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4a4b

Structure of modified phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex

Method: X-RAY DIFFRACTION Dmax: 91.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 UBIQUITIN-PROTEIN LIGASE CBL

HOMO SAPIENS

UniProt P22681

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 47–435 Fragment：TKB DOMAIN, LINKER HELIX REGION, AND RING DOMAIN, RESIDUES 47-435 Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) TYROSINE-PROTEIN KINASE ZAP-70 × 1 （P43403） UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；31-35% PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH), 0.2 M KCL, 50 MM HEPES, PH 7.5 Resolution 2.79 Å R-free 0.267

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 4A4B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B47 STRUCTURE OF THE N-TERMINAL DOMAIN OF CBL IN COMPLEX WITH ITS BINDING SITE IN ZAP-70 Deposited 1999-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 47–350（304 aa） Fragment：N-TERMINAL DOMAIN
Chain B 47–350（304 aa） Fragment：N-TERMINAL DOMAIN
Chain C 47–350（304 aa） Fragment：N-TERMINAL DOMAIN
Not recorded CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.6
Resolution 2.20 Å R-free 0.266
1FBV STRUCTURE OF A CBL-UBCH7 COMPLEX: RING DOMAIN FUNCTION IN UBIQUITIN-PROTEIN LIGASES Deposited 2000-07-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 47–434（388 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；Sodium Citrate, Ammonium Sulfate,, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.90 Å R-free 0.262
1YVH Crystal Structure of the c-Cbl TKB Domain in Complex with the APS pTyr-618 Phosphopeptide Deposited 2005-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–351（329 aa） Fragment：Tyrosine kinase binding domain, residues 25-351
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；277 K；PEG 8000, magnesium acetate, sodium cacodylate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.05 Å R-free 0.247
2CBL N-TERMINAL DOMAIN OF CBL IN COMPLEX WITH ITS BINDING SITE ON ZAP-70 Deposited 1998-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 47–351（305 aa） Fragment：DOMAIN
Not recorded CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.1；pH 6.1
Resolution 2.10 Å R-free 0.245
2JUJ Solution Structure of the UBA domain from c-Cbl Deposited 2007-08-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 851–906（56 aa） Fragment：UBA domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 20mM sodium phosphate, 50mM sodium chloride, 1mM DTT, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 20mM sodium phosphate, 50mM sodium chloride, 1mM DTT, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 20mM sodium phosphate, 50mM sodium chloride, 1mM DTT, 100% D2O | 100% D2O
Resolution not provided
2K4D E2-c-Cbl recognition is necessary but not sufficient for ubiquitination activity Deposited 2008-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 358–437（80 aa） Fragment：RING domain, residues 358-437
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.3；298 K；Ionic strength (raw mmCIF value) 150；Pressure ambient
NMR sample composition 1mM [U-99% 15N] c-Cbl; 50mM potassium phosphate; 100mM sodium chloride; 0.100mM zinc chloride; 0.2mM PMSF; 5mM DTT; 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1mM [U-99% 13C; U-99% 15N] c-Cbl; 50mM potassium phosphate; 100mM sodium chloride; 0.100mM zinc chloride; 0.2mM PMSF; 5mM DTT; 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2OO9 crystal structure of the UBA domain from human c-Cbl ubiquitin ligase Deposited 2007-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 856–895（40 aa） Fragment：UBA domain
Chain B 856–895（40 aa） Fragment：UBA domain
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 8.5；293 K；3.8M sodium formate, 0.1M Tris, 4% (v/v) glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.260
2OO9 crystal structure of the UBA domain from human c-Cbl ubiquitin ligase Deposited 2007-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 856–895（40 aa） Fragment：UBA domain
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；3.8M sodium formate, 0.1M Tris, 4% (v/v) glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.260
2Y1M Structure of native c-Cbl Deposited 2010-12-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 47–435（389 aa） Fragment：RESIDUES 47-435
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；0.1 M TRIS-HCL, PH 9.0-9.5, 3.7-4.0 M SODIUM FORMATE, 5 MM DTT
Resolution 2.67 Å R-free 0.263
2Y1M Structure of native c-Cbl Deposited 2010-12-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 47–435（389 aa） Fragment：RESIDUES 47-435
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；0.1 M TRIS-HCL, PH 9.0-9.5, 3.7-4.0 M SODIUM FORMATE, 5 MM DTT
Resolution 2.67 Å R-free 0.263
2Y1M Structure of native c-Cbl Deposited 2010-12-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 47–435（389 aa） Fragment：RESIDUES 47-435
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；0.1 M TRIS-HCL, PH 9.0-9.5, 3.7-4.0 M SODIUM FORMATE, 5 MM DTT
Resolution 2.67 Å R-free 0.263
2Y1M Structure of native c-Cbl Deposited 2010-12-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 47–435（389 aa） Fragment：RESIDUES 47-435
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；0.1 M TRIS-HCL, PH 9.0-9.5, 3.7-4.0 M SODIUM FORMATE, 5 MM DTT
Resolution 2.67 Å R-free 0.263
