal Structure of the N-terminal domain of HAUSP/USP7 complexed with mdm2 peptide 147-150 Deposited 2006-01-13 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
54–205（152 aa）
Fragment：MATH domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30% PEG4K, 0.1 M Tris, 0.2 M Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 8.5
|
Resolution 2.10 Å R-free 0.250 |
| 2KVR Solution NMR structure of human ubiquitin specific protease Usp7 UBL domain (residues 537-664). NESG target hr4395c/ SGC-Toronto Deposited 2010-03-25 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
537–664（128 aa）
Fragment：ubiquitin-like domain (residues 537-664)
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 250；Pressure ambient
NMR sample composition
0.8-1.2 mM [U-100% 13C; U-100% 15N] protein, 20 mM sodium phosphate, pH 7.0, 250 mM sodium chloride, 2 mM DTT, 0.5 mM PMSF, 1 mM benzamidine, 1 mM TCEP, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2XXN Structure of the vIRF4-HAUSP TRAF domain complex Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
63–205（143 aa）
Fragment：TRAF DOMAIN, RESIDUES 63-205
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；5% PEG3350, 0.2 M MAGNESIUM FORMATE, PH 5.9
|
Resolution 1.60 Å R-free 0.174 |
| 2YLM Mechanism of USP7 (HAUSP) activation by its C-terminal ubiquitin-like domain (HUBL) and allosteric regulation by GMP-synthetase. Deposited 2011-06-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
560–1084（525 aa）
Fragment：USP7 UBIQUITIN-LIKE DOMAIN (HUBL), RESIDUES 560-1084
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；10% PEG 4000, 200 MM NACL, 100 MM MES PH 6.0.
|
Resolution 2.70 Å R-free 0.216 |
| 3MQR Crystal Structure of the USP7:HdmX(AHSS) complex Deposited 2010-04-28 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
54–205（152 aa）
Fragment：UNP residues 54-205
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；30% PEG4000, 0.2M Lithium sulfate, 0.1M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.228 |
| 3MQS Crystal Structure of the USP7:Hdm2(PSTS) complex Deposited 2010-04-28 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
54–205（152 aa）
Fragment：UNP residues 54-205
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；30% PEG4000, 0.2M Lithium Sulfate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.40 Å R-free 0.255 |
| 4JJQ Crystal structure of usp7-ntd with an e2 enzyme Deposited 2013-03-08 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
54–207（154 aa）
Fragment：USP7-NTD, UNP RESIDUES 54-205
|
Mutation：A156D | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30 % PEG 4000, 0.1 M TRIS PH 8.5 AND 0.2 M LITHIUM SULFATE , VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.95 Å R-free 0.217 |
| 4KG9 Crystal Structure Of USP7-NTD with MCM-BP Deposited 2013-04-29 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
54–205（152 aa）
Fragment：USP7-NTD, unp residues 54-205
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30 % PEG 4000, 0.1 M Tris, 0.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277KK, pH 8.5
|
Resolution 1.70 Å R-free 0.233 |
| 4M5W Crystal structure of the USP7/HAUSP catalytic domain Deposited 2013-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–560（354 aa）
Fragment：catalytic domain (UNP residues 207-560)
|
Not recorded | BR BROMIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；285 K；0.1 M HEPES, pH 7.5, 22% PEG3350, 0.2 M sodium bromide, 0.15 mM Cymal-7, VAPOR DIFFUSION, SITTING DROP, temperature 285K
|
Resolution 2.24 Å R-free 0.242 |
| 4M5X Crystal structure of the USP7/HAUSP catalytic domain Deposited 2013-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–560（354 aa）
Fragment：catalytic domain (UNP residues 207-560)
|
Not recorded | BR BROMIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；285 K；0.1 M HEPES, pH 7.5, 22% PEG3350, 0.2 M sodium bromide, 0.15 mM Cymal-7, VAPOR DIFFUSION, SITTING DROP, temperature 285K
|
Resolution 2.19 Å R-free 0.221 |
| 4M5X Crystal structure of the USP7/HAUSP catalytic domain Deposited 2013-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–560（354 aa）
Fragment：catalytic domain (UNP residues 207-560)
|
Not recorded | BR BROMIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；285 K；0.1 M HEPES, pH 7.5, 22% PEG3350, 0.2 M sodium bromide, 0.15 mM Cymal-7, VAPOR DIFFUSION, SITTING DROP, temperature 285K
|
Resolution 2.19 Å R-free 0.221 |
| 4PYZ Crystal structure of the first two Ubl domains of Deubiquitylase USP7 Deposited 2014-03-28 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
537–793（257 aa）
Fragment：UNP residues 537-793
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；15% PEG 4000, 0.2 M NH4Ac, 0.1 M NaCitrate pH5.6, vapor diffusion hanging drop, temperature 291K
|
Resolution 2.84 Å R-free 0.287 |
| 4PYZ Crystal structure of the first two Ubl domains of Deubiquitylase USP7 Deposited 2014-03-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
537–793（257 aa）
Fragment：UNP residues 537-793
|
Not recorded | UNX UNKNOWN LIGAND × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；15% PEG 4000, 0.2 M NH4Ac, 0.1 M NaCitrate pH5.6, vapor diffusion hanging drop, temperature 291K
|
Resolution 2.84 Å R-free 0.287 |
| 4WPH Crystal structure of USP7 ubiquitin-like domains in compact conformation Deposited 2014-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
535–888（354 aa）
Fragment：ubiquitin-like domain (UNP residues 535-888)
|
Not recorded | CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 3000, sodium citrate, L-proline
|
Resolution 2.92 Å R-free 0.262 |
| 4WPH Crystal structure of USP7 ubiquitin-like domains in compact conformation Deposited 2014-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
