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2khw

Solution Structure of the human Polymerase iota UBM2-Ubiquitin Complex

Method: SOLUTION NMR Dmax: 46.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Immunoglobulin G-binding protein G, DNA polymerase iota

Streptococcus sp., Homo sapiens

UniProt P19909

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 304–357 Fragment：UNP residues 304-357, 676-715 Ubiquitin × 1 （P62988） 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

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 2KHW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10DV Room Temperature X-Ray Structure of SARS CoV-2 Main Protease Intermediate Precursor with Ensitrelvir (ESV) Deposited 2026-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 304–357（54 aa）
Chain B 304–357（54 aa）
Mutation：C145A Mutation：C145A 7YY 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；18-21% PEG3350, 0.1 M Bis-Tris, pH 6.5 or 7.0
Resolution 2.05 Å R-free 0.234
1FCC CRYSTAL STRUCTURE OF THE C2 FRAGMENT OF STREPTOCOCCAL PROTEIN G IN COMPLEX WITH THE FC DOMAIN OF HUMAN IGG Deposited 1995-01-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 372–427（56 aa）
Chain D 372–427（56 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.20 Å R-free 0.357
1FCL DELTA1.5: A COMPUTATIONALLY DESIGNED CORE VARIANT OF THE B1 DOMAIN OF STREPTOCOCCAL PROTEIN G Deposited 2000-07-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 302–357（56 aa） Fragment：GB1_DELTA1.5
Mutation：Y3F, L7I, F30L, A34I, V39I, F52W No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate；Pressure Atmospheric
NMR sample composition 1 mM unlabeled protein in 50 mM sodium phosphate, pH 6.0 | either D2O or 90:10 H2O:D2O
Resolution not provided
1FD6 DELTA0: A COMPUTATIONALLY DESIGNED CORE VARIANT OF THE B1 DOMAIN OF STREPTOCOCCAL PROTEIN G Deposited 2000-07-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 302–357（56 aa） Fragment：GB1_DELT0
Mutation：Y3F, L7I, V39I No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate；Pressure ambient
NMR sample composition 3 mM protein in 50 mM sodium phosphate, pH 6.0 | either D2O or 90:10 H2O:D2O
Resolution not provided
1GB4 HYPERTHERMOPHILIC VARIANT OF THE B1 DOMAIN FROM STREPTOCOCCAL PROTEIN G, NMR, 47 STRUCTURES Deposited 1998-01-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 372–427（56 aa） Fragment：B1 DOMAIN
Mutation：V1M, Y4F, V7I, T17I, T19I, T26E, V30I, V40I No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5；308 K；Ionic strength (raw mmCIF value) 50mM；Pressure ATMOSPHERIC
NMR sample composition H2O/D2O
Resolution not provided
1GJS Solution structure of the Albumin binding domain of Streptococcal Protein G Deposited 2001-08-02 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 254–299（46 aa） Fragment：ALBUMIN-BINDING DOMAIN RESIDUES 254-299
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；300 K；Pressure 1
Resolution not provided
1GJT Solution structure of the Albumin binding domain of Streptococcal Protein G Deposited 2001-08-02 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 254–299（46 aa） Fragment：ALBUMIN-BINDING DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；300 K；Pressure 1
Resolution not provided
1IBX NMR STRUCTURE OF DFF40 AND DFF45 N-TERMINAL DOMAIN COMPLEX Deposited 2001-03-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 302–357（56 aa） Fragment：B1 DOMAIN OF PROTEIN G FUSED WITH N-TERMINAL DOMAIN (CIDE DOMAIN) OF DFF45
Mutation：T(-43)Q No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；296 K；Ionic strength (raw mmCIF value) 50 mM NaCl；Pressure ambient
NMR sample composition 0.6 mM DFF40/DFF45 NTD complex 90% deuterated, U-15N/13C labeled DFF40 non-labeled DFF45 | 20 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
NMR sample composition 0.6 mM DFF40/DFF45 NTD complex U-13C labeled DFF45 non-labeled DFF40 | 20 mM Phosphate buffer 5 mM DTT, 50 mM NaCl D2O
NMR sample composition 0.6 mM DFF40/DFF45 NTD complex 90% deuterated, U-15N/13C labeled DFF45 non-labeled DFF40 | 20 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
NMR sample composition 0.6 mM DFF40/DFF45 NTD complex U-15N labeled DFF40 non-labeled DFF45 | 20 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
NMR sample composition 0.6 mM DFF40/DFF45 NTD complex U-15N labeled DFF45 non-labeled DFF40 | 20 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
NMR sample composition 0.6 mM DFF40/DFF45 NTD complex perdeuterated, U-15N labeled DFF40 non-labeled DFF45 | 20 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
NMR sample composition 0.6 mM DFF40/DFF45 NTD complex perdeuterated, U-15N labeled DFF45 non-labeled DFF40 | 20 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
NMR sample composition 0.6 mM DFF40/DFF45 NTD complex 10% 13C labeled DFF40 non-labeled DFF45 | 20 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
NMR sample composition 0.6 mM DFF40/DFF45 NTD complex 10% 13C labeled DFF45 non-labeled DFF40 | 20 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
NMR sample composition 0.6 mM DFF40/DFF45 NTD complex U-13C labeled DFF40 non-labeled DFF45 | 20 mM Phosphate buffer 5 mM DTT, 50 mM NaCl D2O
Resolution not provided
1P7E GB3 solution structure obtained by refinement of X-ray structure with dipolar couplings Deposited 2003-05-01 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 444–497（54 aa） Fragment：THIRD IGG-BINDING DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 25 mM NaH2PO4/Na2HPO4, 0.2 mg/mL NaN3, 1.5 mM GB3 protein and aligning media
Resolution not provided
1P7F GB3 solution structure obtained by refinement of X-ray structure with dipolar couplings Deposited 2003-05-01 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 444–497（54 aa） Fragment：THIRD IGG-BINDING DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 25 mM NaH2PO4/Na2HPO4, 0.2 mg/mL NaN3, 1.5 mM GB3 protein and aligning media
Resolution not provided
1ZXH G311 mutant protein Deposited 2005-06-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 443–497（55 aa）
Mutation：yes No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；275 K；Ionic strength (raw mmCIF value) 0.1M；Pressure ambient
NMR sample composition G311 mutant protein, 0.1 M KPi, pH7.0, ~0.6 M GuHCl. | 0.1 M KPi, pH7.0, ~0.6 M GuHCl.
Resolution not provided
2GI9 Backbone Conformational Constraints in a Microcrystalline U-15N-Labeled Protein by 3D Dipolar-Shift Solid-State NMR Spectroscopy Deposited 2006-03-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 303–357（55 aa）
Mutation：T2Q No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；5mM Acetate 3.8, 150mM NaCl, 50% MPD and 20% IPA, pH 4.5
Resolution 1.14 Å R-free 0.181
2I2Y Solution structure of the RRM of SRp20 bound to the RNA CAUC Deposited 2006-08-17 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: dimeric
Chain A 304–357（54 aa） Fragment：RRM domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.4；315 K；Pressure ambient
NMR sample composition 1mM SRp20 13C-15N labelled + 1 mM CAUC natural abundance in 50 mM sodium dihydrogenophosphate, pH 6.4, 1mM DTT; | 10% D2O,90% H2O or 100% D2O
NMR sample composition 1mM SRp20 15N labelled + 1 mM CAUC natural abundance in 1mM SRp20 15N labelled in 50 mM sodium dihydrogenophosphate, pH 6.4, 1mM DTT | 10% D2O, 90% H2O or 100% D2O
NMR sample composition 1mM SRp20 15N labelled + 1 mM CAUC with 13C labelled riboses and natural abundance bases in 50 mM sodium dihydrogenophosphate, pH 6.4, 1mM DTT; | 10% D2O, 90% H2O or 100% D2O
NMR sample composition 1mM SRp20 15N labelled + 1 mM CAUC with A2 and U3 riboses 13C labelled and natural abundance of other riboses and all bases in 50 mM sodium dihydrogenophosphate, pH 6.4, 1mM DTT; | 10% D2O, 90% H2O or 100% D2O
NMR sample composition 1mM SRp20 15N labelled + 1 mM CAUC with C1 and C4 riboses 13C labelled and natural abundance of other riboses and all bases, in 50 mM sodium dihydrogenophosphate, pH 6.4, 1mM DTT; | 10% D2O, 90% H2O or 100% D2O
Resolution not provided
2I38 Solution structure of the RRM of SRp20 Deposited 2006-08-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 304–357（54 aa） Fragment：RRM domain
Mutation：E129D No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；315 K；Pressure ambient
NMR sample composition 1mM SRp20 13C-15N labelled in 50 mM sodium dihydrogenophosphate, pH 5.8, 1mM DTT; | 10% D2O, 90% H2O or 100% D2O
NMR sample composition 1mM SRp20 15N labelled in 50 mM sodium dihydrogenophosphate, pH 5.8, 1mM DTT; | 10% D2O, 90% H2O or 100% D2O
Resolution not provided
2IGG DETERMINATION OF THE SOLUTION STRUCTURES OF DOMAINS II AND III OF PROTEIN G FROM STREPTOCOCCUS BY 1H NMR Deposited 1992-08-26 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 367–430（64 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2JSV Dipole tensor-based refinement for atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR spectroscopy Deposited 2007-07-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 303–357（55 aa） Fragment：2-1 repeat
Mutation：T2Q No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions pH 5.5；281 K；Pressure ambient
NMR sample composition 14 mg/mL [U-99% 13C; U-99% 15N] protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2O | H2O
NMR sample composition 14 mg/mL [U-99% 15N] protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2O | H2O
NMR sample composition 14 mg/mL [U-100% 13C; U-100% 15N] protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2O | H2O
NMR sample composition 14 mg/mL (1,3) 13C glycerol, U15N protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2O | H2O
NMR sample composition 14 mg/mL 2 13C glycerol, Uniform 15N protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2O | H2O
Resolution not provided
2KHU Solution Structure of the Ubiquitin-Binding Motif of Human Polymerase Iota Deposited 2009-04-11 Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 304–357（54 aa） Fragment：UNP residues 304-357, 676-715
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；25 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition 1-4 mM [U-100% 13C; U-100% 15N] D2O-1, 1-4 mM [U-100% 13C; U-100% 15N] H2O-2, 100% D2O | 100% D2O
Resolution not provided
2KN4 The structure of the RRM domain of SC35 Deposited 2009-08-14 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 304–357（54 aa） Fragment：UNP residues 304-357 from P19909, UNP residues 9-101 from Q01130
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；305 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] SC35-1, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] SC35-2, 100% D2O | 100% D2O
NMR sample composition 0.5 mM [U-100% 15N] SC35-3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM SC35-4, 100% D2O | 100% D2O
Resolution not provided
2KQ4 Atomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy Deposited 2009-10-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 303–357（55 aa） Fragment：UNP residues 303 to 357
Mutation：T2Q No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions Pressure ambient
NMR sample composition 30 mg 1,3-13C glycerol, U 15N entity-1, 50 v/v MPTG-2, solid | solid
NMR sample composition 30 mg 2-13C glycerol, U 15N entity-3, 50 v/v MPTG-4, solid | solid
Resolution not provided
2KWD Supramolecular Protein Structure Determination by Site-Specific Long-Range Intermolecular Solid State NMR Spectroscopy Deposited 2010-04-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 304–357（54 aa）
Chain B 304–357（54 aa）
Chain C 304–357（54 aa）
Chain D 304–357（54 aa）
Chain E 304–357（54 aa）
Mutation：T2Q Mutation：T2Q Mutation：T2Q Mutation：T2Q Mutation：T2Q No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions 273 K；Pressure 1
NMR sample composition 20 mg [U-1,3-13C-glycerol; U-100% 15N] GB1-1, solid | solid
NMR sample composition 50 % [U-1,3-13C-glycerol] GB1-2, 50 % [U-99% 15N] GB1-3, solid | solid
NMR sample composition 20 mg [U-2-13C-glycerol; U-100% 15N] GB1-4, solid | solid
Resolution not provided
2LUM Three-State Ensemble obtained from eNOEs of the Third Immunoglobulin Binding Domain of Protein G (GB3) Deposited 2012-06-18 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 444–497（54 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 4 mM [U-95% 13C; U-95% 15N] Third Immunoglobulin G-binding protein G, 50 mM potassium phosphate, 0.5 mg/mL sodium azide, 50 mM sodium chloride, 97% H2O/3% D2O | 97% H2O/3% D2O
Resolution not provided
2N9K 1H, 13C, and 15N Chemical Shift Assignments for in vitro GB1 Deposited 2015-11-26 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 303–357（55 aa） Fragment：UNP residues 303-357
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；295 K；Ionic strength (raw mmCIF value) 0.31；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Protein G B1-1, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2N9L 1H, 13C, and 15N Chemical Shift Assignments for in-cell GB1 Deposited 2015-11-30 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 303–357（55 aa） Fragment：UNP residues 303-357
