3n3k

The catalytic domain of USP8 in complex with a USP8 specific inhibitor

Method: X-RAY DIFFRACTION D_max: 71.8 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin carboxyl-terminal hydrolase 8

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 734–1110	Fragment：CATALYTIC DOMAIN	Ubiquitin × 1 （P62988） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；24% PEG3350, 0.1 M BIS-TRIS, 0.2 M AMMONIUM ACETATE, 1 MM DTT, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.242

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3N3K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WHB Solution structure of the Rhodanese-like domain in human ubiquitin specific protease 8 (UBP8) Deposited 2004-05-28	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 176–319（144 aa） Fragment：Rhodanese-like domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1mM protein, 20mM d-Tris-HCl, pH 7.0, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2A9U Structure of the N-terminal domain of Human Ubiquitin carboxyl-terminal hydrolase 8 (USP8) Deposited 2005-07-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–142（142 aa） Fragment：N-terminal domain, residues 1-142 Chain B 1–142（142 aa） Fragment：N-terminal domain, residues 1-142	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；27% PEG3350, 0.2 M Li2SO4, 0.1 M bisTris, pH 5.6, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298 K	Resolution 2.10 Å R-free 0.259
2GFO Structure of the Catalytic Domain of Human Ubiquitin Carboxyl-terminal Hydrolase 8 Deposited 2006-03-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 734–1110（377 aa） Fragment：Catalytic Domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；18% PEG3350; 0.1 M bis-Tris, pH 6.3, 0.2 M KSCN, 1 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 298, temperature 298.0K	Resolution 2.00 Å R-free 0.210
2GWF Structure of a USP8-NRDP1 complex Deposited 2006-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 181–318（138 aa） Fragment：Rhodanase domain, residues 181-318	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；12% PEG5000 MME, 0.1 M bis-Tris, 1 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.30 Å R-free 0.237
2GWF Structure of a USP8-NRDP1 complex Deposited 2006-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 181–318（138 aa） Fragment：Rhodanase domain, residues 181-318	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；12% PEG5000 MME, 0.1 M bis-Tris, 1 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.30 Å R-free 0.237
2GWF Structure of a USP8-NRDP1 complex Deposited 2006-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 181–318（138 aa） Fragment：Rhodanase domain, residues 181-318	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；12% PEG5000 MME, 0.1 M bis-Tris, 1 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.30 Å R-free 0.237
6F09 Binary complex of 14-3-3 zeta with ubiquitin specific protease 8 (USP8) pSer718 peptide Deposited 2017-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 712–724（13 aa） Chain D 712–724（13 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) 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；298.15 K；0.1 M phosphate citrate pH 4.4; 40% PEG 300	Resolution 1.59 Å R-free 0.225
6F09 Binary complex of 14-3-3 zeta with ubiquitin specific protease 8 (USP8) pSer718 peptide Deposited 2017-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 712–724（13 aa） Chain C 712–724（13 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) 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；298.15 K；0.1 M phosphate citrate pH 4.4; 40% PEG 300	Resolution 1.59 Å R-free 0.225
6F09 Binary complex of 14-3-3 zeta with ubiquitin specific protease 8 (USP8) pSer718 peptide Deposited 2017-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 712–724（13 aa） Chain D 712–724（13 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) 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；298.15 K；0.1 M phosphate citrate pH 4.4; 40% PEG 300	Resolution 1.59 Å R-free 0.225
6F09 Binary complex of 14-3-3 zeta with ubiquitin specific protease 8 (USP8) pSer718 peptide Deposited 2017-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 712–724（13 aa） Chain C 712–724（13 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) 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；298.15 K；0.1 M phosphate citrate pH 4.4; 40% PEG 300	Resolution 1.59 Å R-free 0.225
8ADM Ternary complex of 14-3-3 sigma, Usp8pS718 phosphopeptide and small molecule stabilizer Deposited 2022-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 715–722（8 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	O6C 1-[2-(4-chloranylphenoxy)-2-methyl-propanoyl]-~{N}-[2-[2-(dimethylamino)ethyldisulfanyl]ethyl]piperidine-4-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1M carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1M buffer system 1 (Imidazole; MES monohydrate) pH 6.5 and 50% precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)	Resolution 1.70 Å R-free 0.222
8XPN The Crystal Structure of USP8 from Biortus. Deposited 2024-01-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 734–1110（377 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG 2000 MME, 0.1M Bis-Tris propane pH6.9	Resolution 2.10 Å R-free 0.216
8XPN The Crystal Structure of USP8 from Biortus. Deposited 2024-01-04	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 734–1110（377 aa）	Not recorded	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG 2000 MME, 0.1M Bis-Tris propane pH6.9	Resolution 2.10 Å R-free 0.216
8XPN The Crystal Structure of USP8 from Biortus. Deposited 2024-01-04	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 734–1110（377 aa）	Not recorded	ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG 2000 MME, 0.1M Bis-Tris propane pH6.9	Resolution 2.10 Å R-free 0.216
8Y9A The Crystal Structure of USP8 from Biortus. Deposited 2024-02-06	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 1–142（142 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；4.0M Na formate	Resolution 3.10 Å R-free 0.268

8 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBP8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–396； UniProt 734–1110

Ubiquitin

Homo sapiens

UniProt P62988

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–76	Mutation：Q2R, F4V, T9M, K11R, T14I, Q62H, K63N, E64H, T66A, H68Y, V70L, R72K	Ubiquitin carboxyl-terminal hydrolase 8 × 1 （P40818） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；24% PEG3350, 0.1 M BIS-TRIS, 0.2 M AMMONIUM ACETATE, 1 MM DTT, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.242