535–888（354 aa）
Fragment：ubiquitin-like domain (UNP residues 535-888)
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 3000, sodium citrate, L-proline
|
Resolution 2.92 Å R-free 0.262 |
| 4WPI Crystal structure of USP7 ubiquitin-like domains in extended conformation Deposited 2014-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
535–888（354 aa）
Fragment：ubiquitin-like domain (UNP residues 535-888)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；sodium chloride, TRIS-HCl, 2-mercaptoethanol, betaine hydrochloride
|
Resolution 3.40 Å R-free 0.281 |
| 4WPI Crystal structure of USP7 ubiquitin-like domains in extended conformation Deposited 2014-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
535–888（354 aa）
Fragment：ubiquitin-like domain (UNP residues 535-888)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；sodium chloride, TRIS-HCl, 2-mercaptoethanol, betaine hydrochloride
|
Resolution 3.40 Å R-free 0.281 |
| 4YOC Crystal Structure of human DNMT1 and USP7/HAUSP complex Deposited 2015-03-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
560–1102（543 aa）
Fragment：UNP RESIDUES 560-1102
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；6-8% PEG 3350, 200 mM potassium acetate
|
Resolution 2.92 Å R-free 0.258 |
| 4YSI Structure of USP7 with a novel viral protein Deposited 2015-03-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
63–205（143 aa）
Fragment：UNP residues 63-205
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30% PEG4K, 0.2M LiSO4, 0.1M TrisHCl
|
Resolution 1.02 Å R-free 0.160 |
| 4Z96 Crystal structure of DNMT1 in complex with USP7 Deposited 2015-04-09 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
544–1067（524 aa）
Fragment：UNP residues 544-1067
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；0.1 M sodium citrate, pH5.5, 10% PEG6000, 15% glycerol
|
Resolution 2.85 Å R-free 0.246 |
| 4Z97 Crystal structure of USP7 in complex with DNMT1(K1115Q) Deposited 2015-04-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
544–1067（524 aa）
Fragment：UNP residues 544-1067
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；297 K；0.1 M sodium citrate, pH5.5, 10% PEG6000, 15% glycerol
|
Resolution 3.00 Å R-free 0.254 |
| 5C56 Crystal structure of USP7/HAUSP in complex with ICP0 Deposited 2015-06-19 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
560–1102（543 aa）
Fragment：UNP RESIDUES 560-1102
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；20% PEG3350, 0.2M Sodium Bromide
|
Resolution 2.69 Å R-free 0.263 |
| 5C6D Crystal structure of USP7 in complex with UHRF1 Deposited 2015-06-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
561–881（321 aa）
Fragment：UNP residues 561-881
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；100 mM CHES (pH 9.0), 20% PEG8000
|
Resolution 2.29 Å R-free 0.234 |
| 5C6D Crystal structure of USP7 in complex with UHRF1 Deposited 2015-06-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
561–881（321 aa）
Fragment：UNP residues 561-881
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；100 mM CHES (pH 9.0), 20% PEG8000
|
Resolution 2.29 Å R-free 0.234 |
| 5FWI structure of usp7 catalytic domain and three ubl-domains Deposited 2016-02-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
207–882（676 aa）
Fragment：RESIDUES 207-882
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
15% PEG 3350 0.2M NA CITRATE
|
Resolution 3.40 Å R-free 0.267 |
| 5J7T Molecular Understanding of USP7 Substrate Recognition and C-Terminal Activation Deposited 2016-04-06 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
195–865（671 aa）
Fragment：USP7
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.3；289 K；PEG 3350, 0.2M tri-potassium citrate
|
Resolution 3.20 Å R-free 0.294 |
| 5JTJ USP7CD-CTP in complex with Ubiquitin Deposited 2016-05-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
193–538（346 aa）
Fragment：UNP residues 193-538 LINKED via GGSGG to Residues 1084-1102
Chain A
1084–1102（19 aa）
Fragment：UNP residues 193-538 LINKED via GGSGG to Residues 1084-1102
|
Not recorded | CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.05 M Calcium chloride, 0.1 M MES pH 6.0 and 45% PEG 200
|
Resolution 3.32 Å R-free 0.209 |
| 5JTJ USP7CD-CTP in complex with Ubiquitin Deposited 2016-05-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
193–538（346 aa）
Fragment：UNP residues 193-538 LINKED via GGSGG to Residues 1084-1102
Chain A
1084–1102（19 aa）
Fragment：UNP residues 193-538 LINKED via GGSGG to Residues 1084-1102
|
Not recorded | CA CALCIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.05 M Calcium chloride, 0.1 M MES pH 6.0 and 45% PEG 200
|
Resolution 3.32 Å R-free 0.209 |
| 5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
191–538（348 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain A
866–1086（221 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
|
Resolution 3.31 Å R-free 0.269 |
| 5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
191–538（348 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain C
866–1086（221 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
|
Resolution 3.31 Å R-free 0.269 |
| 5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
191–538（348 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain E
866–1086（221 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
|
Resolution 3.31 Å R-free 0.269 |
| 5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
191–538（348 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain G
866–1086（221 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
|
Resolution 3.31 Å R-free 0.269 |
| 5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