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；295 K；Ionic strength (raw mmCIF value) 0.31；Pressure ambient
NMR sample composition 250 uM [U-100% 13C; U-100% 15N] Protein G B1-1, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2OED GB3 solution structure obtained by refinement of X-ray structure with dipolar couplings Deposited 2006-12-29 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 444–497（54 aa） Fragment：THIRD IGG-BINDING DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 25 MM NAH2PO4/NA2HPO4, 0.2 MG/ML NAN3, 1.5 MM GB3 PROTEIN AND ALIGNING MEDIA, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2ON8 Gbeta1 stabilization by in vitro evolution and computational design Deposited 2007-01-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 373–427（55 aa）
Mutation：T1M, T2Q, Y3F, V6I, T16I, T18L, T25E, V29K, V39I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；50mM Na acetate, pH 5.0, 17 mg/ml protein mixed with equal volume of 2.3M ammonium suphate, 0.1M sodium acetate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 1.35 Å R-free 0.195
2ONQ Gbeta1 stabilization by in vitro evolution and computational design Deposited 2007-01-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 373–427（55 aa） Fragment：residues 373-427
Mutation：T2Q, Y3F, L7I, T16I, T18I, T25E, V29F, V39I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；50mM sodium acetate, 20mg/ml protein solution mixed in equal volume of crystallization buffer containing 33% PEG monomethylether, 0.1M calcium chloride, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 1.70 Å R-free 0.229
2PLP Ultra high resolution backbone conformation of protein GB1 from residual dipolar couplings alone Deposited 2007-04-20 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 303–356（54 aa） Fragment：First Immunoglobin binding domain (GB1)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.6；300 K；Ionic strength (raw mmCIF value) 50mM salt；Pressure ambient
NMR sample composition perdeuterated (triple labelled 15N, 13C, 2D) | Partially aligned in bacteriophage and lyotrophic alcohol medium.
Resolution not provided
2QMT Crystal Polymorphism of Protein GB1 Examined by Solid-state NMR and X-ray Diffraction Deposited 2007-07-16 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 303–357（55 aa） Fragment：immunoglobulin beta 1 binding domain (residues 303-357)
Mutation：T2Q PO4 PHOSPHATE ION × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 IPA ISOPROPYL ALCOHOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；50 mM NaCl, 50% MPD, 6% IPA, 25 mM Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.05 Å R-free 0.207
3FIL Structural and energetic determinants for hyperstable variants of GB1 obtained from in-vitro evolution Deposited 2008-12-12 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 303–357（55 aa） Fragment：immunoglobulin binding domain, UNP residues 303-357
Chain B 303–357（55 aa） Fragment：immunoglobulin binding domain, UNP residues 303-357
Mutation：T2Q, E15V, T16L, T18I, N37L Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：T2Q, E15V, T16L, T18I, N37L CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293.15 K；protein solution: 50mM sodium acetate pH 5.6, 50mg/ml protein. reservoir solution: 25% PEG 3350, 0.1M citric acids pH 3.5. Drop 400nl protein solution & 400nl reservoir solution, 80 micro-l reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 0.88 Å R-free 0.149
3UI3 Structural and Biochemical Characterization of HP0315 from Helicobacter pylori as a VapD Protein with an Endoribonuclease Activity Deposited 2011-11-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 304–357（54 aa）
Chain B 304–357（54 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；pH 6；293 K；0.2M (NH4)2SO4, 9% PEG3350, 5-8% glycerol, 100mM 2-(N-morpholino)ethanesulfonic acid', pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.284
3V3X Nitroxide Spin Labels in Protein GB1: N8/K28 Double Mutant Deposited 2011-12-14 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 304–357（54 aa）
Chain C 304–357（54 aa）
Mutation：C8N Mutation：C8N MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 3 2PE NONAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；150 mM sodium acetate pH 4.5, 18% w/v PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.288
3V3X Nitroxide Spin Labels in Protein GB1: N8/K28 Double Mutant Deposited 2011-12-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 304–357（54 aa）
Chain D 304–357（54 aa）
Mutation：C8N Mutation：C8N MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 4 GOL GLYCEROL × 1 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；150 mM sodium acetate pH 4.5, 18% w/v PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.288
4WH4 Protein GB1 Quadruple Mutant I6H/N8H/K28H/Q32H Deposited 2014-09-19 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 304–357（54 aa）
Mutation：I6H/N8H/K28H/Q32H SO4 SULFATE ION × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1.75 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES pH 7.5
Resolution 2.20 Å R-free 0.256
4WH4 Protein GB1 Quadruple Mutant I6H/N8H/K28H/Q32H Deposited 2014-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 304–357（54 aa）
Mutation：I6H/N8H/K28H/Q32H GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1.75 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES pH 7.5
Resolution 2.20 Å R-free 0.256
5BMG Nitroxide Spin Labels in Protein GB1: E15 Mutant Deposited 2015-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 304–357（54 aa） Fragment：UNP residues 304-357
Mutation：E15C MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；0.1 M magnesium chloride, 0.1 M Tris pH 4.5, 20% w/v PEG 4000
Resolution 2.20 Å R-free 0.218
5BMG Nitroxide Spin Labels in Protein GB1: E15 Mutant Deposited 2015-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 304–357（54 aa） Fragment：UNP residues 304-357
Mutation：E15C MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；0.1 M magnesium chloride, 0.1 M Tris pH 4.5, 20% w/v PEG 4000
Resolution 2.20 Å R-free 0.218
5BMG Nitroxide Spin Labels in Protein GB1: E15 Mutant Deposited 2015-05-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 304–357（54 aa） Fragment：UNP residues 304-357
Mutation：E15C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；0.1 M magnesium chloride, 0.1 M Tris pH 4.5, 20% w/v PEG 4000
Resolution 2.20 Å R-free 0.218
5BMG Nitroxide Spin Labels in Protein GB1: E15 Mutant Deposited 2015-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 304–357（54 aa） Fragment：UNP residues 304-357
Mutation：E15C MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；0.1 M magnesium chloride, 0.1 M Tris pH 4.5, 20% w/v PEG 4000
Resolution 2.20 Å R-free 0.218
5BMG Nitroxide Spin Labels in Protein GB1: E15 Mutant Deposited 2015-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 304–357（54 aa） Fragment：UNP residues 304-357
Mutation：E15C MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；0.1 M magnesium chloride, 0.1 M Tris pH 4.5, 20% w/v PEG 4000
Resolution 2.20 Å R-free 0.218
5BMG Nitroxide Spin Labels in Protein GB1: E15 Mutant Deposited 2015-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 304–357（54 aa） Fragment：UNP residues 304-357
Mutation：E15C MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；0.1 M magnesium chloride, 0.1 M Tris pH 4.5, 20% w/v PEG 4000
Resolution 2.20 Å R-free 0.218
5BMG Nitroxide Spin Labels in Protein GB1: E15 Mutant Deposited 2015-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 304–357（54 aa） Fragment：UNP residues 304-357
Mutation：E15C MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；0.1 M magnesium chloride, 0.1 M Tris pH 4.5, 20% w/v PEG 4000
Resolution 2.20 Å R-free 0.218
5BMG Nitroxide Spin Labels in Protein GB1: E15 Mutant Deposited 2015-05-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 304–357（54 aa） Fragment：UNP residues 304-357
Mutation：E15C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；0.1 M magnesium chloride, 0.1 M Tris pH 4.5, 20% w/v PEG 4000
Resolution 2.20 Å R-free 0.218
5BMH Nitroxide Spin Labels in Protein GB1: T44 Mutant, Crystal Form B Deposited 2015-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 304–357（54 aa） Fragment：UNP residues 304-357
Mutation：T44C MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M potassium sodium tartrate, 0.2 M sodium citrate pH 6.0, 2 M ammonium sulfate
Resolution 1.60 Å R-free 0.175
5BMI Nitroxide Spin Labels in Protein GB1: T44 Mutant, Crystal Form A Deposited 2015-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 304–357（54 aa） Fragment：UNP residues 304-357
Mutation：T44C MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 1.2 M sodium citrate
Resolution 2.50 Å R-free 0.251
5HFY Backbone Modifications in the Protein GB1 Helix: beta-2-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35 Deposited 2016-01-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 302–357（56 aa） Fragment：UNP residues 302-357
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 4.6；298 K；0.2 M sodium acetate pH 4.6, 20% w/v PEG 4000
Resolution 1.95 Å R-free 0.230
5HFY Backbone Modifications in the Protein GB1 Helix: beta-2-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35 Deposited 2016-01-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 302–357（56 aa） Fragment：UNP residues 302-357
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 4.6；298 K；0.2 M sodium acetate pH 4.6, 20% w/v PEG 4000
Resolution 1.95 Å R-free 0.230
5HG2 Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-2-Asn35 Deposited 2016-01-07 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 302–357（56 aa） Fragment：UNP residues 302-357
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M sodium cacodylate pH 6.5, 0.1 M magnesium acetate, 20% w/v PEG 4000
Resolution 1.80 Å R-free 0.216
5HG2 Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-2-Asn35 Deposited 2016-01-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 302–357（56 aa） Fragment：UNP residues 302-357
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 6.5；298 K；0.1 M sodium cacodylate pH 6.5, 0.1 M magnesium acetate, 20% w/v PEG 4000
Resolution 1.80 Å R-free 0.216
5HG2 Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-2-Asn35 Deposited 2016-01-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 302–357（56 aa） Fragment：UNP residues 302-357
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M sodium cacodylate pH 6.5, 0.1 M magnesium acetate, 20% w/v PEG 4000
Resolution 1.80 Å R-free 0.216
5HG2 Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-2-Asn35 Deposited 2016-01-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 302–357（56 aa） Fragment：UNP residues 302-357
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M sodium cacodylate pH 6.5, 0.1 M magnesium acetate, 20% w/v PEG 4000
Resolution 1.80 Å R-free 0.216
5HI1 Backbone Modifications in the Protein GB1 Helix: Aib24, beta-3-Lys28, beta-3-Lys31, Aib35 Deposited 2016-01-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 302–357（56 aa） Fragment：UNP residues 302-357
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 K；0.2 M ammonium sulfate, 0.1M sodium acetate pH 4.5, 20% (w/v) PEG 4000
Resolution 2.15 Å R-free 0.252
5HI1 Backbone Modifications in the Protein GB1 Helix: Aib24, beta-3-Lys28, beta-3-Lys31, Aib35 Deposited 2016-01-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 302–357（56 aa） Fragment：UNP residues 302-357
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 K；0.2 M ammonium sulfate, 0.1M sodium acetate pH 4.5, 20% (w/v) PEG 4000
Resolution 2.15 Å R-free 0.252
5HI1 Backbone Modifications in the Protein GB1 Helix: Aib24, beta-3-Lys28, beta-3-Lys31, Aib35 Deposited 2016-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 302–357（56 aa） Fragment：UNP residues 302-357
Non-standard monomer：Yes (specific site not provided by mmCIF) ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M ammonium sulfate, 0.1M sodium acetate pH 4.5, 20% (w/v) PEG 4000
Resolution 2.15 Å R-free 0.252
5HI1 Backbone Modifications in the Protein GB1 Helix: Aib24, beta-3-Lys28, beta-3-Lys31, Aib35 Deposited 2016-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 302–357（56 aa） Fragment：UNP residues 302-357
Non-standard monomer：Yes (specific site not provided by mmCIF) ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M ammonium sulfate, 0.1M sodium acetate pH 4.5, 20% (w/v) PEG 4000
Resolution 2.15 Å R-free 0.252
5HI1 Backbone Modifications in the Protein GB1 Helix: Aib24, beta-3-Lys28, beta-3-Lys31, Aib35 Deposited 2016-01-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 302–357（56 aa） Fragment：UNP residues 302-357
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 K；0.2 M ammonium sulfate, 0.1M sodium acetate pH 4.5, 20% (w/v) PEG 4000
Resolution 2.15 Å R-free 0.252
