|
12ZJ
Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980)
Deposited 2026-04-24
|
Different construct
Different ligand/ion
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 ligand/ion
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 ligand/ion
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 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：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 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：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 ligand/ion
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 ligand/ion
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 oligomeric state
Different ligand/ion
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 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 oligomeric state
Different ligand/ion
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 oligomeric state
Different ligand/ion
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 oligomeric state
Different ligand/ion
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 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 oligomeric state
Different ligand/ion
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 oligomeric state
Different ligand/ion
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 oligomeric state
Different ligand/ion
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 oligomeric state
Different ligand/ion
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 oligomeric state
Different ligand/ion
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 ligand/ion
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 ligand/ion
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 ligand/ion
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 oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein monomer
Monomer；Protein × 1
PDB declaration: monomeric
|
Chain A
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 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：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 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 ligand/ion
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 ligand/ion
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 ligand/ion
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 ligand/ion
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 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 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 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 oligomeric state
Different ligand/ion
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 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 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 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 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 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
|
|
4YSI
Structure of USP7 with a novel viral protein
Deposited 2015-03-17
|
Different construct
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 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
|
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 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 ligand/ion
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 ligand/ion
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 ligand/ion
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 oligomeric state
Different ligand/ion
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
|
|
5GG4
Crystal structure of USP7 with RNF169 peptide
Deposited 2016-06-15
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein heterocomplex
Heteromer；Protein × 4
PDB declaration: tetrameric
|
Chain A
560–890（331 aa）
Fragment：UNP residues 560-890
Chain B
560–890（331 aa）
Fragment：UNP residues 560-890
|
Not recorded
|
No recorded non-water small molecule
|
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
|
|
5GG4
Crystal structure of USP7 with RNF169 peptide
Deposited 2016-06-15
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein heterocomplex
Heteromer；Protein × 4
PDB declaration: tetrameric
|
Chain C
560–890（331 aa）
Fragment：UNP residues 560-890
Chain D
560–890（331 aa）
Fragment：UNP residues 560-890
|
Not recorded
|
No recorded non-water small molecule
|
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
|
|
5J7T
Molecular Understanding of USP7 Substrate Recognition and C-Terminal Activation
Deposited 2016-04-06
|
Different construct
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
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 mutation/modification
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 mutation/modification
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 mutation/modification
Different ligand/ion
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 mutation/modification
Different ligand/ion
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 mutation/modification
Different ligand/ion
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 mutation/modification
Different ligand/ion
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 oligomeric state
Different ligand/ion
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 ligand/ion
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 oligomeric state
Different ligand/ion
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 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 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：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 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 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）
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
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 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
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 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 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 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 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 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
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 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
208–554（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 ligand/ion
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 oligomeric state
Different ligand/ion
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 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 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 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 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 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 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 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 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 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 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 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 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 oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein monomer
Monomer；Protein × 1
PDB declaration: monomeric
|
Chain A
560–1083（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 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
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 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 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 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 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 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 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 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
|
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 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
|
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 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
|
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 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）
|
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 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 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
|
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 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 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
|
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 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 ligand/ion
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 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 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 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 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 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 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 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 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 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 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 ligand/ion
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 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 ligand/ion
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 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 ligand/ion
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 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 ligand/ion
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 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
|
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 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 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
|
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 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 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 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
|