191–538（348 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain A
866–1086（221 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain E
191–538（348 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain E
866–1086（221 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
|
Resolution 3.31 Å R-free 0.269 |
| 5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
191–538（348 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain A
866–1086（221 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain C
191–538（348 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain C
866–1086（221 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain E
191–538（348 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain E
866–1086（221 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain G
191–538（348 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain G
866–1086（221 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
|
Resolution 3.31 Å R-free 0.269 |
| 5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
191–538（348 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain C
866–1086（221 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain G
191–538（348 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Chain G
866–1086（221 aa）
Fragment：UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
|
Resolution 3.31 Å R-free 0.269 |
| 5KYB Crystal structure of the apo-form of USP7 catalytic domain [V302K] mutant Deposited 2016-07-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
192–538（347 aa）
Fragment：UNP residues 1-76
|
Mutation：V302K | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；1% Tryptone, 0.05M HEPES Na pH 7.0, 20% PEG3350
|
Resolution 2.20 Å R-free 0.276 |
| 5KYB Crystal structure of the apo-form of USP7 catalytic domain [V302K] mutant Deposited 2016-07-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
192–538（347 aa）
Fragment：UNP residues 1-76
|
Mutation：V302K | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；1% Tryptone, 0.05M HEPES Na pH 7.0, 20% PEG3350
|
Resolution 2.20 Å R-free 0.276 |
| 5KYC Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin (malonate bound) Deposited 2016-07-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
192–538（347 aa）
Fragment：UNP residues 192-538
|
Mutation：V302K | MLA MALONIC ACID × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4；292 K；8% tacsimate pH 4.0, 20% PEG3350
|
Resolution 1.43 Å R-free 0.192 |
| 5KYD Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin Deposited 2016-07-21 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
192–538（347 aa）
Fragment：UNP residues 192-538
|
Mutation：V302K | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；0.2M Ammonium fluoride, 20% PEG3350
|
Resolution 1.62 Å R-free 0.213 |
| 5KYE Crystal structure of USP7 catalytic domain [H294E] mutant in complex with ubiquitin Deposited 2016-07-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
192–538（347 aa）
Fragment：UNP residues 192-538
|
Mutation：H294E | EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5, 25% PEG3350, 0.2M Ammonium acetate
|
Resolution 1.97 Å R-free 0.223 |
| 5KYE Crystal structure of USP7 catalytic domain [H294E] mutant in complex with ubiquitin Deposited 2016-07-21 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
192–538（347 aa）
Fragment：UNP residues 192-538
|
Mutation：H294E | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5, 25% PEG3350, 0.2M Ammonium acetate
|
Resolution 1.97 Å R-free 0.223 |
| 5KYF Crystal structure of USP7 catalytic domain [L299A] mutant in complex with ubiquitin Deposited 2016-07-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
192–538（347 aa）
Fragment：UNP residues 192-538
|
Mutation：L299A | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5, 25% PEG3350
|
Resolution 1.45 Å R-free 0.185 |
| 5N9R Crystal structure of USP7 in complex with a potent, selective and reversible small-molecule inhibitor Deposited 2017-02-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–560（354 aa）
|
Not recorded | SO4 SULFATE ION × 1 GOL GLYCEROL × 1 8RN 7-bromanyl-3-[[4-oxidanyl-1-[(3~{R})-3-phenylbutanoyl]piperidin-4-yl]methyl]thieno[3,2-d]pyrimidin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；PEG 4000, Tris, Li2-Sulfate.
|
Resolution 2.23 Å R-free 0.212 |
| 5N9R Crystal structure of USP7 in complex with a potent, selective and reversible small-molecule inhibitor Deposited 2017-02-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–560（354 aa）
|
Not recorded | SO4 SULFATE ION × 2 GOL GLYCEROL × 2 8RN 7-bromanyl-3-[[4-oxidanyl-1-[(3~{R})-3-phenylbutanoyl]piperidin-4-yl]methyl]thieno[3,2-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；PEG 4000, Tris, Li2-Sulfate.
|
Resolution 2.23 Å R-free 0.212 |
| 5N9T Crystal structure of USP7 in complex with a potent, selective and reversible small-molecule inhibitor Deposited 2017-02-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–560（354 aa）
Fragment：UNP residues 207-560
|
Not recorded | SO4 SULFATE ION × 1 GOL GLYCEROL × 3 8QQ 3-[4-(aminomethyl)phenyl]-2-methyl-6-[[4-oxidanyl-1-[(3~{R})-4,4,4-tris(fluoranyl)-3-phenyl-butanoyl]piperidin-4-yl]methyl]pyrazolo[4,3-d]pyrimidin-7-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Li2 Sulfate, Tris
|
Resolution 1.73 Å R-free 0.224 |
| 5N9T Crystal structure of USP7 in complex with a potent, selective and reversible small-molecule inhibitor Deposited 2017-02-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–560（354 aa）
Fragment：UNP residues 207-560
|
Not recorded | SO4 SULFATE ION × 2 8QQ 3-[4-(aminomethyl)phenyl]-2-methyl-6-[[4-oxidanyl-1-[(3~{R})-4,4,4-tris(fluoranyl)-3-phenyl-butanoyl]piperidin-4-yl]methyl]pyrazolo[4,3-d]pyrimidin-7-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Li2 Sulfate, Tris