5HI1 Backbone Modifications in the Protein GB1 Helix: Aib24, beta-3-Lys28, beta-3-Lys31, Aib35 Deposited 2016-01-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 302–357（56 aa） Fragment：UNP residues 302-357
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 K；0.2 M ammonium sulfate, 0.1M sodium acetate pH 4.5, 20% (w/v) PEG 4000
Resolution 2.15 Å R-free 0.252
5HI1 Backbone Modifications in the Protein GB1 Helix: Aib24, beta-3-Lys28, beta-3-Lys31, Aib35 Deposited 2016-01-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 302–357（56 aa） Fragment：UNP residues 302-357
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 K；0.2 M ammonium sulfate, 0.1M sodium acetate pH 4.5, 20% (w/v) PEG 4000
Resolution 2.15 Å R-free 0.252
5HI1 Backbone Modifications in the Protein GB1 Helix: Aib24, beta-3-Lys28, beta-3-Lys31, Aib35 Deposited 2016-01-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 302–357（56 aa） Fragment：UNP residues 302-357
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 K；0.2 M ammonium sulfate, 0.1M sodium acetate pH 4.5, 20% (w/v) PEG 4000
Resolution 2.15 Å R-free 0.252
5LDE Crystal structure of a vFLIP-IKKgamma stapled peptide dimer Deposited 2016-06-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 304–356（53 aa） Fragment：UNP residues 304-356
Chain B 304–356（53 aa） Fragment：UNP residues 304-356
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；299 K；1.2M Ammonium Sulphate, 0.05M tri-sodium citrate, 3% isopropanol, 0.1-0.2% vitamin B12
Resolution 3.38 Å R-free 0.290
5UB0 Solution NMR Structure of NERD-C, a natively folded tetramutant of the B1 domain of streptococcal protein G (GB1) Deposited 2016-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 373–427（55 aa） Fragment：UNP residues 373-427
Mutation：Y3F/L7I/F30L/V39I No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 10 mM sodium phosphate；Pressure 1
NMR sample composition 1.0 mM [U-98% 15N] protein (GB1), 10 mM sodium phosphate, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM [U-99% 13C; U-98% 15N] protein (GB1), 10 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM [U-99% 13C; U-98% 15N] protein (GB1), 10 mM sodium phosphate, 100% D2O | 100% D2O
Resolution not provided
5UBS Solution NMR Structure of NERD-S, a natively folded pentamutant of the B1 domain of streptococcal protein G (GB1) with a solvent-exposed Trp43 Deposited 2016-12-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 373–427（55 aa） Fragment：UNP residues 373-427
Mutation：Y3F/L7I/A34F/V39L/V54I No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 10 mM sodium phosphate；Pressure 1
NMR sample composition 1 mM [U-98% 15N] protein (GB1), 10 mM sodium phosphate, 100 uM EDTA, 0.02 % sodium azide, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-99% 13C; U-98% 15N] protein (GB1), 10 mM sodium phosphate, 100 uM EDTA, 0.02 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-99% 13C; U-98% 15N] protein (GB1), 10 mM sodium phosphate, 100 uM EDTA, 0.02 % sodium azide, 100% D2O | 100% D2O
Resolution not provided
5UCE Solution NMR structure of the major species of DANCER-2, a dynamic and natively folded pentamutant of the B1 domain of streptococcal protein G (GB1) Deposited 2016-12-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 373–427（55 aa） Fragment：UNP residues 373-427
Mutation：Y3F/L5A/L7I/A34F/V39L No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 10 mM sodium phosphate；Pressure 1
NMR sample composition 200 uM [U-98% 15N] protein (GB1), 10 mM sodium phosphate, 100 uM EDTA, 0.02 % sodium azide, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 200 uM [U-99% 13C; U-98% 15N] protein (GB1), 10 mM sodium phosphate, 100 uM EDTA, 0.02 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 200 uM [U-99% 13C; U-98% 15N] protein (GB1), 10 mM sodium phosphate, 100 uM EDTA, 0.02 % sodium azide, 100% D2O | 100% D2O
Resolution not provided
5UCF Solution NMR-derived model of the minor species of DANCER-2, a dynamic and natively folded pentamutant of the B1 domain of streptococcal protein G (GB1) Deposited 2016-12-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 373–427（55 aa） Fragment：UNP residues 373-427
Mutation：Y3F/L5A/L7I/A34F/V39L No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 10 mM sodium phosphate；Pressure 1
NMR sample composition 200 uM [U-98% 15N] protein (GB1), 10 mM sodium phosphate, 100 uM EDTA, 0.02 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 200 uM [U-99% 13C; U-98% 15N] protein (GB1), 10 mM sodium phosphate, 100 uM EDTA, 0.02 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 200 uM [U-99% 13C; U-98% 15N] protein (GB1), 10 mM sodium phosphate, 100 uM EDTA, 0.02 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6C9O Selenomethionine mutant (V29Sem) of protein GB1 examined by X-ray diffraction Deposited 2018-01-28 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 304–357（54 aa）
Mutation：V29M Non-standard monomer：Yes (specific site not provided by mmCIF) MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；283.15 K；46% MPD, 20% IPA, 25 mM sodium acetate pH 4.5
Resolution 1.20 Å R-free 0.179
6C9O Selenomethionine mutant (V29Sem) of protein GB1 examined by X-ray diffraction Deposited 2018-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 304–357（54 aa）
Mutation：V29M Non-standard monomer：Yes (specific site not provided by mmCIF) MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；283.15 K；46% MPD, 20% IPA, 25 mM sodium acetate pH 4.5
Resolution 1.20 Å R-free 0.179
6CHE Selenomethionine mutant (A34Sem) of protein GB1 examined by X-ray diffraction Deposited 2018-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 304–357（54 aa）
Mutation：A34Sem Non-standard monomer：Yes (specific site not provided by mmCIF) MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 IMD IMIDAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；283.15 K；49% MPD 20% IPA 25 mM sodium acetate pH 4.9 20 mg/ml protein in 25 mM sodium acetate buffer pH 5.5 and 2 mM TCEP
Resolution 1.10 Å R-free 0.147
6CPZ Selenomethionine mutant (I6Sem) of protein GB1 examined by X-ray diffraction Deposited 2018-03-14 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 304–357（54 aa）
Mutation：I6Sem Non-standard monomer：Yes (specific site not provided by mmCIF) MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；283.15 K；48% MPD 20% IPA 25 mM sodium acetate buffer pH 4.7 20 mg/ml protein in 25 mM sodium acetate buffer pH 5.5 and 2 mM TCEP
Resolution 1.12 Å R-free 0.156
6CPZ Selenomethionine mutant (I6Sem) of protein GB1 examined by X-ray diffraction Deposited 2018-03-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 304–357（54 aa）
Mutation：I6Sem Non-standard monomer：Yes (specific site not provided by mmCIF) MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；283.15 K；48% MPD 20% IPA 25 mM sodium acetate buffer pH 4.7 20 mg/ml protein in 25 mM sodium acetate buffer pH 5.5 and 2 mM TCEP
Resolution 1.12 Å R-free 0.156
6CTE 77Se-NMR probes the protein environment of selenomethionine Deposited 2018-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 304–357（54 aa）
Mutation：V39Sem Non-standard monomer：Yes (specific site not provided by mmCIF) MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；283.15 K；49% MPD 20% IPA 25 mM sodium acetate pH 4.7 20 mg/ml protein concentration 25 mM sodium acetate pH 5.5 non-reducing
Resolution 1.20 Å R-free 0.175
6CTE 77Se-NMR probes the protein environment of selenomethionine Deposited 2018-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 304–357（54 aa）
Mutation：V39Sem Non-standard monomer：Yes (specific site not provided by mmCIF) MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 PO4 PHOSPHATE ION × 3 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；283.15 K；49% MPD 20% IPA 25 mM sodium acetate pH 4.7 20 mg/ml protein concentration 25 mM sodium acetate pH 5.5 non-reducing
Resolution 1.20 Å R-free 0.175
6HKA The solution structure of the micelle-associated FATC domain of the human protein kinase ataxia telangiectasia mutated (ATM) Deposited 2018-09-06 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 304–357（54 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 100 mM sodium chloride, 50 mM TRIS, 150 mM [U-100% 2H] DPC, 0.4 mM [U-100% 13C; U-100% 15N] 13C-15N-hATMfatc, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 100 mM sodium chloride, 50 mM TRIS, 150 mM [U-100% 2H] DPC, 0.4 mM [U-10% 13C] 13C-hATMfatc, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 100 mM sodium chloride, 50 mM TRIS, 150 mM [U-100% 2H] DPC, 0.5 mM [U-100% 15N] 15N-hATMfatc, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6HPJ Structure of human SRSF1 RRM1 bound to AACAAA RNA Deposited 2018-09-21 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: dimeric
Chain B 304–357（54 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；313 K；Ionic strength (raw mmCIF value) 120；Pressure atmospheric
NMR sample composition 0.5 mM [U-99% 15N] SRSF1 RRM1, 0.5 mM RNA (5'-R(*AP*AP*CP*AP*AP*A)-3'), 100% D2O | 100% D2O
NMR sample composition 0.5 mM [U-99% 15N] SRSF1 RRM1, 0.5 mM NA RNA (5'-R(*AP*AP*CP*AP*AP*A)-3'), 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N] SRSF1 RRM1, 0.5 mM NA RNA (5'-R(*AP*AP*CP*AP*AP*A)-3'), 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6NJF Solution NMR Structure of DANCER3-F34A, a rigid and natively folded single mutant of the dynamic protein DANCER-3 Deposited 2019-01-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 373–427（55 aa） Fragment：residues 373-427
Mutation：Y3F, V7I, V39L, V54I No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 10 mM sodium phosphate；Pressure 1
NMR sample composition 1.0 mM [U-98% 15N] protein (GB1), 10 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM [U-99% 13C; U-98% 15N] protein (GB1), 10 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM [U-99% 13C; U-98% 15N] protein (GB1), 10 mM sodium phosphate, 100% D2O | 100% D2O
Resolution not provided
6NL6 Crystal structure of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q) Deposited 2019-01-08 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 303–357（55 aa）
Mutation：T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, D36H, N35K, D36A, N37Q ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；70 mM acetic Acid pH 3.6, 30 mM acetic acid pH 5.8, 30% 2,4-methylpentanediol, 100 mM NaCl, and 20 mM zinc sulfate
Resolution 1.40 Å R-free 0.214
6NL6 Crystal structure of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q) Deposited 2019-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 303–357（55 aa）
Mutation：T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, D36H, N35K, D36A, N37Q ZN ZINC ION × 3 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；70 mM acetic Acid pH 3.6, 30 mM acetic acid pH 5.8, 30% 2,4-methylpentanediol, 100 mM NaCl, and 20 mM zinc sulfate
Resolution 1.40 Å R-free 0.214
6NL6 Crystal structure of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q) Deposited 2019-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 303–357（55 aa）
Mutation：T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, D36H, N35K, D36A, N37Q ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；70 mM acetic Acid pH 3.6, 30 mM acetic acid pH 5.8, 30% 2,4-methylpentanediol, 100 mM NaCl, and 20 mM zinc sulfate
Resolution 1.40 Å R-free 0.214
6NL6 Crystal structure of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q) Deposited 2019-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 303–357（55 aa）
Mutation：T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, D36H, N35K, D36A, N37Q ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；70 mM acetic Acid pH 3.6, 30 mM acetic acid pH 5.8, 30% 2,4-methylpentanediol, 100 mM NaCl, and 20 mM zinc sulfate
Resolution 1.40 Å R-free 0.214
6NL7 Crystal structure of B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q) Deposited 2019-01-08 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 303–357（55 aa）
Mutation：T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q ZN ZINC ION × 2 ACT ACETATE ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；80 mM acetic acid pH 3.6, 20 mM acetic acid pH 5.8, 30% 2,4-methylpentanediol, 200 mM NaCl and 20 mM zinc sulfate
Resolution 1.40 Å R-free 0.158
6NL7 Crystal structure of B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q) Deposited 2019-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 303–357（55 aa）
Mutation：T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q ZN ZINC ION × 2 ACT ACETATE ION × 3 NA SODIUM ION × 1 PO4 PHOSPHATE ION × 1 DPO DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；80 mM acetic acid pH 3.6, 20 mM acetic acid pH 5.8, 30% 2,4-methylpentanediol, 200 mM NaCl and 20 mM zinc sulfate
Resolution 1.40 Å R-free 0.158
6NL7 Crystal structure of B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q) Deposited 2019-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 303–357（55 aa）