2Y1M Structure of native c-Cbl Deposited 2010-12-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 47–435（389 aa） Fragment：RESIDUES 47-435
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；0.1 M TRIS-HCL, PH 9.0-9.5, 3.7-4.0 M SODIUM FORMATE, 5 MM DTT
Resolution 2.67 Å R-free 0.263
2Y1M Structure of native c-Cbl Deposited 2010-12-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 47–435（389 aa） Fragment：RESIDUES 47-435
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；0.1 M TRIS-HCL, PH 9.0-9.5, 3.7-4.0 M SODIUM FORMATE, 5 MM DTT
Resolution 2.67 Å R-free 0.263
2Y1N Structure of c-Cbl-ZAP-70 peptide complex Deposited 2010-12-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 47–435（389 aa） Fragment：RESIDUES 47-435
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 18-20% (W/V) PEG 3350, 0.2 M AMMONIUM FORMATE
Resolution 2.00 Å R-free 0.180
2Y1N Structure of c-Cbl-ZAP-70 peptide complex Deposited 2010-12-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 47–435（389 aa） Fragment：RESIDUES 47-435
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 18-20% (W/V) PEG 3350, 0.2 M AMMONIUM FORMATE
Resolution 2.00 Å R-free 0.180
3BUM Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Sprouty2 Deposited 2008-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 25–351（327 aa） Fragment：c-Cbl TKB domain, UNP residues 25-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；ammonium sulfate, PEG3350, pH7.5, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.00 Å R-free 0.263
3BUM Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Sprouty2 Deposited 2008-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 25–351（327 aa） Fragment：c-Cbl TKB domain, UNP residues 25-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；ammonium sulfate, PEG3350, pH7.5, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.00 Å R-free 0.263
3BUN Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Sprouty4 Deposited 2008-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 23–351（329 aa） Fragment：c-Cbl TKB domain, CBL N-terminal, UNP residues 23-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2M NA/K TARTRATE, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.242
3BUN Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Sprouty4 Deposited 2008-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–351（329 aa） Fragment：c-Cbl TKB domain, CBL N-terminal, UNP residues 23-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2M NA/K TARTRATE, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.242
3BUO Crystal structure of c-Cbl-TKB domain complexed with its binding motif in EGF receptor' Deposited 2008-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–351（329 aa） Fragment：c-Cbl TKB domain, CBL N-terminal, UNP residues 23-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.25M Na formate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.278
3BUO Crystal structure of c-Cbl-TKB domain complexed with its binding motif in EGF receptor' Deposited 2008-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 23–351（329 aa） Fragment：c-Cbl TKB domain, CBL N-terminal, UNP residues 23-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.25M Na formate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.278
3BUW Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Syk Deposited 2008-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 23–351（329 aa） Fragment：c-Cbl TKB domain, CBL N-terminal, UNP residues 23-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.12M ammonium acetate, 18% PEG 3350, pH 6.5, vapor diffusion, hanging drop, temperature 298K
Resolution 1.45 Å R-free 0.238
3BUW Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Syk Deposited 2008-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 23–351（329 aa） Fragment：c-Cbl TKB domain, CBL N-terminal, UNP residues 23-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.12M ammonium acetate, 18% PEG 3350, pH 6.5, vapor diffusion, hanging drop, temperature 298K
Resolution 1.45 Å R-free 0.238
3BUW Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Syk Deposited 2008-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–351（329 aa） Fragment：c-Cbl TKB domain, CBL N-terminal, UNP residues 23-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.12M ammonium acetate, 18% PEG 3350, pH 6.5, vapor diffusion, hanging drop, temperature 298K
Resolution 1.45 Å R-free 0.238
3BUW Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Syk Deposited 2008-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 23–351（329 aa） Fragment：c-Cbl TKB domain, CBL N-terminal, UNP residues 23-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.12M ammonium acetate, 18% PEG 3350, pH 6.5, vapor diffusion, hanging drop, temperature 298K
Resolution 1.45 Å R-free 0.238
3BUX Crystal structure of c-Cbl-TKB domain complexed with its binding motif in c-Met Deposited 2008-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 23–351（329 aa） Fragment：c-Cbl TKB domain, CBL N-terminal, UNP residues 23-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.15M malic acid, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.35 Å R-free 0.240
3BUX Crystal structure of c-Cbl-TKB domain complexed with its binding motif in c-Met Deposited 2008-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 23–351（329 aa） Fragment：c-Cbl TKB domain, CBL N-terminal, UNP residues 23-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.15M malic acid, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.35 Å R-free 0.240