|
Resolution 1.73 Å R-free 0.224 |
| 5NGE Crystal structure of USP7 in complex with the non-covalent inhibitor, FT671 Deposited 2017-03-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
192–544（353 aa）
|
Not recorded | 8WK 5-[[1-[(3~{S})-4,4-bis(fluoranyl)-3-(3-fluoranylpyrazol-1-yl)butanoyl]-4-oxidanyl-piperidin-4-yl]methyl]-1-(4-fluorophenyl)pyrazolo[3,4-d]pyrimidin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；25% (w/v) polyethylene glycol (PEG) 1500, 100 mM MMT pH 8.0
|
Resolution 2.35 Å R-free 0.272 |
| 5NGE Crystal structure of USP7 in complex with the non-covalent inhibitor, FT671 Deposited 2017-03-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
192–544（353 aa）
|
Not recorded | 8WK 5-[[1-[(3~{S})-4,4-bis(fluoranyl)-3-(3-fluoranylpyrazol-1-yl)butanoyl]-4-oxidanyl-piperidin-4-yl]methyl]-1-(4-fluorophenyl)pyrazolo[3,4-d]pyrimidin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；25% (w/v) polyethylene glycol (PEG) 1500, 100 mM MMT pH 8.0
|
Resolution 2.35 Å R-free 0.272 |
| 5NGF Crystal structure of USP7 in complex with the covalent inhibitor, FT827 Deposited 2017-03-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
208–560（353 aa）
|
Not recorded | 8WN ~{N}-[2-[4-[4-[(1-methyl-4-oxidanylidene-pyrazolo[3,4-d]pyrimidin-5-yl)methyl]-4-oxidanyl-piperidin-1-yl]carbonylphenyl]phenyl]ethanesulfonamide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20 % (w/v) PEG3350, 100 mM Bis-Tris propane pH 7.5, 0.2 M sodium formate
|
Resolution 2.33 Å R-free 0.247 |
| 5NGF Crystal structure of USP7 in complex with the covalent inhibitor, FT827 Deposited 2017-03-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
208–560（353 aa）
|
Not recorded | 8WN ~{N}-[2-[4-[4-[(1-methyl-4-oxidanylidene-pyrazolo[3,4-d]pyrimidin-5-yl)methyl]-4-oxidanyl-piperidin-1-yl]carbonylphenyl]phenyl]ethanesulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20 % (w/v) PEG3350, 100 mM Bis-Tris propane pH 7.5, 0.2 M sodium formate
|
Resolution 2.33 Å R-free 0.247 |
| 5UQV USP7 in complex with GNE6640 (4-(2-amino-4-ethyl-5-(1H-indazol-5-yl)pyridin-3-yl)phenol) Deposited 2017-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
192–538（347 aa）
Fragment：UNP residues 192-538
|
Not recorded | 8JM 4-[2-amino-4-ethyl-5-(1H-indazol-5-yl)pyridin-3-yl]phenol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；PEG 1000, 0.1M Tris-HCl 7.0
|
Resolution 2.84 Å R-free 0.293 |
| 5UQV USP7 in complex with GNE6640 (4-(2-amino-4-ethyl-5-(1H-indazol-5-yl)pyridin-3-yl)phenol) Deposited 2017-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
192–538（347 aa）
Fragment：UNP residues 192-538
|
Not recorded | 8JM 4-[2-amino-4-ethyl-5-(1H-indazol-5-yl)pyridin-3-yl]phenol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；PEG 1000, 0.1M Tris-HCl 7.0
|
Resolution 2.84 Å R-free 0.293 |
| 5UQX USP7 in complex with GNE6776 (6'-amino-4'-ethyl-5'-(4-hydroxyphenyl)-N-methyl-[3,3'-bipyridine]-6-carboxamide) Deposited 2017-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
192–539（348 aa）
Fragment：UNP residues 192-539
|
Not recorded | 8JP 6'-amino-4'-ethyl-5'-(4-hydroxyphenyl)-N-methyl[3,3'-bipyridine]-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；PEG 1000, 0.1M Tris-HCl 7.0
|
Resolution 2.23 Å R-free 0.223 |
| 5UQX USP7 in complex with GNE6776 (6'-amino-4'-ethyl-5'-(4-hydroxyphenyl)-N-methyl-[3,3'-bipyridine]-6-carboxamide) Deposited 2017-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
192–539（348 aa）
Fragment：UNP residues 192-539
|
Not recorded | 8JP 6'-amino-4'-ethyl-5'-(4-hydroxyphenyl)-N-methyl[3,3'-bipyridine]-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；PEG 1000, 0.1M Tris-HCl 7.0
|
Resolution 2.23 Å R-free 0.223 |
| 5VS6 Structure of DUB complex Deposited 2017-05-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
192–544（353 aa）
Fragment：UNP residues 192-544
Chain B
192–544（353 aa）
Fragment：UNP residues 192-544
|
Not recorded | 9QD N-[3-({4-hydroxy-1-[(3R)-3-phenylbutanoyl]piperidin-4-yl}methyl)-4-oxo-3,4-dihydroquinazolin-7-yl]-3-(4-methylpiperazin-1-yl)propanamide × 2 ACT ACETATE ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, NaFormate
|
Resolution 2.27 Å R-free 0.232 |
| 5VSB Structure of DUB complex Deposited 2017-05-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
192–544（353 aa）
Fragment：UNP residues 192-544
Chain B
192–544（353 aa）
Fragment：UNP residues 192-544
|
Not recorded | 9QA 7-chloro-3-{[4-hydroxy-1-(3-phenylpropanoyl)piperidin-4-yl]methyl}quinazolin-4(3H)-one × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, NaFormate
|
Resolution 1.85 Å R-free 0.249 |
| 5VSK Structure of DUB complex Deposited 2017-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
192–544（353 aa）
|
Not recorded | 9HS 7-chloro-3-({4-hydroxy-1-[(3S)-3-phenylbutanoyl]piperidin-4-yl}methyl)quinazolin-4(3H)-one × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, NaFormate
|
Resolution 3.33 Å R-free 0.274 |
| 5VSK Structure of DUB complex Deposited 2017-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
192–544（353 aa）
|
Not recorded | 9HS 7-chloro-3-({4-hydroxy-1-[(3S)-3-phenylbutanoyl]piperidin-4-yl}methyl)quinazolin-4(3H)-one × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, NaFormate
|
Resolution 3.33 Å R-free 0.274 |
| 5WHC USP7 in complex with Cpd2 (4-(3-(1-methylpiperidin-4-yl)-1,2,4-oxadiazol-5-yl)phenol) Deposited 2017-07-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
209–554（346 aa）
Fragment：residues 209-554
|
Not recorded | AJJ 4-[3-(1-methylpiperidin-4-yl)-1,2,4-oxadiazol-5-yl]phenol × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；PEG 1000, 0.1M Tris-HCl 7.0