Mutation：T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q ACT ACETATE ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；80 mM acetic acid pH 3.6, 20 mM acetic acid pH 5.8, 30% 2,4-methylpentanediol, 200 mM NaCl and 20 mM zinc sulfate
Resolution 1.40 Å R-free 0.158
6NL7 Crystal structure of B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q) Deposited 2019-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 303–357（55 aa）
Mutation：T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；80 mM acetic acid pH 3.6, 20 mM acetic acid pH 5.8, 30% 2,4-methylpentanediol, 200 mM NaCl and 20 mM zinc sulfate
Resolution 1.40 Å R-free 0.158
6NL8 Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-zinc Deposited 2019-01-08 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 303–357（55 aa）
Mutation：L12H, T16L, V29H, Y33H, N37L ZN ZINC ION × 4 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；18.5% PEG 400 0.1M HEPES pH 7.5 50 mM MgCl2, 5mM zinc sulfate
Resolution 1.50 Å R-free 0.163
6NL9 Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-apo Deposited 2019-01-08 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 303–357（55 aa）
Mutation：L12H, T16L, V29H, Y33H, N37L MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；30% PEG 4000 0.1M HEPES pH 7.5 200 mM MgCl2
Resolution 1.70 Å R-free 0.224
6NL9 Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-apo Deposited 2019-01-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 303–357（55 aa）
Mutation：L12H, T16L, V29H, Y33H, N37L No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；30% PEG 4000 0.1M HEPES pH 7.5 200 mM MgCl2
Resolution 1.70 Å R-free 0.224
6NL9 Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-apo Deposited 2019-01-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 303–357（55 aa）
Mutation：L12H, T16L, V29H, Y33H, N37L No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；30% PEG 4000 0.1M HEPES pH 7.5 200 mM MgCl2
Resolution 1.70 Å R-free 0.224
6NL9 Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-apo Deposited 2019-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 303–357（55 aa）
Mutation：L12H, T16L, V29H, Y33H, N37L NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；30% PEG 4000 0.1M HEPES pH 7.5 200 mM MgCl2
Resolution 1.70 Å R-free 0.224
6NLA Crystal structure of de novo designed metal-controlled dimer of B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-zinc Deposited 2019-01-08 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 303–357（55 aa）
Mutation：L12H, E15V, T16L, T18I, V29H, Y33H, N37L ZN ZINC ION × 4 CL CHLORIDE ION × 6 GOL GLYCEROL × 2 NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；4M NaCl 0.1M HEPES pH 7.5 50mM MgCl2, 5mM zinc sulfate
Resolution 1.34 Å R-free 0.128
6NLB Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-apo Deposited 2019-01-08 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 303–357（55 aa）
Mutation：L12H, E15V, T16L, T18I, V29H, Y33H, N37L MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；31% PEG 4,000 0.1M Tris pH 8.5 200mM MgCl2
Resolution 2.30 Å R-free 0.258
6NLB Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-apo Deposited 2019-01-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 303–357（55 aa）
Mutation：L12H, E15V, T16L, T18I, V29H, Y33H, N37L No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；31% PEG 4,000 0.1M Tris pH 8.5 200mM MgCl2
Resolution 2.30 Å R-free 0.258
6NLB Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-apo Deposited 2019-01-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 303–357（55 aa）
Mutation：L12H, E15V, T16L, T18I, V29H, Y33H, N37L No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；31% PEG 4,000 0.1M Tris pH 8.5 200mM MgCl2
Resolution 2.30 Å R-free 0.258
6NLB Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-apo Deposited 2019-01-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 303–357（55 aa）
Mutation：L12H, E15V, T16L, T18I, V29H, Y33H, N37L No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；31% PEG 4,000 0.1M Tris pH 8.5 200mM MgCl2
Resolution 2.30 Å R-free 0.258
6O41 Crystal structure of the unbound PGZL1 germline Fab fragment (PGZL1_gVmDmJ) Deposited 2019-02-27 Different construct 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 M 438–497（60 aa）
Not recorded GOL GLYCEROL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；20% PEG3350, 0.2 M lithium citrate
Resolution 2.46 Å R-free 0.219
6O41 Crystal structure of the unbound PGZL1 germline Fab fragment (PGZL1_gVmDmJ) Deposited 2019-02-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain O 438–497（60 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；20% PEG3350, 0.2 M lithium citrate
Resolution 2.46 Å R-free 0.219
6O41 Crystal structure of the unbound PGZL1 germline Fab fragment (PGZL1_gVmDmJ) Deposited 2019-02-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain N 438–497（60 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；20% PEG3350, 0.2 M lithium citrate
Resolution 2.46 Å R-free 0.219
6OC7 HMP42 Fab in complex with Protein G Deposited 2019-03-22 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 438–497（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；17% PEG 4000, 15% glycerol, 8.5% 2-propanol and 85 mM HEPES pH 7.5
Resolution 1.30 Å R-free 0.184
6UUH Crystal structure of broad and potent HIV-1 neutralizing antibody 438-B11 Deposited 2019-10-30 Different construct 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 E 438–497（60 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.085M sodium acetate (pH=4.0), 0.17M ammonium acetate, 5% %(v/v) glycerol, 27.882 %(w/v) PEG4000, 15% glycerol
Resolution 2.70 Å R-free 0.260
6UUH Crystal structure of broad and potent HIV-1 neutralizing antibody 438-B11 Deposited 2019-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 438–497（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.085M sodium acetate (pH=4.0), 0.17M ammonium acetate, 5% %(v/v) glycerol, 27.882 %(w/v) PEG4000, 15% glycerol
Resolution 2.70 Å R-free 0.260
6UYG Structure of Hepatitis C Virus Envelope Glycoprotein E2c3 core from genotype 6a bound to broadly neutralizing antibody AR3A and non neutralizing antibody E1 Deposited 2019-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain G 438–497（60 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M magnesium chloride, 10% (w/v) PEG 3000, 15% ethylene glycol, 0.1M Na-cacodylate, pH=6.5
Resolution 3.38 Å R-free 0.305
6W00 Crystal structure of Fab239 in complex with NPNA2 peptide from circumsporozoite protein Deposited 2020-02-28 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 440–497（58 aa） Fragment：domain III (UNP residues 438-497)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M sodium chloride, 20% w/v PEG3350
Resolution 1.85 Å R-free 0.206
6WFW Crystal structure of Fab364 in complex with NPNA2 peptide from circumsporozoite protein Deposited 2020-04-04 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 439–497（59 aa） Fragment：domain III (UNP residues 438-497)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；20% PEG8000, 0.05 M potassium phosphate dibasic
Resolution 2.09 Å R-free 0.257
7DA8 X-ray structure of a GB1:T2Q/D46K mutant Deposited 2020-10-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 303–357（55 aa）
Mutation：T303Q, D347K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；MES monohydrate pH 6.5 (buffer system 1), 40% v/v PEG 500* MME, 20 % w/v PEG 20000 (Precipitant mix1) (Morpheus Screen ID 25).
Resolution 2.40 Å R-free 0.305
8DIJ NMR Structure of Streptococcal Protein GB1 Backbone Modified Variant: beta-ACPC24, beta-3-Lys28, beta-3-Lys31, beta-ACPC35 Deposited 2022-06-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 302–357（56 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 40；Pressure 1
NMR sample composition 0.65 mM Streptococcal Protein GB1 Backbone Modified Variant: beta-ACPC24, beta-3-Lys28, beta-3-Lys31, beta-ACPC35, 20 mM sodium phosphate, 0.1 mM DSS, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
8TFR Apo Fab from C10-S66K antibody Deposited 2023-07-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 438–497（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；20% PEG 3350, 0.2 M Na3-citrate, pH 8.2
Resolution 2.99 Å R-free 0.262
8UM7 Site-specific Aspartic Acid Dehydration and Isomerization in Streptococcal Protein GB1: Wild-type Protein Deposited 2023-10-17 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 304–357（54 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 41；Pressure 1
NMR sample composition 0.12 mM B1 Domain of Streptococcal Protein G, 20 mM sodium phosphate, 0.1 mM DSS, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
8UM9 Site-specific Aspartic Acid Dehydration and Isomerization in Streptococcal Protein GB1: D-Asp40 Variant Deposited 2023-10-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 304–357（54 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 41；Pressure 1
NMR sample composition 0.12 mM B1 Domain of Streptococcal Protein G, D-Asp40 Variant, 20 mM sodium phosphate, 0.1 mM DSS, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
8UMA Site-specific Aspartic Acid Dehydration and Isomerization in Streptococcal Protein GB1: D-isoAsp40 Variant Deposited 2023-10-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 304–357（54 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 41；Pressure 1
NMR sample composition 0.17 mM B1 Domain of Streptococcal Protein G, D-isoAsp40 Variant, 20 mM sodium phosphate, 0.1 mM DSS, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
8UMB Site-specific Aspartic Acid Dehydration and Isomerization in Streptococcal Protein GB1: L-Aspartyl Succinimide 40-41 Variant Deposited 2023-10-17 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 304–357（54 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 41；Pressure 1
NMR sample composition 0.07 mM B1 Domain of Streptococcal Protein G, L-Aspartyl Succinimide 40-41 Variant, 20 mM sodium phosphate, 0.1 mM DSS, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
8UMS Site-specific Aspartic Acid Dehydration and Isomerization in Streptococcal Protein GB1: L-isoAsp40 Variant Deposited 2023-10-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 304–357（54 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 41；Pressure 1
NMR sample composition 0.18 mM B1 Domain of Streptococcal Protein G, L-isoAsp40 Variant, 20 mM sodium phosphate, 0.1 mM DSS, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
8WCJ Crystal structure of GB3 penta mutation L5V/K10H/T16S/K19E/Y33I Deposited 2023-09-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 444–497（54 aa）
Mutation：L446V, K451H, T457S, K460E, Y474I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；60% v/v Tacsimate pH 7.0
Resolution 1.55 Å R-free 0.233
9AWE The crystal structure of an engineered Protein GF with Human Kappa Fab Deposited 2024-03-05 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 368–430（63 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium Cacodylate pH 6.0, 0.1M Calcium acetate hydrate, 10% PEG 8000
Resolution 2.80 Å R-free 0.293
9BDE Middle Region of Apolipoprotein B 100 bound to Low Density Lipoprotein Receptor Deposited 2024-04-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 440–497（58 aa） Fragment：;residues 27-384 (Uniprot numbering),residues 278-327 (Uniprot numbering),103-151 (Uniprot numbering),residues 440-497 (Uniprot numbering) ;
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
9I2I X-ray structure of the B1 domain of streptococcal protein G triple mutant T2Q, N8D, and N37D (GB1-QDD). Deposited 2025-01-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 303–357（55 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；278 K；50% MPD, 25% isopropyl alcohol,
Resolution 1.08 Å R-free 0.210
9I2I X-ray structure of the B1 domain of streptococcal protein G triple mutant T2Q, N8D, and N37D (GB1-QDD). Deposited 2025-01-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 303–357（55 aa）
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；278 K；50% MPD, 25% isopropyl alcohol,
Resolution 1.08 Å R-free 0.210
9QBJ Legobody dimer Deposited 2025-03-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain I 440–496（57 aa）
Chain J 440–497（58 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9T8Z Room temperature X-ray structure of the B1 domain of streptococcal protein G triple mutant T2Q, N8D, and N37D (GB1-QDD). Deposited 2025-11-13 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 303–357（55 aa）
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；278 K；50 % 2-methyl-2,4-pentanediol (MPD), 25 % isopropanol
Resolution 1.69 Å R-free 0.197
9T8Z Room temperature X-ray structure of the B1 domain of streptococcal protein G triple mutant T2Q, N8D, and N37D (GB1-QDD). Deposited 2025-11-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 303–357（55 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；278 K；50 % 2-methyl-2,4-pentanediol (MPD), 25 % isopropanol
Resolution 1.69 Å R-free 0.197