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3N3K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C3T ROTAMER STRAIN AS A DETERMINANT OF PROTEIN STRUCTURAL SPECIFICITY Deposited 1999-07-28	Different construct Different mutation/modification Different 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 87–162（76 aa）	Mutation：I3L,I13L,L15V,V17L,I23V,V26L,I61L,L67I	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.8；303 K；Ionic strength (raw mmCIF value) 50 mM；Pressure 1 NMR sample composition 2 MM 13C/15N 1D8 UBIQUITIN, 25 MM SODIUM PHOSPHATE, 25 MM SODIUM ACETATE (D3), 0.02% SODIUM AZIDE, PH 5.8	Resolution not provided
1D3Z UBIQUITIN NMR STRUCTURE Deposited 1999-10-01	Different construct Different mutation/modification 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 136–211（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；308 K；Ionic strength (raw mmCIF value) 20 mM；Pressure AMBIENT NMR sample composition UBIQUITIN HUMAN SEQUENCE	Resolution not provided
1F9J STRUCTURE OF A NEW CRYSTAL FORM OF TETRAUBIQUITIN Deposited 2000-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；lithium sulfate, ammonium sulfate, sodium citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.70 Å R-free 0.292
1FXT STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTER COMPLEX Deposited 2000-09-26	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；30 K；Ionic strength (raw mmCIF value) 450mM NaCl；Pressure ambient NMR sample composition Yeast Ubc1 \| 0.8 mM Ubc1 10uM E1 0.8 mM Ub 10mM ATP, 5 mM MgCl, 40 mM Hepes, 450 mM NaCl,, 1 mM EDTA in water NMR sample composition Human Ub \| 0.8 mM Ubc1 10uM E1 0.8 mM Ub 10mM ATP, 5 mM MgCl, 40 mM Hepes, 450 mM NaCl,, 1 mM EDTA in water	Resolution not provided
1G6J STRUCTURE OF RECOMBINANT HUMAN UBIQUITIN IN AOT REVERSE MICELLES Deposited 2000-11-06	Different mutation/modification 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 293 K；Pressure ambient NMR measurement conditions 293 K；Pressure 50 NMR sample composition 4 mg c13/n15 ubiquitin in 13.5 ul of buffer (50mM Sodium acetate, 250mM Sodium Chloride, pH 5.0) and 1 ml D12-pentane \| 75mM bis(2-ethyl hexyl) sulfosuccinate in d-pentane NMR sample composition 8 mg 13/n15 ubiquitin in 27 ul of buffer (50mM Sodium acetate, 250mM Sodium Chloride, pH 5.0) \| 75mM bis(2-ethyl hexyl) sulfosuccinate in butane NMR sample composition 4 mg n15 ubiquitin in 13.5 ul of buffer (50mM Sodium acetate, 250mM Sodium Chloride, pH 5.0) \| 75mM bis(2-ethyl hexyl) sulfosuccinate in d-pentane	Resolution not provided
1NBF Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde Deposited 2002-12-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；296 K；PEG3000, citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.30 Å R-free 0.262
1NBF Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde Deposited 2002-12-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；296 K；PEG3000, citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.30 Å R-free 0.262
1Q5W Ubiquitin Recognition by Npl4 Zinc-Fingers Deposited 2003-08-11	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 5.5；291 K；Ionic strength (raw mmCIF value) 70mM；Pressure ambient NMR measurement conditions pH 5.5；291 K；Ionic strength (raw mmCIF value) 70mM；Pressure ambient NMR measurement conditions pH 5.5；291 K；Ionic strength (raw mmCIF value) 70mM；Pressure ambient NMR measurement conditions pH 5.5；291 K；Ionic strength (raw mmCIF value) 70mM；Pressure ambient NMR sample composition 1mM Npl4 NZF U-15N,13C; 2mM unlabeled-Ubiquitin; 20mM phosphate buffer pH 5.5, 50mM NaCl; 90% H2O, 10% \| 90% H2O/10% D2O NMR sample composition 1mM Ubiquitin U-15N,13C; 2mM unlabeled-Npl4 NZF; 20mM phosphate buffer pH 5.5, 50mM NaCl; 90% H2O, 10% \| 90% H2O/10% D2O NMR sample composition 1mM Ubiquitin U-15N; 2mM unlabeled-Npl4 NZF; 20mM phosphate buffer pH 5.5, 50mM \| 90% H2O/10% D2O NMR sample composition 1mM Npl4 NZF U-15N; 2mM unlabeled-Ubiquitin; 20mM phosphate buffer pH 5.5, 50mM NaCl; 90% H2O, 10% \| 90% H2O/10% D2O	Resolution not provided
1S1Q TSG101(UEV) domain in complex with Ubiquitin Deposited 2004-01-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；1.4M Ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.00 Å R-free 0.240
1S1Q TSG101(UEV) domain in complex with Ubiquitin Deposited 2004-01-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 SO4 SULFATE ION × 2 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；1.4M Ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.00 Å R-free 0.240
1SIF Crystal structure of a multiple hydrophobic core mutant of ubiquitin Deposited 2004-02-29	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–76（76 aa）	Mutation：M1L, I3L, V5I, I13F, L15V, V17M, V26L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；288 K；31% Peg 4K, 0.05M citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K	Resolution 2.18 Å R-free 0.248
1TBE STRUCTURE OF TETRAUBIQUITIN SHOWS HOW MULTIUBIQUITIN CHAINS CAN BE FORMED Deposited 1993-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1UBI SYNTHETIC STRUCTURAL AND BIOLOGICAL STUDIES OF THE UBIQUITIN SYSTEM. PART 1 Deposited 1994-02-03	Different 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1UBQ STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION Deposited 1987-01-02	Different 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1XD3 Crystal structure of UCHL3-UbVME complex Deposited 2004-09-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 229–303（75 aa）	Not recorded	MG MAGNESIUM ION × 3 GVE METHYL 4-AMINOBUTANOATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.45 Å R-free 0.192
1XD3 Crystal structure of UCHL3-UbVME complex Deposited 2004-09-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 229–303（75 aa）	Not recorded	MG MAGNESIUM ION × 7 GVE METHYL 4-AMINOBUTANOATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.45 Å R-free 0.192
1YX5 Solution Structure of S5a UIM-1/Ubiquitin Complex Deposited 2005-02-19	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：Sequence Database Residues 1-76	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1 NMR sample composition 0.5 mM S5a U-15N, 2H 2.0 mM ubiquitin unlabeled \| 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O NMR sample composition 0.5 mM S5a U-15N, 2H 2.0 mM ubiquitin U-13C \| 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O NMR sample composition 0.5 mM S5a U-13C 2.0 mM ubiquitin unlabeled \| 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O	Resolution not provided
1YX6 Solution Structure of S5a UIM-2/Ubiquitin Complex Deposited 2005-02-19	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：Sequence Database Residues 1-76	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1 NMR sample composition 0.5 mM S5a U-15N, 2H; 2.0 mM ubiquitin unlabeled \| 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O NMR sample composition 0.5 mM S5a U-15N, 2H; 2.0 mM ubiquitin U-13C \| 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O NMR sample composition 0.5 mM S5a U-13C; 2.0 mM ubiquitin unlabeled \| 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O	Resolution not provided
2AYO Structure of USP14 bound to ubquitin aldehyde Deposited 2005-09-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；Tris, calsium chloride, PEG1000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 3.50 Å R-free 0.330
2AYO Structure of USP14 bound to ubquitin aldehyde Deposited 2005-09-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；Tris, calsium chloride, PEG1000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 3.50 Å R-free 0.330
2BGF NMR structure of Lys48-linked di-ubiquitin using chemical shift perturbation data together with RDCs and 15N-relaxation data Deposited 2004-12-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20；Pressure 1.0 NMR sample composition 90% WATER/10% D20	Resolution not provided
2FUH Solution Structure of the UbcH5c/Ub Non-covalent Complex Deposited 2006-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：Ubiquitin	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 150mM NaCl；Pressure ambient NMR sample composition 1mM UbcH5c U-15N,13C 25mM sodium phosphate 150mM NaCl \| 90% H20 10% D20 NMR sample composition 1mM Ubiquitin U-15N,13C 25mM sodium phosphate 150mM NaCl \| 90% H20 10% D20 NMR sample composition 1mM UbcH5c U-15N,13C 1mM Ubiquitin 25mM sodium phosphate 150mM NaCl \| 90% H20 10% D20 NMR sample composition 1mM Ubiquitin U-15N,13C 1mM UbcH5c 25mM sodium phosphate 150mM NaCl \| 90% H20 10% D20 NMR sample composition 1mM UbcH5c U-15N,13C 1mM Ubiquitin 25mM sodium phosphate 150mM NaCl \| 100% D20 NMR sample composition 1mM Ubiquitin U-15N,13C 1mM UbcH5c 25mM sodium phosphate 150mM NaCl \| 100% D20	Resolution not provided
2G45 Co-crystal structure of znf ubp domain from the deubiquitinating enzyme isopeptidase T (isot) in complex with ubiquitin Deposited 2006-02-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；300 K；16% polyethylene glycol 8000, 80 mM sodium cacodylate pH 6.5, 160 mM magenesium or calcium acetate, 20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 6.50	Resolution 1.99 Å R-free 0.268
2G45 Co-crystal structure of znf ubp domain from the deubiquitinating enzyme isopeptidase T (isot) in complex with ubiquitin Deposited 2006-02-21	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；300 K；16% polyethylene glycol 8000, 80 mM sodium cacodylate pH 6.5, 160 mM magenesium or calcium acetate, 20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 6.50	Resolution 1.99 Å R-free 0.268
2GBJ Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin. Deposited 2006-03-10	Different 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；279.15 K；27-32% PEG 4000, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K	Resolution 1.35 Å R-free 0.226
2GBJ Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin. Deposited 2006-03-10	Different 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；279.15 K；27-32% PEG 4000, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K	Resolution 1.35 Å R-free 0.226
2GBK Crystal Structure of the 9-10 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293.15 K；27-32% PEG 6000, 4-12% Acetone, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.99 Å R-free 0.287