|
Resolution 2.55 Å R-free 0.260 |
| 5WHC USP7 in complex with Cpd2 (4-(3-(1-methylpiperidin-4-yl)-1,2,4-oxadiazol-5-yl)phenol) Deposited 2017-07-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
209–554（346 aa）
Fragment：residues 209-554
|
Not recorded | AJJ 4-[3-(1-methylpiperidin-4-yl)-1,2,4-oxadiazol-5-yl]phenol × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；PEG 1000, 0.1M Tris-HCl 7.0
|
Resolution 2.55 Å R-free 0.260 |
| 6F5H Crystal structure of USP7 in complex with a 4-hydroxypiperidine based inhibitor Deposited 2017-12-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
207–560（354 aa）
Chain B
207–560（354 aa）
|
Not recorded | SO4 SULFATE ION × 3 GOL GLYCEROL × 1 CQ5 3-[[4-oxidanyl-1-[(3~{R})-3-phenylbutanoyl]piperidin-4-yl]methyl]-6-(2-pyrrolidin-1-ylethylamino)pyrimidin-4-one × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；PEG 4000, Tris, Li2-Sulfate, pH 7.75
|
Resolution 2.16 Å R-free 0.262 |
| 6M1K USP7 in complex with a novel inhibitor Deposited 2020-02-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
208–554（347 aa）
Chain B
208–554（347 aa）
|
Not recorded | EZF methyl 4-[[4-[[3-[4-(aminomethyl)phenyl]-2-methyl-7-oxidanylidene-pyrazolo[4,3-d]pyrimidin-6-yl]methyl]-4-oxidanyl-piperidin-1-yl]methyl]-3-chloranyl-benzoate × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；0.1M Tris (hydroxymethyl)aminomethane hydrochloride, pH 7.0, 20% (v/v) PEG 1000
|
Resolution 2.25 Å R-free 0.269 |
| 6P5L Crystal Structure of Ubl123 with an EZH2 peptide Deposited 2019-05-30 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
535–890（356 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；167 mM NaCl, 20mM Tris, 5mM b-ME, 10mM betaine hydrochlorid
|
Resolution 3.30 Å R-free 0.289 |
| 6P5L Crystal Structure of Ubl123 with an EZH2 peptide Deposited 2019-05-30 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
535–890（356 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；167 mM NaCl, 20mM Tris, 5mM b-ME, 10mM betaine hydrochlorid
|
Resolution 3.30 Å R-free 0.289 |
| 6VN2 USP7 IN COMPLEX WITH LIGAND COMPOUND 18 Deposited 2020-01-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–555（349 aa）
|
Not recorded | R44 1-({7-[(2R)-5-chloro-2-(piperazine-1-carbonyl)-2,3-dihydro-1-benzofuran-7-yl]thieno[3,2-b]pyridin-2-yl}methyl)-1H-pyrrole-2,5-dione × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；NULL
|
Resolution 2.93 Å R-free 0.290 |
| 6VN2 USP7 IN COMPLEX WITH LIGAND COMPOUND 18 Deposited 2020-01-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–555（349 aa）
|
Not recorded | R44 1-({7-[(2R)-5-chloro-2-(piperazine-1-carbonyl)-2,3-dihydro-1-benzofuran-7-yl]thieno[3,2-b]pyridin-2-yl}methyl)-1H-pyrrole-2,5-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；NULL
|
Resolution 2.93 Å R-free 0.290 |
| 6VN3 USP7 IN COMPLEX WITH LIGAND COMPOUND 23 Deposited 2020-01-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–555（349 aa）
|
Not recorded | R3Y 1-{[7-(5-chloro-2-{[(3R,4S)-4-fluoropyrrolidin-3-yl]oxy}-3-methylphenyl)thieno[3,2-b]pyridin-2-yl]methyl}-1H-pyrrole-2,5-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；NULL
|
Resolution 2.73 Å R-free 0.290 |
| 6VN3 USP7 IN COMPLEX WITH LIGAND COMPOUND 23 Deposited 2020-01-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–555（349 aa）
|
Not recorded | R3Y 1-{[7-(5-chloro-2-{[(3R,4S)-4-fluoropyrrolidin-3-yl]oxy}-3-methylphenyl)thieno[3,2-b]pyridin-2-yl]methyl}-1H-pyrrole-2,5-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；NULL
|
Resolution 2.73 Å R-free 0.290 |
| 6VN4 USP7 IN COMPLEX WITH LIGAND COMPOUND 1 Deposited 2020-01-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–555（349 aa）
|
Not recorded | R4D 3-({4-hydroxy-1-[(2R)-2-methyl-3-phenylpropanoyl]piperidin-4-yl}methyl)quinazolin-4(3H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；NULL
|
Resolution 2.69 Å R-free 0.300 |
| 6VN4 USP7 IN COMPLEX WITH LIGAND COMPOUND 1 Deposited 2020-01-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–555（349 aa）
|
Not recorded | R4D 3-({4-hydroxy-1-[(2R)-2-methyl-3-phenylpropanoyl]piperidin-4-yl}methyl)quinazolin-4(3H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；NULL
|
Resolution 2.69 Å R-free 0.300 |
| 6VN5 USP7 IN COMPLEX WITH LIGAND COMPOUND 7 Deposited 2020-01-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–555（349 aa）
|
Not recorded | R41 [(2R)-7-(2-aminopyridin-4-yl)-5-chloro-2,3-dihydro-1-benzofuran-2-yl](piperazin-1-yl)methanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K
|
Resolution 2.90 Å R-free 0.268 |
| 6VN5 USP7 IN COMPLEX WITH LIGAND COMPOUND 7 Deposited 2020-01-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–555（349 aa）
|
Not recorded | R41 [(2R)-7-(2-aminopyridin-4-yl)-5-chloro-2,3-dihydro-1-benzofuran-2-yl](piperazin-1-yl)methanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K
|
Resolution 2.90 Å R-free 0.268 |
| 6VN6 USP7 IN COMPLEX WITH LIGAND COMPOUND 14 Deposited 2020-01-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–555（349 aa）
|
Not recorded | R4J [(2R)-5-chloro-7-{2-[(2S)-1-chloro-2,3-dihydroxypropan-2-yl]thieno[3,2-b]pyridin-7-yl}-2,3-dihydro-1-benzofuran-2-yl](piperazin-1-yl)methanone × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；NULL
|
Resolution 2.99 Å R-free 0.267 |
| 6VN6 USP7 IN COMPLEX WITH LIGAND COMPOUND 14 Deposited 2020-01-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–555（349 aa）
|
Not recorded | R4J [(2R)-5-chloro-7-{2-[(2S)-1-chloro-2,3-dihydroxypropan-2-yl]thieno[3,2-b]pyridin-7-yl}-2,3-dihydro-1-benzofuran-2-yl](piperazin-1-yl)methanone × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；NULL
|
Resolution 2.99 Å R-free 0.267 |