76 other PDB entries and 116 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPG2_STRSG
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–56； UniProt 304–357

Immunoglobulin G-binding protein G, DNA polymerase iota

Streptococcus sp., Homo sapiens

UniProt Q9UNA4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 676–715 Fragment：UNP residues 304-357, 676-715 Ubiquitin × 1 （P62988） 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

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 2KHW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1T3N Structure of the catalytic core of DNA polymerase Iota in complex with DNA and dTTP Deposited 2004-04-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 27–414（388 aa）
Chain B 27–414（388 aa）
Not recorded MG MAGNESIUM ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å R-free 0.286
2ALZ Ternary Complex of hPoli with DNA and dCTP Deposited 2005-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 25–414（390 aa）
Not recorded MG MAGNESIUM ION × 4 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；16% PEG 5K MME, 0.4 M Ammonium Sulfate, 0.1 M MES buffer, pH 6.5, hanging drop, pH 6.50
Resolution 2.50 Å R-free 0.272
2DPI Ternary complex of hPoli with DNA and dCTP Deposited 2006-05-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 1–420（420 aa） Fragment：residues 1-420
Not recorded MG MAGNESIUM ION × 4 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；16% PEG 5K MME, 0.4M Ammonium Sulfate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.30 Å R-free 0.278
2DPJ structure of hPoli with DNA and dTTP Deposited 2006-05-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 1–420（420 aa） Fragment：residues 1-420
Not recorded MG MAGNESIUM ION × 4 TTP THYMIDINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；16% PEG 5K MME, 0.4M Ammonium Sulfate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.30 Å R-free 0.277
2FLL Ternary complex of human DNA polymerase iota with DNA and dTTP Deposited 2006-01-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 1–420（420 aa）
Not recorded MG MAGNESIUM ION × 4 TTP THYMIDINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；pH 6.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.60 Å R-free 0.277
2FLN binary complex of catalytic core of human DNA polymerase iota with DNA (template A) Deposited 2006-01-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 1–420（420 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；pH 6.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.50 Å R-free 0.279
2FLP Binary complex of the catalytic core of human DNA polymerase iota with DNA (template G) Deposited 2006-01-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 1–420（420 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；pH 6.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.40 Å R-free 0.276
2KHU Solution Structure of the Ubiquitin-Binding Motif of Human Polymerase Iota Deposited 2009-04-11 Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 676–715（40 aa） Fragment：UNP residues 304-357, 676-715
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；25 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition 1-4 mM [U-100% 13C; U-100% 15N] D2O-1, 1-4 mM [U-100% 13C; U-100% 15N] H2O-2, 100% D2O | 100% D2O
Resolution not provided
2KTF Solution NMR structure of human polymerase iota UBM2 in complex with ubiquitin Deposited 2010-02-01 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 679–707（29 aa） Fragment：Ubiquitin biding motif UBM2
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
2L0F Solution NMR structure of human polymerase iota UBM2 (P692A mutant) in complex with ubiquitin Deposited 2010-07-01 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 674–715（42 aa）
Not recorded 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
2L0G Solution NMR structure of ubiquitin-binding motif (UBM2) of human polymerase iota Deposited 2010-07-01 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 679–707（29 aa）
Not recorded 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, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MBB Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex Deposited 2013-07-29 Different construct Different experimental conditions Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 516–555（40 aa） Fragment：UNP P06654 residues 229-282, UNP Q9UNA4 residues 516-555
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 sample composition 3 mM [U-100% 15N] GB1-UBM1, 3 mM [U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
NMR sample composition 3 mM GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
Resolution not provided
3EPG Structure of Human DNA Polymerase Iota complexed with N2-ethylguanine Deposited 2008-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 1–420（420 aa） Fragment：Catalytic Fragment (UNP residues 1-420)
Not recorded DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 NA SODIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；12-15% PEG MME 5000, 0.2-0.4M Ammonium Sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Resolution 2.50 Å R-free 0.283
3EPI Structure of Human DNA Polymerase Iota complexed with N2-ethylguanine and incoming TTP Deposited 2008-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 1–420（420 aa） Fragment：Catalytic Fragment (UNP residues 1-420)
Not recorded NA SODIUM ION × 2 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；12-15% PEG MME 5000, 0.2-0.4M Ammonium Sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Resolution 2.90 Å R-free 0.282
3G6V DNA synthesis across an abasic lesion by human DNA polymerase-iota Deposited 2009-02-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–420（420 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Crystals grew over a period of one day, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.251
3G6X Ternary complex of DNA Polymerase iota:DNA:dGTP with an abasic site at the templating position Deposited 2009-02-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–420（420 aa）
Not recorded DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Crystals grew in 24 hours, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.08 Å R-free 0.265
3G6Y Ternary complex of DNA Polymerase iota:DNA:dTTP with an abasic site at the templating position Deposited 2009-02-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–420（420 aa）
Not recorded TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；crystals grew in 24 hours, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.253
3GV5 Human DNA polymerase iota in complex with T template DNA and incoming ddADP Deposited 2009-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–420（420 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 4 GOL GLYCEROL × 1 ADI 2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.5；298 K；15% PEG 3350, 0.15 M CaCl2, 5% glycerol, 0.005M DTT, pH 7.5, hanging drop, temperature 298K
Resolution 2.00 Å R-free 0.253
3GV5 Human DNA polymerase iota in complex with T template DNA and incoming ddADP Deposited 2009-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 1–420（420 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 4 ADI 2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.5；298 K；15% PEG 3350, 0.15 M CaCl2, 5% glycerol, 0.005M DTT, pH 7.5, hanging drop, temperature 298K
Resolution 2.00 Å R-free 0.253
3GV7 Human DNA polymerase iota in complex with T template DNA and incoming dTTP Deposited 2009-03-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–420（420 aa）
Not recorded MG MAGNESIUM ION × 2 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；15% PEG 5000MME, 0.2M NH4SO4, 0.1M MES 6.5, 5% glycerol, hanging drop
Resolution 2.20 Å R-free 0.258
3GV8 Human DNA polymerase iota in complex with T template DNA and incoming dGTP Deposited 2009-03-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–420（420 aa）
Not recorded MG MAGNESIUM ION × 2 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；15% PEG 5000MME, 0.2M NH4SO4, 0.1M MES 6.5, 5% glycerol, hanging drop
Resolution 2.00 Å R-free 0.248
3H40 Binary complex of human DNA polymerase iota with template U/T Deposited 2009-04-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 26–414（389 aa） Fragment：UNP residues 26-414, UmuC domain, DNA binding domain
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；10-15 % PEG 5K MME, 0.2-0.4 M Ammonium sulfate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.30 Å R-free 0.277
3H4B Ternary complex of human DNA polymerase iota with template U/T and incoming dATP Deposited 2009-04-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 25–414（390 aa）
Not recorded DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；10-15% PEG 5K MME, 0.2-0.4 M Ammonium sulfate, 0.1 M MES , pH 6.5 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.85 Å R-free 0.281
3H4D Ternary complex of human DNA polymerase iota with template U/T and incoming dGTP Deposited 2009-04-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 25–414（390 aa） Fragment：polymerase iota
Not recorded MG MAGNESIUM ION × 2 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；10-15% PEG 5K MME, 0.2-0.4 M Ammonium sulfate, 0.1 M MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.270
3NGD Structural Basis for Proficient Incorporation of dTTP Opposite O6-methylguanine by Human DNA Polymerase Iota Deposited 2010-06-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–420（420 aa） Fragment：Catalytic Fragment, 1-420
Not recorded DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M ammonium sulfate, 12.5% PEG 5000 monomethylether, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.284
3OSN Structural Basis for Proficient Incorporation of dTTP Opposite O6-Methylguanine by Human DNA Polymerase Iota Deposited 2010-09-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–420（420 aa） Fragment：Catalytic fragment, residues 1-420
Not recorded TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M Ammonium Sulfate, 12.5% PEG 5000 monomethylether, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.90 Å R-free 0.241
3Q8P Human DNA polymerase iota incorporating dCTP opposite 8-oxo-guanine Deposited 2011-01-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–420（420 aa） Fragment：UNP residues 1-420
Not recorded DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15% PEG 5000MME, 0.15M NH4SO4, 0.1M MES pH 6.5, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Resolution 1.95 Å R-free 0.257
3Q8Q Human DNA polymerase iota incorporating dATP opposite 8-oxo-guanine Deposited 2011-01-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–420（420 aa） Fragment：UNP residues 1-420
Not recorded MG MAGNESIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15% PEG 5000MME, 0.15M NH4SO4, 0.1M MES 6.5, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Resolution 2.03 Å R-free 0.253
3Q8R Human DNA polymerase iota incorporating dGTP opposite 8-oxo-guanine Deposited 2011-01-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–420（420 aa） Fragment：UNP residues 1-420
Not recorded DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15% PEG 5000MME, 0.15M NH4SO4, 0.1M MES 6.5, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Resolution 2.45 Å R-free 0.280
3Q8S Human DNA polymerase iota incorporating dTTP opposite 8-oxo-guanine Deposited 2011-01-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–420（420 aa） Fragment：UNP residues 1-420
Not recorded MG MAGNESIUM ION × 2 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15% PEG 5000MME, 0.15M NH4SO4, 0.1M MES 6.5, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Resolution 2.09 Å R-free 0.266
4EBC Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota Deposited 2012-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 26–445（420 aa） Fragment：UNP residues 26-445
Not recorded 0OH North-methanocarba-2'-deoxyadenosine triphosphate × 1 CA CALCIUM ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；20 mM Tris-HCl, pH 7.9, 5% glycerol, 10 mM 2-mercaptoethanol, 150 mM calcium chloride, 12% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.90 Å R-free 0.253
4EBD Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota Deposited 2012-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 26–445（420 aa） Fragment：UNP residues 26-445
Not recorded 0OJ South-methanocarba-2'-deoxyadenosine triphosphate × 1 CA CALCIUM ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；20 mM Tris-HCl, pH 7.9, 5% glycerol, 10 mM 2-mercaptoethanol, 150 mM calcium chloride, 12% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.57 Å R-free 0.263
4EBE Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota Deposited 2012-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 26–445（420 aa） Fragment：UNP residues 26-445
Not recorded DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；20 mM Tris-HCl, pH 7.9, 5% glycerol, 10 mM 2-mercaptoethanol, 150 mM calcium chloride, 10% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.10 Å R-free 0.265
4EYH Human DNA polymerase iota incorporating dCTP opposite N-(deoxyguanosin-8-yl)-1-aminopyrene lesion Deposited 2012-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 26–445（420 aa） Fragment：UNP residues 26-445
Not recorded DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15% PEG 5000MME, 0.2 M MH4SO4, 0.1 M MES pH 6.5, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Resolution 2.90 Å R-free 0.281
4EYI Human DNA polymerase iota incorporating dATP opposite N-(deoxyguanosin-8-yl)-1-aminopyrene lesion Deposited 2012-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 26–445（420 aa） Fragment：UNP residues 26-445
Not recorded DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15% PEG 5000MME, 0.2 M NH4SO4, 0.1M MES pH 6.5, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Resolution 2.90 Å R-free 0.264
4FS1 Base pairing mechanism of N2,3-ethenoguanine with dTTP by human polymerase iota Deposited 2012-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 26–445（420 aa）
Not recorded MG MAGNESIUM ION × 3 NA SODIUM ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.9；277 K；210 microM polymerase iota, 253 microM DNA complex, 10 mM MgCl2, 20 mM dTTP; mix 1:1 ratio with precipitant, 0.1 M MES (pH 6.5), 0.3 M (NH4)2SO4, 17% PEG 5000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.50 Å R-free 0.270
4FS2 Base pairing mechanism of N2,3-ethenoguanine with dCTP by human polymerase iota Deposited 2012-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 26–445（420 aa）
Not recorded MG MAGNESIUM ION × 3 NA SODIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.9；277 K；210 microM polymerase iota, 253 microM DNA complex, 10 mM MgCl2, 20 mM dTTP; mix 1:1 ratio with precipitant, 0.1 M MES (pH 6.5), 0.3 M (NH4)2SO4, 17% PEG 5000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.05 Å R-free 0.261
5KT2 Teranry complex of human DNA polymerase iota(26-445) inserting dCMPNPP opposite template G in the presence of Mg2+ Deposited 2016-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 26–445（420 aa） Fragment：UNP residues 26-445
Not recorded 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；13% PEG MME 5000, 0.1M MES, 0.3M ammonium sulfate
Resolution 2.49 Å R-free 0.249
5KT3 Teranry complex of human DNA polymerase iota(26-445) inserting dCMPNPP opposite template G in the presence of Mn2+ Deposited 2016-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 26–445（420 aa） Fragment：UNP residues 26-445
Not recorded 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 MN MANGANESE (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；18% PEG MME 5000, 0.1M MES buffer, 0.3M ammonium sulfate
Resolution 2.64 Å R-free 0.248
5KT4 Teranry complex of human DNA polymerase iota R96G inserting dCMPNPP opposite template G in the presence of Mg2+ Deposited 2016-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–445（445 aa） Fragment：UNP residues 1-445
Not recorded 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；18% PEG MME 5000, 0.1M MES buffer, 0.3M ammonium sulfate
Resolution 2.78 Å R-free 0.249
5KT5 Teranry complex of human DNA polymerase iota R96G inserting dCMPNPP opposite template G in the presence of Mn2+ Deposited 2016-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–445（445 aa） Fragment：UNP residues 1-445
Not recorded MN MANGANESE (II) ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；18% PEG MME 5000, 0.1M MES buffer, 0.3M ammonium sulfate
Resolution 2.80 Å R-free 0.266
5KT6 Teranry complex of human DNA polymerase iota(1-445) inserting dCMPNPP opposite template G in the presence of Mg2+ Deposited 2016-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–445（445 aa） Fragment：UNP residues 1-445
Not recorded 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；18% PEG MME 5000, 0.1M MES buffer, 0.3M ammonium sulfate
Resolution 3.54 Å R-free 0.244
5KT7 Teranry complex of human DNA polymerase iota(1-445) inserting dCMPNPP opposite template G in the presence of Mn2+ Deposited 2016-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–445（445 aa）
Not recorded MN MANGANESE (II) ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；18% PEG MME 5000, 0.1M MES buffer, 0.3M ammonium sulfate
Resolution 3.15 Å R-free 0.236
5ULW Structure of human DNA polymerase iota bound to template 1-methyl-deoxyadenosine Deposited 2017-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 26–445（420 aa）
Not recorded TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；50 mM MES, pH 6.0, 18 % PEG 5KMME, 0.4 M Ammonium Sulfate
Resolution 2.62 Å R-free 0.248
5ULX Structure of human DNA polymerase iota bound to template 1-methyl-deoxyadenosine crystallized in the presence of dCTP Deposited 2017-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 26–445（420 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；100 mM MES, pH 6.0, 14 % PEG 5KMME, 0.4 M Ammonium Sulfate
Resolution 1.96 Å R-free 0.239
9DDR Ternary substrate complex of DNA polymerase iota with DNA (template A), Ca2+, and dTTP Deposited 2024-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 26–445（420 aa）
Not recorded TTP THYMIDINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM HEPES pH 7 1.5-1.8 M Ammonium Sulfate 5 mM EDTA
Resolution 2.15 Å R-free 0.280
9DQT Binary substrate complex of DNA polymerase iota with DNA (template A) Deposited 2024-09-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 26–445（420 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；100 mM HEPES pH 7 1.5 -1.8 M Ammonium Sulfate 5 mM EDTA
Resolution 3.19 Å R-free 0.364
9DQU Product complex of DNA polymerase iota with Pyrophosphate Deposited 2024-09-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 26–445（420 aa）
Not recorded POP PYROPHOSPHATE 2- × 2 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；100 mM HEPES pH 7 1.5 -1.8 M Ammonium Sulfate 5 mM EDTA
Resolution 2.20 Å R-free 0.278
9DR7 Product complex of DNA polymerase iota with 2 monophosphates Deposited 2024-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 26–445（420 aa）
Not recorded PO4 PHOSPHATE ION × 4 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；100 mM HEPES pH 7 1.5 -1.8 M Ammonium Sulfate 5 mM EDTA
Resolution 2.45 Å R-free 0.312
9DR9 Binary product complex of DNA polymerase iota with DNA Deposited 2024-09-25 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 26–445（420 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；100 mM HEPES pH 7 1.5 - 1.8 M Ammonium Sulfate 5 mM EDTA
Resolution 2.21 Å R-free 0.297
9DRB Binary complex of DNA polymerase iota with product DNA Deposited 2024-09-25 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 26–445（420 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；100 mM HEPES pH 7 1.5 - 1.8 M Ammonium Sulfate 5 mM EDTA
Resolution 2.36 Å R-free 0.324
9DRC Ternary substrate complex of DNA polymerase iota R71A mutant with DNA (template A) and dTTP Deposited 2024-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 26–445（420 aa）
Not recorded TTP THYMIDINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；100 mM HEPES pH 7 1.5 - 1.8 M Ammonium Sulfate 5 mM EDTA
Resolution 2.45 Å R-free 0.294
9NJH Translocated product complex of DNA polymerase iota with DNA (template A) Deposited 2025-02-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 26–445（420 aa）
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；100 mM HEPES pH 7 1.5 -1.8 M Ammonium Sulfate 5 mM EDTA
Resolution 2.29 Å R-free 0.288