2GBK Crystal Structure of the 9-10 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293.15 K；27-32% PEG 6000, 4-12% Acetone, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.99 Å R-free 0.287
2GBK Crystal Structure of the 9-10 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293.15 K；27-32% PEG 6000, 4-12% Acetone, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.99 Å R-free 0.287
2GBK Crystal Structure of the 9-10 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293.15 K；27-32% PEG 6000, 4-12% Acetone, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.99 Å R-free 0.287
2GBK Crystal Structure of the 9-10 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain C 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293.15 K；27-32% PEG 6000, 4-12% Acetone, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.99 Å R-free 0.287
2GBK Crystal Structure of the 9-10 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Chain D 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293.15 K；27-32% PEG 6000, 4-12% Acetone, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.99 Å R-free 0.287
2GBM Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；293.15 K；25-30% PEG 4000, 50 mM Sodium Cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 5.50	Resolution 1.55 Å R-free 0.227
2GBM Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different 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 1–76（76 aa）	Not recorded	ARS ARSENIC × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；293.15 K；25-30% PEG 4000, 50 mM Sodium Cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 5.50	Resolution 1.55 Å R-free 0.227
2GBM Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–76（76 aa）	Not recorded	ARS ARSENIC × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；293.15 K；25-30% PEG 4000, 50 mM Sodium Cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 5.50	Resolution 1.55 Å R-free 0.227
2GBM Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–76（76 aa）	Not recorded	ARS ARSENIC × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；293.15 K；25-30% PEG 4000, 50 mM Sodium Cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 5.50	Resolution 1.55 Å R-free 0.227
2GBN Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；279.15 K；25-30% PEG 4000, 50 mM Sodium Cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K	Resolution 1.60 Å R-free 0.265
2GBR Crystal Structure of the 35-36 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different 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 1–76（76 aa）	Not recorded	CD CADMIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.9；293.15 K；24-30% PEG 4000, 50-80 mM Cadmium Chloride, 100 mM Sodium Acetate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 2.00 Å R-free 0.290
2GBR Crystal Structure of the 35-36 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different 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 1–76（76 aa）	Not recorded	CD CADMIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.9；293.15 K；24-30% PEG 4000, 50-80 mM Cadmium Chloride, 100 mM Sodium Acetate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 2.00 Å R-free 0.290
2GBR Crystal Structure of the 35-36 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–76（76 aa）	Not recorded	CD CADMIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.9；293.15 K；24-30% PEG 4000, 50-80 mM Cadmium Chloride, 100 mM Sodium Acetate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 2.00 Å R-free 0.290
2GBR Crystal Structure of the 35-36 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa） Chain C 1–76（76 aa）	Not recorded	CD CADMIUM ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.9；293.15 K；24-30% PEG 4000, 50-80 mM Cadmium Chloride, 100 mM Sodium Acetate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 2.00 Å R-free 0.290
2GBR Crystal Structure of the 35-36 MoaD Insertion Mutant of Ubiquitin Deposited 2006-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	CD CADMIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.9；293.15 K；24-30% PEG 4000, 50-80 mM Cadmium Chloride, 100 mM Sodium Acetate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 2.00 Å R-free 0.290
2HTH Structural basis for ubiquitin recognition by the human EAP45/ESCRT-II GLUE domain Deposited 2006-07-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；10% PEG8000; 10% Ethylene glycol; 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.289
2IBI Covalent Ubiquitin-USP2 Complex Deposited 2006-09-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–75（75 aa）	Not recorded	ZN ZINC ION × 1 NEH ETHANAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；298 K；22% PEG1500, 0.1 M Bicine, 0.2 M NaCl, 1 mM DTT, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 9.00	Resolution 2.20 Å R-free 0.259
2J7Q Crystal structure of the ubiquitin-specific protease encoded by murine cytomegalovirus tegument protein M48 in complex with a ubquitin-based suicide substrate Deposited 2006-10-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–75（75 aa） Fragment：UBIQUITIN FUSED TO VINYLMETHYLESTER, UBVME, RESIDUES 1-75	Not recorded	MG MAGNESIUM ION × 2 GVE METHYL 4-AMINOBUTANOATE × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；200 MM MAGNESIUM FORMATE, 14% PEG 3350, pH 7.50	Resolution 1.80 Å R-free 0.214
2J7Q Crystal structure of the ubiquitin-specific protease encoded by murine cytomegalovirus tegument protein M48 in complex with a ubquitin-based suicide substrate Deposited 2006-10-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–75（75 aa） Fragment：UBIQUITIN FUSED TO VINYLMETHYLESTER, UBVME, RESIDUES 1-75	Not recorded	MG MAGNESIUM ION × 1 GVE METHYL 4-AMINOBUTANOATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；200 MM MAGNESIUM FORMATE, 14% PEG 3350, pH 7.50	Resolution 1.80 Å R-free 0.214
2JF5 crystal structure of Lys63-linked di-ubiquitin Deposited 2007-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	CD CADMIUM ION × 2 MG MAGNESIUM ION × 1 CO COBALT (II) ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；12 % (W/V) PEG 3350, 5 MM NICKEL CHLORIDE, 5 MM COBALT CHLORIDE, 5 MM CADMIUM CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 0.1 M HEPES [PH 7.5]	Resolution 1.95 Å R-free 0.250
2JZZ Solid-State NMR Structure of Microcrystalline Ubiquitin Deposited 2008-01-22	Different mutation/modification 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLID-STATE NMR NMR measurement conditions 270 K；Pressure ambient NMR sample composition 5.5 mg/mL [U-99% 13C; U-98% 15N] Ubiquitin, 20 mM ammonium acetate, 20 mM citric acid, 60 v/v 2-methyl-2,4-pentandiol, 0.05 % sodium azide, 100 % H2O \| 100 % H2O	Resolution not provided
2K6D CIN85 Sh3-C domain in complex with ubiquitin Deposited 2008-07-07	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–75（75 aa） Fragment：ubiquitin	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 0.150；Pressure ambient NMR sample composition 0.1 mM CIN85, 0.1 mM [U-100% 15N] ubiquitin, 50 mM sodium phosphate, 2 mM DTT, 5 mM DSS, 150 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.1 mM [U-100% 15N] CIN85, 0.1 mM ubiquitiny, 50 mM sodium phosphate, 2 mM DTT, 5 mM DSS, 150 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] CIN85, 50 mM sodium phosphate, 2 mM DTT, 5 mM DSS, 150 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2K8B Solution structure of PLAA family ubiquitin binding domain (PFUC) cis isomer in complex with ubiquitin Deposited 2008-09-04	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient NMR sample composition 0.2 mM Ubiquitin, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.2 mM PFUC_cis, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2K8C Solution structure of PLAA family ubiquitin binding domain (PFUC) trans isomer in complex with ubiquitin Deposited 2008-09-04	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient NMR sample composition 0.2 mM [U-100% 15N] Ubiquitin, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.2 mM [U-100% 15N] PFUC_trans, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KDF NMR structure of minor S5a (196-306):K48 linked diubiquitin species Deposited 2009-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–76（76 aa） Chain C 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 20 mM NaPO4; 100 mM NaCl；Pressure ambient NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 20 mM NaPO4; 50 mM NaCl；Pressure ambient NMR sample composition 0.4 mM [U-100% 15N; U-50% 2H] S5a (196-306)-1, 1.2 mM K48 linked diubiquitin-2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-100% 13C] S5a (196-306)-3, 1.5 mM K48 linked diubiquitin-4, 100% D2O \| 100% D2O NMR sample composition 0.5 mM [U-100% 13C of the proximal Ub; natural abundance of the distal subunit] K48 linked diubiquitin-5, 1.0 mM S5a (196-306)-6, 100% D2O \| 100% D2O NMR sample composition 0.5 mM [U-100% 13C of the distal subunit; natural abundance of the proximal Ub] K48 linked diubiquitin-7, 1.0 mM S5a (196-306)-8, 100% D2O \| 100% D2O NMR sample composition 0.4 mM [U-100% 13C] S5a (196-306)-9, 1.2 mM [U-100% 2H of the proximal Ub; natural abundance of the distal subunit] K48 linked diubiquitin-10, 100% D2O \| 100% D2O	Resolution not provided
2KHW Solution Structure of the human Polymerase iota UBM2-Ubiquitin Complex Deposited 2009-04-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition 1 mM [U-100% 15N] entity_1-1, 4 mM entity_2-2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 3 mM [U-100% 15N] entity_1-3, 3 mM [U-100% 15N] entity_2-4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 3 mM [U-100% 13C; U-100% 15N] entity_1-5, 3 mM [U-100% 13C; U-100% 15N] entity_2-6, 100% D2O \| 100% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_1-7, 4 mM entity_2-8, 100% D2O \| 100% D2O	Resolution not provided