| 7CM2 The Crystal Structure of human USP7 USP domain from Biortus Deposited 2020-07-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
208–560（353 aa）
Fragment：UNP residues 208-560
|
Not recorded | GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Tris pH8.5, 25% PEG3,350
|
Resolution 2.25 Å R-free 0.236 |
| 7CM2 The Crystal Structure of human USP7 USP domain from Biortus Deposited 2020-07-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
208–560（353 aa）
Fragment：UNP residues 208-560
|
Not recorded | GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Tris pH8.5, 25% PEG3,350
|
Resolution 2.25 Å R-free 0.236 |
| 7VIJ Crystal structure of USP7-HUBL domain Deposited 2021-09-27 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
560–1083（524 aa）
Fragment：HUBL domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；2% v/v Tacsimate pH 7.0, 0.1M imidazole pH 7.0, 8% w/v polyethylene glycol 3350, 5% v/v 2-propanol
|
Resolution 2.30 Å R-free 0.263 |
| 7XHH High-resolution X-ray cocrystal structure of USP7 in complex with X4 Deposited 2022-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
207–554（348 aa）
Chain B
207–554（348 aa）
|
Not recorded | DYO 3-[4-(aminomethyl)phenyl]-6-[[1-[[2-chloranyl-4-(1,2,4-oxadiazol-3-yl)phenyl]methyl]-4-oxidanyl-piperidin-4-yl]methyl]-2-methyl-pyrazolo[4,3-d]pyrimidin-7-one × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；0.1M Tris (hydroxymethyl)aminomethane hydrochloride, pH 7.0, 20% (v/v) PEG 1000
|
Resolution 2.10 Å R-free 0.218 |
| 7XHK High-resolution X-ray cocrystal structure of USP7 in complex with LX04-46 Deposited 2022-04-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
211–553（343 aa）
|
Not recorded | DVU ~{N}-[[4-[6-[[1-[[2-chloranyl-4-(furan-2-yl)phenyl]methyl]-4-oxidanyl-piperidin-4-yl]methyl]-2-methyl-7-oxidanylidene-pyrazolo[4,3-d]pyrimidin-3-yl]phenyl]methyl]methanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；20mg/ml Crystal, 100mM Tris,20% PEG 1000, PH 7.0
|
Resolution 2.30 Å R-free 0.264 |
| 7XPY Crystal structure of USP7 in complex with its inhibitor Deposited 2022-05-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
560–1102（543 aa）
Fragment：UNP RESIDUES 560-1102
|
Not recorded | EIB [(3S,3aR,4R,6Z,9S,10E,11aR)-9-acetyloxy-6-(acetyloxymethyl)-3,10-dimethyl-2-oxidanylidene-3a,4,5,8,9,11a-hexahydro-3H-cyclodeca[b]furan-4-yl] (E)-2-methyl-4-oxidanyl-but-2-enoate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；2% v/v Tacsimate pH 7.0, 0.1 M Imidazole pH 7.0, 8% w/v Polyethylene glycol 3350, 5% v/v 2-Propanol
|
Resolution 2.35 Å R-free 0.266 |
| 8D4Z Crystal structure of USP7 in complex with allosteric inhibitor FX1-3763 Deposited 2022-06-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–560（354 aa）
|
Not recorded | QBL 1-({(7M)-7-[1-(azetidin-3-yl)-6-chloro-1,2,3,4-tetrahydroquinolin-8-yl]thieno[3,2-b]pyridin-2-yl}methyl)pyrrolidine-2,5-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.10 M Bis-Tris-Propane pH 8.50, 0.10 M K-formate, 26.0 % (w/v) PEG 3350
|
Resolution 2.26 Å R-free 0.260 |
| 8D4Z Crystal structure of USP7 in complex with allosteric inhibitor FX1-3763 Deposited 2022-06-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–560（354 aa）
|
Not recorded | QBL 1-({(7M)-7-[1-(azetidin-3-yl)-6-chloro-1,2,3,4-tetrahydroquinolin-8-yl]thieno[3,2-b]pyridin-2-yl}methyl)pyrrolidine-2,5-dione × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.10 M Bis-Tris-Propane pH 8.50, 0.10 M K-formate, 26.0 % (w/v) PEG 3350
|
Resolution 2.26 Å R-free 0.260 |
| 9DEK USP7 in complex with macrocycle inhibitor MC02 Deposited 2024-08-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
192–538（347 aa）
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M BIS-TRIS pH 6.5 and 20% w/v PEG 5000 MME
|
Resolution 2.00 Å R-free 0.225 |
| 9DEK USP7 in complex with macrocycle inhibitor MC02 Deposited 2024-08-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
192–538（347 aa）
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M BIS-TRIS pH 6.5 and 20% w/v PEG 5000 MME
|
Resolution 2.00 Å R-free 0.225 |
| 9DEL USP7 in complex with macrocycle MC03 Deposited 2024-08-29 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
192–538（347 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；25 %w/v PEG 1500, 0.1 M MMT pH 7
|
Resolution 2.50 Å R-free 0.272 |
| 9DEL USP7 in complex with macrocycle MC03 Deposited 2024-08-29 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
192–538（347 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；25 %w/v PEG 1500, 0.1 M MMT pH 7
|
Resolution 2.50 Å R-free 0.272 |
| 9DEM USP7 in complex with macrocycle MC04 Deposited 2024-08-29 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
192–538（347 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；20% v/v 2-Propanol, 0.1M Tris pH 8.0 and 5% PEG 8000
|
Resolution 1.77 Å R-free 0.237 |
| 9DEN USP7 in complex with macrocycle MC07 Deposited 2024-08-29 | Different construct 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
192–538（347 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；25% w/v PEG 1500 and 0.1 M MMT (malic acid, MES, Tris) buffer pH 7
|
Resolution 2.93 Å R-free 0.250 |
| 9DEN USP7 in complex with macrocycle MC07 Deposited 2024-08-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
192–538（347 aa）
|
Not recorded | EOH ETHANOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；25% w/v PEG 1500 and 0.1 M MMT (malic acid, MES, Tris) buffer pH 7
|
Resolution 2.93 Å R-free 0.250 |
| 9DEO USP7 in complex with macrocycle inhibitor MC08 Deposited 2024-08-29 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