52 other PDB entries and 53 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLI_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 61–100； UniProt 676–715

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 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–76 Not recorded Immunoglobulin G-binding protein G, DNA polymerase iota × 1 （P19909,Q9UNA4） 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

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 2KHW 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 experimental conditions 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 oligomeric state Different experimental conditions 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 experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；lithium sulfate, ammonium sulfate, sodium citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.292
1FXT STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTER COMPLEX Deposited 2000-09-26 Different oligomeric state Different experimental conditions 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 oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions 293 K；Pressure ambient
NMR measurement conditions 293 K；Pressure 50
NMR sample composition 4 mg c13/n15 ubiquitin in 13.5 ul of buffer (50mM Sodium acetate, 250mM Sodium Chloride, pH 5.0) and 1 ml D12-pentane | 75mM bis(2-ethyl hexyl) sulfosuccinate in d-pentane
NMR sample composition 8 mg 13/n15 ubiquitin in 27 ul of buffer (50mM Sodium acetate, 250mM Sodium Chloride, pH 5.0) | 75mM bis(2-ethyl hexyl) sulfosuccinate in butane
NMR sample composition 4 mg n15 ubiquitin in 13.5 ul of buffer (50mM Sodium acetate, 250mM Sodium Chloride, pH 5.0) | 75mM bis(2-ethyl hexyl) sulfosuccinate in d-pentane
Resolution not provided
1NBF Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde Deposited 2002-12-02 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；296 K；PEG3000, citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.30 Å R-free 0.262
1NBF Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde Deposited 2002-12-02 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；296 K；PEG3000, citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.30 Å R-free 0.262
1Q5W Ubiquitin Recognition by Npl4 Zinc-Fingers Deposited 2003-08-11 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 5.5；291 K；Ionic strength (raw mmCIF value) 70mM；Pressure ambient
NMR measurement conditions pH 5.5；291 K；Ionic strength (raw mmCIF value) 70mM；Pressure ambient
NMR measurement conditions pH 5.5；291 K；Ionic strength (raw mmCIF value) 70mM；Pressure ambient
NMR measurement conditions pH 5.5；291 K；Ionic strength (raw mmCIF value) 70mM；Pressure ambient
NMR sample composition 1mM Npl4 NZF U-15N,13C; 2mM unlabeled-Ubiquitin; 20mM phosphate buffer pH 5.5, 50mM NaCl; 90% H2O, 10% | 90% H2O/10% D2O
NMR sample composition 1mM Ubiquitin U-15N,13C; 2mM unlabeled-Npl4 NZF; 20mM phosphate buffer pH 5.5, 50mM NaCl; 90% H2O, 10% | 90% H2O/10% D2O
NMR sample composition 1mM Ubiquitin U-15N; 2mM unlabeled-Npl4 NZF; 20mM phosphate buffer pH 5.5, 50mM | 90% H2O/10% D2O
NMR sample composition 1mM Npl4 NZF U-15N; 2mM unlabeled-Ubiquitin; 20mM phosphate buffer pH 5.5, 50mM NaCl; 90% H2O, 10% | 90% H2O/10% D2O
Resolution not provided
1S1Q TSG101(UEV) domain in complex with Ubiquitin Deposited 2004-01-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；1.4M Ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.00 Å R-free 0.240
1S1Q TSG101(UEV) domain in complex with Ubiquitin Deposited 2004-01-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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）
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 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 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 oligomeric state 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 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 oligomeric state 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 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
1XD3 Crystal structure of UCHL3-UbVME complex Deposited 2004-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 229–303（75 aa）
Not recorded MG MAGNESIUM ION × 3 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.45 Å R-free 0.192
1XD3 Crystal structure of UCHL3-UbVME complex Deposited 2004-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 229–303（75 aa）
Not recorded MG MAGNESIUM ION × 7 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.45 Å R-free 0.192
1YX5 Solution Structure of S5a UIM-1/Ubiquitin Complex Deposited 2005-02-19 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：Sequence Database Residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1
NMR sample composition 0.5 mM S5a U-15N, 2H 2.0 mM ubiquitin unlabeled | 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O
NMR sample composition 0.5 mM S5a U-15N, 2H 2.0 mM ubiquitin U-13C | 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O
NMR sample composition 0.5 mM S5a U-13C 2.0 mM ubiquitin unlabeled | 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O
Resolution not provided
1YX6 Solution Structure of S5a UIM-2/Ubiquitin Complex Deposited 2005-02-19 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：Sequence Database Residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1
NMR sample composition 0.5 mM S5a U-15N, 2H; 2.0 mM ubiquitin unlabeled | 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O
NMR sample composition 0.5 mM S5a U-15N, 2H; 2.0 mM ubiquitin U-13C | 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O
NMR sample composition 0.5 mM S5a U-13C; 2.0 mM ubiquitin unlabeled | 20 mM Phosphate buffer, 100 mM NaCl, 10% D2O
Resolution not provided
2AYO Structure of USP14 bound to ubquitin aldehyde Deposited 2005-09-07 Different mutation/modification Different oligomeric state Different 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）
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 experimental method 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 experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20；Pressure 1.0
NMR sample composition 90% WATER/10% D20
Resolution not provided
2FUH Solution Structure of the UbcH5c/Ub Non-covalent Complex Deposited 2006-01-26 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：Ubiquitin
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 150mM NaCl；Pressure ambient
NMR sample composition 1mM UbcH5c U-15N,13C 25mM sodium phosphate 150mM NaCl | 90% H20 10% D20
NMR sample composition 1mM Ubiquitin U-15N,13C 25mM sodium phosphate 150mM NaCl | 90% H20 10% D20
NMR sample composition 1mM UbcH5c U-15N,13C 1mM Ubiquitin 25mM sodium phosphate 150mM NaCl | 90% H20 10% D20
NMR sample composition 1mM Ubiquitin U-15N,13C 1mM UbcH5c 25mM sodium phosphate 150mM NaCl | 90% H20 10% D20
NMR sample composition 1mM UbcH5c U-15N,13C 1mM Ubiquitin 25mM sodium phosphate 150mM NaCl | 100% D20
NMR sample composition 1mM Ubiquitin U-15N,13C 1mM UbcH5c 25mM sodium phosphate 150mM NaCl | 100% D20
Resolution not provided
2G45 Co-crystal structure of znf ubp domain from the deubiquitinating enzyme isopeptidase T (isot) in complex with ubiquitin Deposited 2006-02-21 Different oligomeric state Different ligand/ion Different experimental 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 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；300 K；16% polyethylene glycol 8000, 80 mM sodium cacodylate pH 6.5, 160 mM magenesium or calcium acetate, 20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 6.50
Resolution 1.99 Å R-free 0.268
2G45 Co-crystal structure of znf ubp domain from the deubiquitinating enzyme isopeptidase T (isot) in complex with ubiquitin Deposited 2006-02-21 Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state 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 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 oligomeric state Different experimental method 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 oligomeric state 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 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 experimental method 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 experimental method 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 oligomeric state 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state 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 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded CD CADMIUM ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.9；293.15 K；24-30% PEG 4000, 50-80 mM Cadmium Chloride, 100 mM Sodium Acetate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.00 Å R-free 0.290
2HTH Structural basis for ubiquitin recognition by the human EAP45/ESCRT-II GLUE domain Deposited 2006-07-25 Different oligomeric state Different 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 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；10% PEG8000; 10% Ethylene glycol; 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.70 Å R-free 0.289
2IBI Covalent Ubiquitin-USP2 Complex Deposited 2006-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded ZN ZINC ION × 1 NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；298 K；22% PEG1500, 0.1 M Bicine, 0.2 M NaCl, 1 mM DTT, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 9.00
Resolution 2.20 Å R-free 0.259
2J7Q Crystal structure of the ubiquitin-specific protease encoded by murine cytomegalovirus tegument protein M48 in complex with a ubquitin-based suicide substrate Deposited 2006-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental 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 FUSED TO VINYLMETHYLESTER, UBVME, RESIDUES 1-75
Not recorded MG MAGNESIUM ION × 2 GVE METHYL 4-AMINOBUTANOATE × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；200 MM MAGNESIUM FORMATE, 14% PEG 3350, pH 7.50
Resolution 1.80 Å R-free 0.214
2J7Q Crystal structure of the ubiquitin-specific protease encoded by murine cytomegalovirus tegument protein M48 in complex with a ubquitin-based suicide substrate Deposited 2006-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method 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 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 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 oligomeric state Different experimental method Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions 270 K；Pressure ambient
NMR sample composition 5.5 mg/mL [U-99% 13C; U-98% 15N] Ubiquitin, 20 mM ammonium acetate, 20 mM citric acid, 60 v/v 2-methyl-2,4-pentandiol, 0.05 % sodium azide, 100 % H2O | 100 % H2O
Resolution not provided
2K6D CIN85 Sh3-C domain in complex with ubiquitin Deposited 2008-07-07 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa） Fragment：ubiquitin
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 0.150；Pressure ambient
NMR sample composition 0.1 mM CIN85, 0.1 mM [U-100% 15N] ubiquitin, 50 mM sodium phosphate, 2 mM DTT, 5 mM DSS, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.1 mM [U-100% 15N] CIN85, 0.1 mM ubiquitiny, 50 mM sodium phosphate, 2 mM DTT, 5 mM DSS, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] CIN85, 50 mM sodium phosphate, 2 mM DTT, 5 mM DSS, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2K8B Solution structure of PLAA family ubiquitin binding domain (PFUC) cis isomer in complex with ubiquitin Deposited 2008-09-04 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient
NMR sample composition 0.2 mM Ubiquitin, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.2 mM PFUC_cis, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2K8C Solution structure of PLAA family ubiquitin binding domain (PFUC) trans isomer in complex with ubiquitin Deposited 2008-09-04 Different oligomeric state Different experimental conditions 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 experimental conditions 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
2KJH NMR based structural model of the UBCH8-UBIQUITIN complex Deposited 2009-05-28 Different mutation/modification Different oligomeric state Different experimental conditions 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 oligomeric state Different experimental conditions 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 oligomeric state Different experimental conditions 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 oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions Pressure ambient
NMR sample composition [U-100% 13C; U-100% 15N] Ubiquitin-1, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2KTF Solution NMR structure of human polymerase iota UBM2 in complex with ubiquitin Deposited 2010-02-01 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；301 K；Ionic strength (raw mmCIF value) 0.08；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] protein, 3.5 mM peptide, 20 mM sodium phosphate, 30 mM sodium chloride, 0.001 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 2.5 mM protein, 0.5 mM [U-100% 13C; U-100% 15N] peptide, 20 mM sodium phosphate, 30 mM sodium chloride, 0.001 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2KWU Solution Structure of UBM2 of murine Polymerase iota in Complex with Ubiquitin Deposited 2010-04-19 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) 0.189；Pressure ambient