2KJH NMR based structural model of the UBCH8-UBIQUITIN complex Deposited 2009-05-28	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Mutation：G76C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 250；Pressure ambient NMR sample composition 0.35 mM [U-100% 13C; U-100% 15N] UbcH8-1, 0.35 mM Ubiquitin-2, 20 mM sodium phosphate-3, 1 mM EDTA-4, 250 mM sodium chloride-5, 50 mM Arginine-6, 50 mM Glutamic Acid-7, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.35 mM UbcH8-8, 0.35 mM [U-100% 13C; U-100% 15N] Ubiquitin-9, 20 mM sodium phosphate-10, 1 mM EDTA-11, 250 mM sodium chloride-12, 50 mM Arginine-13, 50 mM Glutamic Acid-14, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.35 mM [U-100% 15N; U-99% 2H] UbcH8-15, 0.35 mM Ubiquitin-16, 20 mM sodium phosphate-17, 1 mM EDTA-18, 250 mM sodium chloride-19, 50 mM Arginine-20, 50 mM Glutamic Acid-21, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.35 mM UbcH8-22, 0.35 mM [U-100% 15N; U-99% 2H] Ubiquitin-23, 20 mM sodium phosphate-24, 1 mM EDTA-25, 250 mM sodium chloride-26, 50 mM Arginine-27, 50 mM Glutamic Acid-28, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KLG PERE NMR structure of ubiquitin Deposited 2009-07-02	Different mutation/modification 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 50mM potassium phosphate-1, 3mM sodium azide-2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KN5 A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family Deposited 2009-08-14	Different mutation/modification 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；308 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N] human ubiquitin, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6-0.9 mM [U-100% 13C; U-100% 15N] human ubiquitin, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KOX NMR residual dipolar couplings identify long range correlated motions in the backbone of the protein ubiquitin Deposited 2009-10-02	Different mutation/modification 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions Pressure ambient NMR sample composition [U-100% 13C; U-100% 15N] Ubiquitin-1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KTF Solution NMR structure of human polymerase iota UBM2 in complex with ubiquitin Deposited 2010-02-01	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；301 K；Ionic strength (raw mmCIF value) 0.08；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] protein, 3.5 mM peptide, 20 mM sodium phosphate, 30 mM sodium chloride, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2.5 mM protein, 0.5 mM [U-100% 13C; U-100% 15N] peptide, 20 mM sodium phosphate, 30 mM sodium chloride, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KWU Solution Structure of UBM2 of murine Polymerase iota in Complex with Ubiquitin Deposited 2010-04-19	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) 0.189；Pressure ambient NMR sample composition 1-2 mM [U-99% 15N] DNA polymerase iota UBM2, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1-2 mM [U-95% 13C; U-99% 15N] DNA polymerase iota UBM2, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 4-8 mM DNA polymerase iota UBM2, 1-2 mM [U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 4-8 mM DNA polymerase iota UBM2, 1-2 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.7 mM DNA polymerase iota UBM2, 6.8 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2KWV Solution Structure of UBM1 of murine Polymerase iota in Complex with Ubiquitin Deposited 2010-04-20	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) 0.189；Pressure ambient NMR sample composition 1-2 mM [U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1-2 mM [U-95% 13C; U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.0 mM DNA polymerase iota UBM1, 4 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2L0F Solution NMR structure of human polymerase iota UBM2 (P692A mutant) in complex with ubiquitin Deposited 2010-07-01	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa）	Mutation：P692A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.18；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] UBM2, 3 mM ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 5 mM UBM2, 1.5 mM [U-100% 13C; U-100% 15N] ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] UBM2, 3 mM ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 100% D2O \| 100% D2O NMR sample composition 5 mM UBM2, 1.5 mM [U-100% 13C; U-100% 15N] ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 100% D2O \| 100% D2O	Resolution not provided
2L0T Solution structure of the complex of ubiquitin and the VHS domain of Stam2 Deposited 2010-07-15	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；288 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 250 uM [U-99% 15N] Ubiquitin protein, 250 uM [U-99% 15N] VHS domain of Stam2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2NR2 The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteins Deposited 2006-11-01	Different mutation/modification 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2O6V Crystal structure and solution NMR studies of Lys48-linked tetraubiquitin at neutral pH Deposited 2006-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–76（76 aa） Chain B 1–76（76 aa） Chain C 1–76（76 aa） Chain D 1–76（76 aa）	Mutation：K63R Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；2M ammonium sulfate, 4% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.20 Å R-free 0.262
2O6V Crystal structure and solution NMR studies of Lys48-linked tetraubiquitin at neutral pH Deposited 2006-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–76（76 aa） Chain F 1–76（76 aa） Chain G 1–76（76 aa） Chain H 1–76（76 aa）	Mutation：K63R Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；2M ammonium sulfate, 4% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.20 Å R-free 0.262
2O6V Crystal structure and solution NMR studies of Lys48-linked tetraubiquitin at neutral pH Deposited 2006-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–76（76 aa） Chain B 1–76（76 aa） Chain C 1–76（76 aa） Chain D 1–76（76 aa）	Mutation：K63R Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；2M ammonium sulfate, 4% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.20 Å R-free 0.262
2OJR Structure of ubiquitin solved by SAD using the Lanthanide-Binding Tag Deposited 2007-01-13	Different 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 1–76（76 aa）	Not recorded	TB TERBIUM(III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；298 K；0.1M HEPES pH 7.5, 3.7 M NaCl, 33% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50	Resolution 2.60 Å R-free 0.254
2PE9 NMR Based Structure of the Open Conformation of LYS48-Linked Di-UBiquitin Using Experimental Global Rotational Diffusion Tensor from NMR Relaxation Measurements Deposited 2007-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM；Pressure AMBIENT NMR sample composition DI-UBIQUITIN, 90% WATER/10% D20	Resolution not provided
2PEA NMR Based Structure of the Closed Conformation of LYS48-Linked Di-Ubiquitin Using Experimental Global Rotational Diffusion Tensor from NMR Relaxation Measurements Deposited 2007-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM；Pressure AMBIENT NMR sample composition DI-UBIQUITIN, 90% WATER/10% D20	Resolution not provided
2W9N crystal structure of linear di-ubiquitin Deposited 2009-01-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；22% PEG 3350 AND 200 MM ZNOAC, pH 7	Resolution 2.25 Å R-free 0.276
2WDT Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME Deposited 2009-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–75（75 aa） Fragment：RESIDUES 1-75	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；100 MM BIS-TRIS PH 5.5, 200 MM NACL, 25 % PEG 3350	Resolution 2.30 Å R-free 0.235
2WDT Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME Deposited 2009-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–75（75 aa） Fragment：RESIDUES 1-75	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；100 MM BIS-TRIS PH 5.5, 200 MM NACL, 25 % PEG 3350	Resolution 2.30 Å R-free 0.235
2XEW Crystal structure of K11-linked diubiquitin Deposited 2010-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–76（76 aa） Chain B 1–76（76 aa） Chain C 1–76（76 aa） Chain D 1–76（76 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.5；3M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE PH3.5	Resolution 2.20 Å R-free 0.252
2XEW Crystal structure of K11-linked diubiquitin Deposited 2010-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–76（76 aa） Chain F 1–76（76 aa） Chain G 1–76（76 aa） Chain H 1–76（76 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3 FLC CITRATE ANION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.5；3M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE PH3.5	Resolution 2.20 Å R-free 0.252
2XEW Crystal structure of K11-linked diubiquitin Deposited 2010-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain I 1–76（76 aa） Chain J 1–76（76 aa） Chain K 1–76（76 aa） Chain L 1–76（76 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.5；3M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE PH3.5	Resolution 2.20 Å R-free 0.252
2XK5 Crystal structure of K6-linked diubiquitin Deposited 2010-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；19-20 % PEG 3350, 0.2 M ZINC ACETATE, pH 7	Resolution 3.00 Å R-free 0.248
2Z59 Complex Structures of Mouse Rpn13 (22-130aa) and ubiquitin Deposited 2007-07-01	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Pressure ambient NMR sample composition 0.6mM MmRpn13 U-15N, 13C; U-70% 2H; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6mM MmRpn13 U-15N; U-50% 2H; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6mM MmRpn13 U-15N, 13C; U-70% 2H; 0.6mM ubiquitin; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.4mM MmRpn13 U-15N; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.4mM ubiquitin U-15N; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.4mM MmRpn13 U-13C; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 100% D2O \| 100% D2O	Resolution not provided
2ZCB Crystal Structure of ubiquitin P37A/P38A Deposited 2007-11-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–76（76 aa）	Mutation：P37A, P38A	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；293 K；0.2M Zinc Acetate dehydrate, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.224