192–538（347 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；25% w/v PEG 1500, 0.1 M MMT pH 7
|
Resolution 2.70 Å R-free 0.296 |
| 9DEO USP7 in complex with macrocycle inhibitor MC08 Deposited 2024-08-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
192–538（347 aa）
|
Not recorded | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；25% w/v PEG 1500, 0.1 M MMT pH 7
|
Resolution 2.70 Å R-free 0.296 |
| 9DEP USP7 in complex with macrocycle MC09 Deposited 2024-08-29 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
192–538（347 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 1500 and 0.1 M MMT (malic acid, MES, Tris) buffer pH 7
|
Resolution 2.57 Å R-free 0.284 |
| 9DEP USP7 in complex with macrocycle MC09 Deposited 2024-08-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
192–538（347 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% w/v PEG 1500 and 0.1 M MMT (malic acid, MES, Tris) buffer pH 7
|
Resolution 2.57 Å R-free 0.284 |
| 9DEP USP7 in complex with macrocycle MC09 Deposited 2024-08-29 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
192–538（347 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 1500 and 0.1 M MMT (malic acid, MES, Tris) buffer pH 7
|
Resolution 2.57 Å R-free 0.284 |
| 9FIO Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
208–560（353 aa）
|
Not recorded | R4D 3-({4-hydroxy-1-[(2R)-2-methyl-3-phenylpropanoyl]piperidin-4-yl}methyl)quinazolin-4(3H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 2.60 Å R-free 0.321 |
| 9FIO Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
208–560（353 aa）
|
Not recorded | R4D 3-({4-hydroxy-1-[(2R)-2-methyl-3-phenylpropanoyl]piperidin-4-yl}methyl)quinazolin-4(3H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 2.60 Å R-free 0.321 |
| 9FIP Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–560（354 aa）
|
Not recorded | A1ICU 3-[[4-oxidanyl-1-[(1~{R},2~{R})-2-phenylcyclohexyl]carbonyl-piperidin-4-yl]methyl]quinazolin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 3.06 Å R-free 0.264 |
| 9FIP Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–560（354 aa）
|
Not recorded | A1ICU 3-[[4-oxidanyl-1-[(1~{R},2~{R})-2-phenylcyclohexyl]carbonyl-piperidin-4-yl]methyl]quinazolin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 3.06 Å R-free 0.264 |
| 9FIQ Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–560（354 aa）
|
Not recorded | A1ICV 3-[[4-oxidanyl-1-[(3~{S},4~{S})-3-phenyl-1-(phenylmethyl)piperidin-4-yl]carbonyl-piperidin-4-yl]methyl]quinazolin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 2.86 Å R-free 0.278 |
| 9FIQ Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–560（354 aa）
|
Not recorded | A1ICV 3-[[4-oxidanyl-1-[(3~{S},4~{S})-3-phenyl-1-(phenylmethyl)piperidin-4-yl]carbonyl-piperidin-4-yl]methyl]quinazolin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 2.86 Å R-free 0.278 |
| 9FIR Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–560（354 aa）
|
Not recorded | A1ICS 3-[[1-[(2~{S},3~{S})-1-methyl-6-oxidanylidene-2-phenyl-piperidin-3-yl]carbonyl-4-oxidanyl-piperidin-4-yl]methyl]quinazolin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 2.76 Å R-free 0.322 |
| 9FIR Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–560（354 aa）
|
Not recorded | A1ICS 3-[[1-[(2~{S},3~{S})-1-methyl-6-oxidanylidene-2-phenyl-piperidin-3-yl]carbonyl-4-oxidanyl-piperidin-4-yl]methyl]quinazolin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 2.76 Å R-free 0.322 |
| 9FIS Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
208–560（353 aa）
|
Not recorded | A1ICW 3-[[4-oxidanyl-1-[(3~{R},4~{R})-3-phenyl-1-(2-phenylethyl)piperidin-4-yl]carbonyl-piperidin-4-yl]methyl]quinazolin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 2.77 Å R-free 0.243 |
| 9FIS Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
208–560（353 aa）
|
Not recorded | A1ICW 3-[[4-oxidanyl-1-[(3~{R},4~{R})-3-phenyl-1-(2-phenylethyl)piperidin-4-yl]carbonyl-piperidin-4-yl]methyl]quinazolin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 2.77 Å R-free 0.243 |
| 9FIT Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–560（354 aa）
|
Mutation：F409A | A1ICT 7-methyl-3-[[4-oxidanyl-1-[(3~{R},4~{R})-3-phenyl-1-[(5-pyrimidin-5-ylthiophen-2-yl)methyl]piperidin-4-yl]carbonyl-piperidin-4-yl]methyl]pyrrolo[2,3-d]pyrimidin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 2.70 Å R-free 0.328 |
| 9FIT Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–560（354 aa）
|
Mutation：F409A | A1ICT 7-methyl-3-[[4-oxidanyl-1-[(3~{R},4~{R})-3-phenyl-1-[(5-pyrimidin-5-ylthiophen-2-yl)methyl]piperidin-4-yl]carbonyl-piperidin-4-yl]methyl]pyrrolo[2,3-d]pyrimidin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 2.70 Å R-free 0.328 |
| 9FIU Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–560（354 aa）
|
Mutation：F409A | A1ICX 3-[[1-[(3~{R},4~{R})-1-[5-(3-methoxypyridin-4-yl)thiophen-2-yl]carbonyl-3-phenyl-piperidin-4-yl]carbonyl-4-oxidanyl-piperidin-4-yl]methyl]-7-methyl-pyrrolo[2,3-d]pyrimidin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 3.37 Å R-free 0.297 |
| 9FIU Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–560（354 aa）
|
Mutation：F409A | A1ICX 3-[[1-[(3~{R},4~{R})-1-[5-(3-methoxypyridin-4-yl)thiophen-2-yl]carbonyl-3-phenyl-piperidin-4-yl]carbonyl-4-oxidanyl-piperidin-4-yl]methyl]-7-methyl-pyrrolo[2,3-d]pyrimidin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 3.37 Å R-free 0.297 |
| 9FIV Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–560（354 aa）
|
Mutation：F409A | A1ICO 7-methyl-3-[[4-oxidanyl-1-[(3~{R},4~{R})-3-phenyl-1-[(5-pyridin-4-yl-1,3-thiazol-2-yl)methyl]piperidin-4-yl]carbonyl-piperidin-4-yl]methyl]pyrrolo[2,3-d]pyrimidin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 2.70 Å R-free 0.330 |