NMR sample composition 1-2 mM [U-99% 15N] DNA polymerase iota UBM2, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1-2 mM [U-95% 13C; U-99% 15N] DNA polymerase iota UBM2, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 4-8 mM DNA polymerase iota UBM2, 1-2 mM [U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 4-8 mM DNA polymerase iota UBM2, 1-2 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1.7 mM DNA polymerase iota UBM2, 6.8 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2KWV Solution Structure of UBM1 of murine Polymerase iota in Complex with Ubiquitin Deposited 2010-04-20 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) 0.189；Pressure ambient
NMR sample composition 1-2 mM [U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1-2 mM [U-95% 13C; U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1.0 mM DNA polymerase iota UBM1, 4 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2L0F Solution NMR structure of human polymerase iota UBM2 (P692A mutant) in complex with ubiquitin Deposited 2010-07-01 Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Mutation：P692A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.18；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] UBM2, 3 mM ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 5 mM UBM2, 1.5 mM [U-100% 13C; U-100% 15N] ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] UBM2, 3 mM ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 100% D2O | 100% D2O
NMR sample composition 5 mM UBM2, 1.5 mM [U-100% 13C; U-100% 15N] ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 100% D2O | 100% D2O
Resolution not provided
2L0T Solution structure of the complex of ubiquitin and the VHS domain of Stam2 Deposited 2010-07-15 Different oligomeric state Different experimental conditions 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 oligomeric state Different experimental conditions 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 method 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 method 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 method 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 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 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 experimental conditions 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 experimental conditions 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；22% PEG 3350 AND 200 MM ZNOAC, pH 7
Resolution 2.25 Å R-free 0.276
2WDT Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME Deposited 2009-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa） Fragment：RESIDUES 1-75
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；100 MM BIS-TRIS PH 5.5, 200 MM NACL, 25 % PEG 3350
Resolution 2.30 Å R-free 0.235
2WDT Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME Deposited 2009-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 method 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 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 ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；19-20 % PEG 3350, 0.2 M ZINC ACETATE, pH 7
Resolution 3.00 Å R-free 0.248
2Z59 Complex Structures of Mouse Rpn13 (22-130aa) and ubiquitin Deposited 2007-07-01 Different oligomeric state Different experimental conditions 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 method 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 method 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 experimental method 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 method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Mutation：P37A, P38A Mutation：P37A, P38A Mutation：P37A, P38A ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；293 K；0.2M Zinc Acetate dehydrate, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.60 Å R-free 0.224
3A33 UbcH5b~Ubiquitin Conjugate Deposited 2009-06-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；2.0M NaCl, 0.1M Potassium acetate, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.280
3BY4 Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin Deposited 2008-01-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded 3CN 3-AMINOPROPANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；Bis-Tris, Magnesium Chloride, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.55 Å R-free 0.211
3C0R Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin Deposited 2008-01-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded 3CN 3-AMINOPROPANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；277 K；MES, ammonium acetate, PEG3350, pH 6.5, hanging drop, temperature 277K
Resolution 2.31 Å R-free 0.243
3C0R Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin Deposited 2008-01-21 Different construct Different oligomeric state Different ligand/ion Different experimental method 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 experimental method 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 experimental method 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 experimental method 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 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 CD CADMIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 200mM cadmium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.300
3EEC X-ray structure of human ubiquitin Cd(II) adduct Deposited 2008-09-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Not recorded CD CADMIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 200mM cadmium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.300
3EEC X-ray structure of human ubiquitin Cd(II) adduct Deposited 2008-09-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Not recorded CD CADMIUM ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 200mM cadmium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.300
3EEC X-ray structure of human ubiquitin Cd(II) adduct Deposited 2008-09-04 Different oligomeric state Different ligand/ion Different experimental method 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 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 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 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 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 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）
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 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded ZN ZINC ION × 1 NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；13% PEG 3350, 0.1 M Bis-Tris, 0.1 M Ammonium sulfate, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.59 Å R-free 0.218
3I3T Crystal structure of covalent ubiquitin-USP21 complex Deposited 2009-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded ZN ZINC ION × 1 NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；13% PEG 3350, 0.1 M Bis-Tris, 0.1 M Ammonium sulfate, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.59 Å R-free 0.218
3I3T Crystal structure of covalent ubiquitin-USP21 complex Deposited 2009-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded ZN ZINC ION × 1 NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；13% PEG 3350, 0.1 M Bis-Tris, 0.1 M Ammonium sulfate, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.59 Å R-free 0.218
3I3T Crystal structure of covalent ubiquitin-USP21 complex Deposited 2009-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–75（75 aa）
Not recorded ZN ZINC ION × 1 NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；13% PEG 3350, 0.1 M Bis-Tris, 0.1 M Ammonium sulfate, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.59 Å R-free 0.218
3IFW Crystal structure of the S18Y variant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester. Deposited 2009-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；2.4 M ammonium sulfate, 0.1M BICINE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.40 Å R-free 0.256
3IHP Covalent Ubiquitin-Usp5 Complex Deposited 2009-07-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa）
Not recorded ZN ZINC ION × 1 NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；298 K；Crystals of the covalent ubiquitin complex of Usp5 were grown at 298 K using the hanging drop method by mixing equal volumes of protein solution (25 mg/ml) and Crystallization Buffer (1.45 M ammonium sulfate, 0.1 M bis-Tris, pH 6.5, 0.2 M sodium acetate, 5% ethyleneglycol and 1 mM dithiothreitol). The crystals were cryoprotected by immersion in Paratone N in paraffin oil 30% (v/v) and placed in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.80 Å R-free 0.276
3IHP Covalent Ubiquitin-Usp5 Complex Deposited 2009-07-30 Different construct Different oligomeric state Different ligand/ion Different experimental method 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 experimental method 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 experimental method 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 experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Y 1–76（76 aa）
Mutation：Ubiquitin G76 ester linked to UbcH5B S85 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, pH 5.1-5.2, 2.4-2.5 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.30 Å R-free 0.267
3JW0 E2~Ubiquitin-HECT Deposited 2009-09-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain X 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, 2.4M sodium chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.287
3JW0 E2~Ubiquitin-HECT Deposited 2009-09-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Y 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, 2.4M sodium chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.287
3K9P The crystal structure of E2-25K and ubiquitin complex Deposited 2009-10-16 Different oligomeric state Different 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 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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100mM HEPES-NaOH (pH 7.5), 25% (w/v) PEG 3350, 50mM Sodium Fluoride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.296
3KVF Crystal structure of the I93M mutant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester Deposited 2009-11-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.1M BICINE, 2.4M Ammonium Sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.284
3KW5 Crystal structure of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester Deposited 2009-11-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.1M BICINE, 2.4M Ammonium Sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.83 Å R-free 0.286
3LDZ Crystal structure of human STAM1 VHS domain in complex with ubiquitin Deposited 2010-01-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–73（73 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2M Na thiocyanate, 20% PEG3350, 0.1M imidazole pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.234
3LDZ Crystal structure of human STAM1 VHS domain in complex with ubiquitin Deposited 2010-01-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–73（73 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2M Na thiocyanate, 20% PEG3350, 0.1M imidazole pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.234
3LDZ Crystal structure of human STAM1 VHS domain in complex with ubiquitin Deposited 2010-01-13 Different construct Different oligomeric state Different experimental method 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Hepes pH 6.5, 10% (w/v) PEG 8000, 20% (v/v) Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.89 Å R-free 0.208
3MTN Usp21 in complex with a ubiquitin-based, USP21-specific inhibitor Deposited 2010-04-30 Different oligomeric state Different ligand/ion Different experimental 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 CL CHLORIDE ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；291 K；11% PEG 4000, 0.1 M SODIUM CITRATE, 0.1 M AMMONIUM ACETATE, 5 MM TCEP, PH 5.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
Resolution 2.70 Å R-free 0.273
3MTN Usp21 in complex with a ubiquitin-based, USP21-specific inhibitor Deposited 2010-04-30 Different oligomeric state Different ligand/ion Different experimental method 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 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 PT PLATINUM (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；30% PEG 1450, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.79 Å R-free 0.258
3N3K The catalytic domain of USP8 in complex with a USP8 specific inhibitor Deposited 2010-05-20 Different mutation/modification Different oligomeric state Different 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：Q2R, F4V, T9M, K11R, T14I, Q62H, K63N, E64H, T66A, H68Y, V70L, R72K ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；24% PEG3350, 0.1 M BIS-TRIS, 0.2 M AMMONIUM ACETATE, 1 MM DTT, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.242
3NHE High Resolution Structure (1.26A) of USP2a in Complex with Ubiquitin Deposited 2010-06-14 Different oligomeric state Different 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 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 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 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 method 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 method 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 method 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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