2ZCB Crystal Structure of ubiquitin P37A/P38A Deposited 2007-11-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–76（76 aa）	Mutation：P37A, P38A	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；293 K；0.2M Zinc Acetate dehydrate, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.224
2ZCB Crystal Structure of ubiquitin P37A/P38A Deposited 2007-11-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–76（76 aa）	Mutation：P37A, P38A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；293 K；0.2M Zinc Acetate dehydrate, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.224
2ZCB Crystal Structure of ubiquitin P37A/P38A Deposited 2007-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa） Chain C 1–76（76 aa）	Mutation：P37A, P38A Mutation：P37A, P38A Mutation：P37A, P38A	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；293 K；0.2M Zinc Acetate dehydrate, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.224
3A33 UbcH5b~Ubiquitin Conjugate Deposited 2009-06-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–76（76 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；2.0M NaCl, 0.1M Potassium acetate, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.280
3BY4 Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin Deposited 2008-01-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–75（75 aa）	Not recorded	3CN 3-AMINOPROPANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；Bis-Tris, Magnesium Chloride, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.55 Å R-free 0.211
3C0R Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin Deposited 2008-01-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–75（75 aa）	Not recorded	3CN 3-AMINOPROPANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 6.5；277 K；MES, ammonium acetate, PEG3350, pH 6.5, hanging drop, temperature 277K	Resolution 2.31 Å R-free 0.243
3C0R Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin Deposited 2008-01-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–75（75 aa）	Not recorded	3CN 3-AMINOPROPANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 6.5；277 K；MES, ammonium acetate, PEG3350, pH 6.5, hanging drop, temperature 277K	Resolution 2.31 Å R-free 0.243
3DVG Crystal structure of K63-specific fab Apu.3A8 bound to K63-linked di-ubiquitin Deposited 2008-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain X 1–76（76 aa） Chain Y 1–76（76 aa）	Mutation：D77 Mutation：K63R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；291 K；protein: 17.0 mg/mL in 20 mM Tris-HCl pH 7.3, 150 mM NaCl well solution: 0.1M Tris-HCl pH 8.0, 1.6M LiS04 , VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.60 Å R-free 0.261
3DVN Crystal structure of K63-specific fab Apu2.16 bound to K63-linked di-ubiquitin Deposited 2008-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain X 1–76（76 aa） Chain Y 1–76（76 aa）	Mutation：D77 Mutation：K63R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；291 K；protein: 12.7 mg/mL in 10 mM Tris-HCl pH 8.0, 75 mM NaCl well: 0.2M Na Cl, 0.1 M Tris pH 8.2, 0.1 M citrate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.70 Å R-free 0.268
3DVN Crystal structure of K63-specific fab Apu2.16 bound to K63-linked di-ubiquitin Deposited 2008-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain U 1–76（76 aa） Chain V 1–76（76 aa）	Mutation：D77 Mutation：K63R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；291 K；protein: 12.7 mg/mL in 10 mM Tris-HCl pH 8.0, 75 mM NaCl well: 0.2M Na Cl, 0.1 M Tris pH 8.2, 0.1 M citrate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.70 Å R-free 0.268
3EEC X-ray structure of human ubiquitin Cd(II) adduct Deposited 2008-09-04	Different 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 1–76（76 aa）	Not recorded	CD CADMIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 200mM cadmium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.300
3EEC X-ray structure of human ubiquitin Cd(II) adduct Deposited 2008-09-04	Different 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 1–76（76 aa）	Not recorded	CD CADMIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 200mM cadmium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.300
3EEC X-ray structure of human ubiquitin Cd(II) adduct Deposited 2008-09-04	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa）	Not recorded	CD CADMIUM ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 200mM cadmium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.300
3EEC X-ray structure of human ubiquitin Cd(II) adduct Deposited 2008-09-04	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 1–76（76 aa）	Not recorded	CD CADMIUM ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 200mM cadmium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.300
3EFU X-ray structure of human ubiquitin-Hg(II) adduct Deposited 2008-09-10	Different 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 1–76（76 aa）	Not recorded	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% PEG 1450, 50mM HEPES, 2.92mM mercurium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.84 Å R-free 0.293
3EHV X-ray structure of human ubiquitin Zn(II) adduct Deposited 2008-09-15	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 25mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.81 Å R-free 0.271
3EHV X-ray structure of human ubiquitin Zn(II) adduct Deposited 2008-09-15	Different 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 25mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.81 Å R-free 0.271
3EHV X-ray structure of human ubiquitin Zn(II) adduct Deposited 2008-09-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 25mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.81 Å R-free 0.271
3H7P Crystal structure of K63-linked di-ubiquitin Deposited 2009-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Mutation：K63R	CD CADMIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH UNDER OIL；pH 5.2；291 K；0.2 M Cadmium sulfate, 5% w/v PEG 8000 and 0.1 M Imidazole-Cl pH 6.5, Al's oil, MICROBATCH UNDER OIL, temperature 291K	Resolution 1.90 Å R-free 0.236
3H7S Crystal structures of K63-linked di- and tri-ubiquitin reveal a highly extended chain architecture Deposited 2009-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH UNDER OIL；pH 5.2；291 K；0.2 M Zinc acetate, 6% w/v PEG 8000 and 0.1 M Imidazole-Cl pH 6.5, Al's oil, MICROBATCH UNDER OIL, temperature 291K	Resolution 2.30 Å R-free 0.253
3H7S Crystal structures of K63-linked di- and tri-ubiquitin reveal a highly extended chain architecture Deposited 2009-04-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–76（76 aa）	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH UNDER OIL；pH 5.2；291 K；0.2 M Zinc acetate, 6% w/v PEG 8000 and 0.1 M Imidazole-Cl pH 6.5, Al's oil, MICROBATCH UNDER OIL, temperature 291K	Resolution 2.30 Å R-free 0.253
3H7S Crystal structures of K63-linked di- and tri-ubiquitin reveal a highly extended chain architecture Deposited 2009-04-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH UNDER OIL；pH 5.2；291 K；0.2 M Zinc acetate, 6% w/v PEG 8000 and 0.1 M Imidazole-Cl pH 6.5, Al's oil, MICROBATCH UNDER OIL, temperature 291K	Resolution 2.30 Å R-free 0.253
3HM3 The Structure and conformation of Lys-63 linked tetra-ubiquitin Deposited 2009-05-28	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 1–76（76 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M Sodium acetate, 5% PEG 3000, 50 mM Zinc acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.96 Å R-free 0.236
3HM3 The Structure and conformation of Lys-63 linked tetra-ubiquitin Deposited 2009-05-28	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M Sodium acetate, 5% PEG 3000, 50 mM Zinc acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.96 Å R-free 0.236
3HM3 The Structure and conformation of Lys-63 linked tetra-ubiquitin Deposited 2009-05-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–76（76 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M Sodium acetate, 5% PEG 3000, 50 mM Zinc acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.96 Å R-free 0.236
3HM3 The Structure and conformation of Lys-63 linked tetra-ubiquitin Deposited 2009-05-28	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M Sodium acetate, 5% PEG 3000, 50 mM Zinc acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.96 Å R-free 0.236
3I3T Crystal structure of covalent ubiquitin-USP21 complex Deposited 2009-06-30	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 1–75（75 aa）	Not recorded	ZN ZINC ION × 1 NEH ETHANAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；13% PEG 3350, 0.1 M Bis-Tris, 0.1 M Ammonium sulfate, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.59 Å R-free 0.218
3I3T Crystal structure of covalent ubiquitin-USP21 complex Deposited 2009-06-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–75（75 aa）	Not recorded	ZN ZINC ION × 1 NEH ETHANAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；13% PEG 3350, 0.1 M Bis-Tris, 0.1 M Ammonium sulfate, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.59 Å R-free 0.218
3I3T Crystal structure of covalent ubiquitin-USP21 complex Deposited 2009-06-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–75（75 aa）	Not recorded	ZN ZINC ION × 1 NEH ETHANAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；13% PEG 3350, 0.1 M Bis-Tris, 0.1 M Ammonium sulfate, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.59 Å R-free 0.218
3I3T Crystal structure of covalent ubiquitin-USP21 complex Deposited 2009-06-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–75（75 aa）	Not recorded	ZN ZINC ION × 1 NEH ETHANAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；13% PEG 3350, 0.1 M Bis-Tris, 0.1 M Ammonium sulfate, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.59 Å R-free 0.218
3IFW Crystal structure of the S18Y variant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester. Deposited 2009-07-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–75（75 aa）	Not recorded	GVE METHYL 4-AMINOBUTANOATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；2.4 M ammonium sulfate, 0.1M BICINE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.40 Å R-free 0.256