| 9FIV Structure-guided discovery of selective USP7 inhibitors with in vivo activity Deposited 2024-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–560（354 aa）
|
Mutation：F409A | A1ICO 7-methyl-3-[[4-oxidanyl-1-[(3~{R},4~{R})-3-phenyl-1-[(5-pyridin-4-yl-1,3-thiazol-2-yl)methyl]piperidin-4-yl]carbonyl-piperidin-4-yl]methyl]pyrrolo[2,3-d]pyrimidin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；23% peg 3350,
0.6 M sodium formate,
10 mM DTT
|
Resolution 2.70 Å R-free 0.330 |
| 9IJU Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-06-25 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
208–560（353 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
|
Resolution 2.46 Å R-free 0.270 |
| 9IJU Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-06-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
208–560（353 aa）
|
Not recorded | SRE (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
|
Resolution 2.46 Å R-free 0.270 |
| 9IJU Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-06-25 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
208–560（353 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
|
Resolution 2.46 Å R-free 0.270 |
| 9IJU Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-06-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
208–560（353 aa）
|
Not recorded | SRE (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
|
Resolution 2.46 Å R-free 0.270 |
| 9IML Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-07-03 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
208–560（353 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
|
Resolution 2.78 Å R-free 0.280 |
| 9IML Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-07-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
208–560（353 aa）
|
Not recorded | XB7 1-[(4-fluorophenyl)methyl]-N-{1-[2-(4-methoxyphenyl)ethyl]piperidin-4-yl}-1H-benzimidazol-2-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
|
Resolution 2.78 Å R-free 0.280 |
| 9IML Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-07-03 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
208–560（353 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
|
Resolution 2.78 Å R-free 0.280 |
| 9IML Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-07-03 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
208–560（353 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
|
Resolution 2.78 Å R-free 0.280 |
| 9K2W Cryo-EM structure of USP7:DNMT1 complex; closed conformation Deposited 2024-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1102（1102 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.54 Å |
| 9K2X Cryo-EM structure of USP7:DNMT1 complex; open conformation Deposited 2024-10-18 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1102（1102 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.75 Å |
| 9QJE USP7 Covalently Bound to N-(6-Fluoro-3-nitropyridin-2-yl)-5-(1-methyl-1H-pyrazol-4-yl)isoquinolin-3-amine (GCL36, 7a) with Partial Occupancy Deposited 2025-03-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
207–560（354 aa）
|
Not recorded | A1I71 5-(1-methyl-1H-pyrazol-4-yl)-N-(3-nitropyridin-2-yl)isoquinolin-3-amine × 1 EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 BR BROMIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；USP7 (17.5 mg/mL) was incubated with the Compound (500 uM in reservoir solution) prior to crystallization. The reservoir solution contained 0.1 M HEPES pH 7.5, 0.2 M sodium bromide, 22% PEG3350
|
Resolution 2.26 Å R-free 0.248 |
| 9QJE USP7 Covalently Bound to N-(6-Fluoro-3-nitropyridin-2-yl)-5-(1-methyl-1H-pyrazol-4-yl)isoquinolin-3-amine (GCL36, 7a) with Partial Occupancy Deposited 2025-03-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
207–560（354 aa）
|
Not recorded | A1I71 5-(1-methyl-1H-pyrazol-4-yl)-N-(3-nitropyridin-2-yl)isoquinolin-3-amine × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 BR BROMIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；USP7 (17.5 mg/mL) was incubated with the Compound (500 uM in reservoir solution) prior to crystallization. The reservoir solution contained 0.1 M HEPES pH 7.5, 0.2 M sodium bromide, 22% PEG3350
|
Resolution 2.26 Å R-free 0.248 |
| 9SZN Crystal structure of the catalytic domain of USP7 in complex with Compound 43 Deposited 2025-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
208–560（353 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1JSJ 3-((7-(3-((S)-3-aminopyrrolidine-1-carbonyl)-4-methyl-6-(trifluoromethyl)pyridin-2-yl)thieno[3,2-b]pyridin-2-yl)methyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2,4-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；277 K；8 % w/v PEG 20,000/8 % v/v PEG 550 MME; 0.1 M Sodium acetate pH 4.5; 0.25 M Potassium bromide
|
Resolution 1.99 Å R-free 0.226 |
| 9SZO Crystal structure of the catalytic domain of USP7 in complex with Compound 13 Deposited 2025-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
208–560（353 aa）
|
Not recorded | A1JSK (43S,Z)-25-chloro-23-methyl-3-oxa-1(7,2)-thieno[3,2-b]pyridina-4(3,1)-piperidina-11(1,3)-imidazolidina-2(1,2)-benzenacyclododecaphan-7-ene-112,114-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；277 K；8 % w/v PEG 20,000/8 % v/v PEG 550 MME; 0.1 M Sodium acetate pH 4.5; 0.25 M Potassium bromide
|
Resolution 2.57 Å R-free 0.280 |
84 other PDB entries and 144 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | UBP7_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 4–334； UniProt 560–890 Author chain B； PDBConstruct 4–334； UniProt 560–890 Author chain C； PDBConstruct 4–334； UniProt 560–890 Author chain D； PDBConstruct 4–334； UniProt 560–890 |