SAXS profile for 2khw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2khw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2khw
Deposition date deposition_date2009-04-13
Structure title titleSolution Structure of the human Polymerase iota UBM2-Ubiquitin Complex
Keywords keywords;UBM, ubiquitin-binding domain, polymerase iota, translesion synthesis, TLS, Cytoplasm, Nucleus, protein binding, transcription regulator activity, Transferase-protein binding COMPLEX ;; Transferase/protein binding
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.43 Å
Radius of gyration Rg (electron density) rg_electron14.09 Å
Forward intensity I(0) i01166680000.00
Molecular weight molecular_weight304100.0 kDa
Excluded volume excluded_volume386610 ų
Envelope volume envelope_volume22327 ų
Hydration-shell volume shell_volume12770 ų
Envelope diameter envelope_diameter54.5 Å
Shell Rg shell_rg20.69 Å
Envelope Rg envelope_rg15.71 Å
Shape Rg shape_rg14.06 Å
Total Rg total_rg14.27 Å
Total atoms total_atoms43575
Residues n_residues2650
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax46.5 Å
Rg (real space) rg_real14.40 Å
Rg uncertainty (real space) rg_real_error0.36 Å
I(0) (real space) i0_real1.1670e+09
I(0) uncertainty (real space) i0_real_error1.4200e+07
Rg (reciprocal space) rg_reciprocal14.40 Å
I(0) (reciprocal space) i0_reciprocal1167000000.0000
Solution quality estimate total_estimate0.7886
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.5 Å
Skewness Skewness skewness0.277
Kurtosis Kurtosis kurtosis-0.133
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha216700.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.751; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2khwb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related

CATH v4.4 (1 domains)

Domain ID domain_id2khwB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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8. Citations (1)

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9. Files and Curves (10)