3IHP Covalent Ubiquitin-Usp5 Complex Deposited 2009-07-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–75（75 aa）	Not recorded	ZN ZINC ION × 1 NEH ETHANAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；298 K；Crystals of the covalent ubiquitin complex of Usp5 were grown at 298 K using the hanging drop method by mixing equal volumes of protein solution (25 mg/ml) and Crystallization Buffer (1.45 M ammonium sulfate, 0.1 M bis-Tris, pH 6.5, 0.2 M sodium acetate, 5% ethyleneglycol and 1 mM dithiothreitol). The crystals were cryoprotected by immersion in Paratone N in paraffin oil 30% (v/v) and placed in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.80 Å R-free 0.276
3IHP Covalent Ubiquitin-Usp5 Complex Deposited 2009-07-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–75（75 aa）	Not recorded	ZN ZINC ION × 1 NEH ETHANAMINE × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；298 K；Crystals of the covalent ubiquitin complex of Usp5 were grown at 298 K using the hanging drop method by mixing equal volumes of protein solution (25 mg/ml) and Crystallization Buffer (1.45 M ammonium sulfate, 0.1 M bis-Tris, pH 6.5, 0.2 M sodium acetate, 5% ethyleneglycol and 1 mM dithiothreitol). The crystals were cryoprotected by immersion in Paratone N in paraffin oil 30% (v/v) and placed in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.80 Å R-free 0.276
3JSV Crystal structure of mouse NEMO CoZi in complex with Lys63-linked di-ubiquitin Deposited 2009-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Mutation：K63R Mutation：X77D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.294
3JVZ E2~Ubiquitin-HECT Deposited 2009-09-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain X 1–76（76 aa）	Mutation：Ubiquitin G76 ester linked to UbcH5B S85	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, pH 5.1-5.2, 2.4-2.5 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.30 Å R-free 0.267
3JVZ E2~Ubiquitin-HECT Deposited 2009-09-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Y 1–76（76 aa）	Mutation：Ubiquitin G76 ester linked to UbcH5B S85	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, pH 5.1-5.2, 2.4-2.5 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.30 Å R-free 0.267
3JW0 E2~Ubiquitin-HECT Deposited 2009-09-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain X 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, 2.4M sodium chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.10 Å R-free 0.287
3JW0 E2~Ubiquitin-HECT Deposited 2009-09-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Y 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, 2.4M sodium chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.10 Å R-free 0.287
3K9P The crystal structure of E2-25K and ubiquitin complex Deposited 2009-10-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100mM HEPES-NaOH (pH 7.5), 25% (w/v) PEG 3350, 50mM Sodium Fluoride, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.296
3K9P The crystal structure of E2-25K and ubiquitin complex Deposited 2009-10-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100mM HEPES-NaOH (pH 7.5), 25% (w/v) PEG 3350, 50mM Sodium Fluoride, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.296
3KVF Crystal structure of the I93M mutant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester Deposited 2009-11-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–75（75 aa）	Not recorded	GVE METHYL 4-AMINOBUTANOATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.1M BICINE, 2.4M Ammonium Sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.284
3KW5 Crystal structure of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester Deposited 2009-11-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–75（75 aa）	Not recorded	GVE METHYL 4-AMINOBUTANOATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.1M BICINE, 2.4M Ammonium Sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.83 Å R-free 0.286
3LDZ Crystal structure of human STAM1 VHS domain in complex with ubiquitin Deposited 2010-01-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–73（73 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2M Na thiocyanate, 20% PEG3350, 0.1M imidazole pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.234
3LDZ Crystal structure of human STAM1 VHS domain in complex with ubiquitin Deposited 2010-01-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–73（73 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2M Na thiocyanate, 20% PEG3350, 0.1M imidazole pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.234
3LDZ Crystal structure of human STAM1 VHS domain in complex with ubiquitin Deposited 2010-01-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–73（73 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2M Na thiocyanate, 20% PEG3350, 0.1M imidazole pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.234
3MHS Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde Deposited 2010-04-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Hepes pH 6.5, 10% (w/v) PEG 8000, 20% (v/v) Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.89 Å R-free 0.208
3MTN Usp21 in complex with a ubiquitin-based, USP21-specific inhibitor Deposited 2010-04-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 1 CL CHLORIDE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；291 K；11% PEG 4000, 0.1 M SODIUM CITRATE, 0.1 M AMMONIUM ACETATE, 5 MM TCEP, PH 5.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K	Resolution 2.70 Å R-free 0.273
3MTN Usp21 in complex with a ubiquitin-based, USP21-specific inhibitor Deposited 2010-04-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–76（76 aa）	Not recorded	ZN ZINC ION × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；291 K；11% PEG 4000, 0.1 M SODIUM CITRATE, 0.1 M AMMONIUM ACETATE, 5 MM TCEP, PH 5.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K	Resolution 2.70 Å R-free 0.273
3N30 Crystal Structure of cubic Zn3-hUb (human ubiquitin) adduct Deposited 2010-05-19	Different 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 1–76（76 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25 mg/ml milliQ water protein solution, 25% (w/v) PEG 1450, 50 mM HEPES, 200 mM Zn acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.318
3N30 Crystal Structure of cubic Zn3-hUb (human ubiquitin) adduct Deposited 2010-05-19	Different 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 1–76（76 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25 mg/ml milliQ water protein solution, 25% (w/v) PEG 1450, 50 mM HEPES, 200 mM Zn acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.318
3N32 The crystal structure of human Ubiquitin adduct with Zeise's salt Deposited 2010-05-19	Different 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 1–76（76 aa）	Not recorded	PT PLATINUM (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；30% PEG 1450, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.79 Å R-free 0.258
3NHE High Resolution Structure (1.26A) of USP2a in Complex with Ubiquitin Deposited 2010-06-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；5% PEG4000, 0.1M Hepes, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.26 Å R-free 0.189
3NOB Structure of K11-linked di-ubiquitin Deposited 2010-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；292 K；25 mg/mL protein in 50 mM Tris 7.5 and 75 mM NaCl were grown in 0.2 M ammonium sulfate, 20% PEG3350. Seeds from this were further microseeded into 0.17 M Ammonium sulfate, 15% glycerol, 20% PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.19 Å R-free 0.281
3NOB Structure of K11-linked di-ubiquitin Deposited 2010-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–76（76 aa） Chain D 1–76（76 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；292 K；25 mg/mL protein in 50 mM Tris 7.5 and 75 mM NaCl were grown in 0.2 M ammonium sulfate, 20% PEG3350. Seeds from this were further microseeded into 0.17 M Ammonium sulfate, 15% glycerol, 20% PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.19 Å R-free 0.281
3NOB Structure of K11-linked di-ubiquitin Deposited 2010-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–76（76 aa） Chain F 1–76（76 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；292 K；25 mg/mL protein in 50 mM Tris 7.5 and 75 mM NaCl were grown in 0.2 M ammonium sulfate, 20% PEG3350. Seeds from this were further microseeded into 0.17 M Ammonium sulfate, 15% glycerol, 20% PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.19 Å R-free 0.281
3NOB Structure of K11-linked di-ubiquitin Deposited 2010-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 1–76（76 aa） Chain H 1–76（76 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；292 K；25 mg/mL protein in 50 mM Tris 7.5 and 75 mM NaCl were grown in 0.2 M ammonium sulfate, 20% PEG3350. Seeds from this were further microseeded into 0.17 M Ammonium sulfate, 15% glycerol, 20% PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.19 Å R-free 0.281
3NS8 Crystal structure of an open conformation of Lys48-linked diubiquitin at pH 7.5 Deposited 2010-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	GOL GLYCEROL × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；HEPES, PEG 8000, Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.71 Å R-free 0.237
3NS8 Crystal structure of an open conformation of Lys48-linked diubiquitin at pH 7.5 Deposited 2010-07-01	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–76（76 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；HEPES, PEG 8000, Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.71 Å R-free 0.237
3NS8 Crystal structure of an open conformation of Lys48-linked diubiquitin at pH 7.5 Deposited 2010-07-01	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–76（76 aa）	Not recorded	GOL GLYCEROL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；HEPES, PEG 8000, Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.71 Å R-free 0.237
3PHD Crystal structure of human HDAC6 in complex with ubiquitin Deposited 2010-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–76（76 aa） Chain F 1–76（76 aa） Chain G 1–76（76 aa） Chain H 1–76（76 aa）	Not recorded	ZN ZINC ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；297 K；15% PEG 3350, 0.1M Ammonium Sulphate, 0.1M Bis-Tris, pH 5.6, temperature 297K	Resolution 3.00 Å R-free 0.265

83 other PDB entries and 138 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBIQ_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–79； UniProt 1–76

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3n3k
Deposition date deposition_date	2010-05-20
Structure title title	The catalytic domain of USP8 in complex with a USP8 specific inhibitor
Keywords keywords	;HYDROLASE, PROTEASE, THIOL PROTEASE, UBL CONJUGATION PATHWAY, DEUBIQUITINATING ENZYME, DUB, ZINC RIBBON, INHIBITOR, UBIQUITIN, Isopeptide bond, Nucleus, Phosphoprotein, Structural Genomics, Structural Genomics Consortium, SGC ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	23.03 Å
Radius of gyration Rg (electron density) rg_electron	21.53 Å
Forward intensity I(0) i0	40428200.00
Molecular weight molecular_weight	49236.0 kDa
Excluded volume excluded_volume	61645 Å³
Envelope volume envelope_volume	72991 Å³
Hydration-shell volume shell_volume	27456 Å³
Envelope diameter envelope_diameter	71.9 Å
Shell Rg shell_rg	29.08 Å
Envelope Rg envelope_rg	21.62 Å
Shape Rg shape_rg	21.50 Å
Total Rg total_rg	22.51 Å
Total atoms total_atoms	3464
Residues n_residues	429
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	71.8 Å
Rg (real space) rg_real	22.88 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	4.0430e+07
I(0) uncertainty (real space) i0_real_error	5.6800e+05
Rg (reciprocal space) rg_reciprocal	22.92 Å
I(0) (reciprocal space) i0_reciprocal	40430000.0000
Solution quality estimate total_estimate	0.8968
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.8 Å
Skewness Skewness skewness	0.149
Kurtosis Kurtosis kurtosis	-0.373
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6567000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.990

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase 8
Molecular weight formula_weight	45418.5 kDa
EC 编号 ec_number	3.1.2.15
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3601

MGSSHHHHHHSSGLVPRGSPTVTPTVNRENKPTCYPKAEISRLSASQIRNLNPVFGGSGPALTGLRNLGNTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIMKALWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNRKRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFMYLSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQKLQTSVDFPLENLDLSQYVIGPKNNLKKYNLFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDDHEVSDISVSSVKSSAAYILFYTSLG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin
Molecular weight formula_weight	9267.6 kDa
Mutation mutation	Q2R, F4V, T9M, K11R, T14I, Q62H, K63N, E64H, T66A, H68Y, V70L, R72K
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSHMRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLLKLRGGGGGGSG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	112

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3n3ka_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.9 — Ubiquitin carboxyl-terminal hydrolase, UCH

Domain ID domain_id	d3n3kb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (2 domains)

Domain ID domain_id	3n3kA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	3n3kB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (2)

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Unit-cell length a length_a	69.983 Å
Unit-cell length b length_b	69.983 Å
Unit-cell length c length_c	181.549 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	34.990 Å
R factor r_factor	0.1808
R_work r_work	0.1778
R_free r_free	0.2424

fit	/app/data/saxs_computation/n3/3n3k/3n3k.fit
pddf	/app/data/pr_computation/n3/3n3k/3n3k.pr.out
profile	/app/data/saxs_computation/n3/3n3k/3n3k.dat

The catalytic domain of USP8 in complex with a USP8 specific inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin carboxyl-terminal hydrolase 8

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)