3BUX Crystal structure of c-Cbl-TKB domain complexed with its binding motif in c-Met Deposited 2008-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–351（329 aa） Fragment：c-Cbl TKB domain, CBL N-terminal, UNP residues 23-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.15M malic acid, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.35 Å R-free 0.240
3BUX Crystal structure of c-Cbl-TKB domain complexed with its binding motif in c-Met Deposited 2008-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 23–351（329 aa） Fragment：c-Cbl TKB domain, CBL N-terminal, UNP residues 23-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.15M malic acid, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.35 Å R-free 0.240
3OB1 Crystal structure of c-Cbl TKB domain in complex with double phosphorylated Spry2 peptide Deposited 2010-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 25–351（327 aa） Fragment：c-Cbl TKB domain, residues 25-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；20% PEG 3350, 0.2M K/Na tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.223
3OB2 Crystal structure of c-Cbl TKB domain in complex with double phosphorylated EGFR peptide Deposited 2010-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 25–351（327 aa） Fragment：c-Cbl TKB domain, residues 25-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；20% (w/v) PEG 3350, 150mM NaK tartrate, 0.1 M Bis-Tris propane pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.217
3PLF Reverse Binding Mode of MetRD peptide complexed with c-Cbl TKB domain Deposited 2010-11-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 25–351（327 aa） Fragment：TKB domain
Not recorded CA CALCIUM ION × 1 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；298 K；100mM Bis-tris propane, 50mM ammonium sulfate, pH 6.5, hanging drop, temperature 298K
Resolution 1.92 Å R-free 0.180
3PLF Reverse Binding Mode of MetRD peptide complexed with c-Cbl TKB domain Deposited 2010-11-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 25–351（327 aa） Fragment：TKB domain
Not recorded CA CALCIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；298 K；100mM Bis-tris propane, 50mM ammonium sulfate, pH 6.5, hanging drop, temperature 298K
Resolution 1.92 Å R-free 0.180
4A49 Structure of phosphoTyr371-c-Cbl-UbcH5B complex Deposited 2011-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 354–435（82 aa） Fragment：C-CBL RESIDUES 354-435
Mutation：Y368F Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 291 K；20% (W/V) PEG 3350 AND 0.2 M POTASSIUM THIOCYANATE AT 18 DEGREES CELSIUS.
Resolution 2.21 Å R-free 0.205
4A4C Structure of phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex Deposited 2011-10-08 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 47–435（389 aa） Fragment：TKB DOMAIN, LINKER HELIX REGION, AND RING DOMAIN, RESIDUES 47-435
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；50 MM HEPES, PH 7.5, 0.2 M KCL AND 31-35% (V/V) PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH) AT 4 DEGREES CELSIUS.
Resolution 2.70 Å R-free 0.268
4GPL Structure of Cbl(TKB) bound to a phosphorylated pentapeptide Deposited 2012-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 47–351（305 aa） Fragment：human Cbl TKB domain residues 47-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.25M potassium sodium tartrate tetrahydrate, 20% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.248
4GPL Structure of Cbl(TKB) bound to a phosphorylated pentapeptide Deposited 2012-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 47–351（305 aa） Fragment：human Cbl TKB domain residues 47-351
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.25M potassium sodium tartrate tetrahydrate, 20% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.248
5HKW Crystal Structure of Apo c-Cbl TKBD Refined to 2.25 A Resolution Deposited 2016-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 47–351（305 aa） Fragment：Tyrosine kinase binding domain (TKBD), residues 47-351
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG 3350, 0.2M sodium citrate dibasic trihyrate
Resolution 2.25 Å R-free 0.234
5HKW Crystal Structure of Apo c-Cbl TKBD Refined to 2.25 A Resolution Deposited 2016-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 47–351（305 aa） Fragment：Tyrosine kinase binding domain (TKBD), residues 47-351
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG 3350, 0.2M sodium citrate dibasic trihyrate
Resolution 2.25 Å R-free 0.234
5HKW Crystal Structure of Apo c-Cbl TKBD Refined to 2.25 A Resolution Deposited 2016-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 47–351（305 aa） Fragment：Tyrosine kinase binding domain (TKBD), residues 47-351
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG 3350, 0.2M sodium citrate dibasic trihyrate
Resolution 2.25 Å R-free 0.234
5HKX Crystal Structure of c-Cbl TKBD-RING domains (Y371E mutant) Refined to 1.85 A Resolution Deposited 2016-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 47–435（389 aa） Fragment：Tyrosine kinase binding and RING domains (TKBD-RING), residues 47-435
Mutation：Y371E EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% (w/v) PEG 5000 MME, 0.1M MES, 12% (v/v) 1-propanol
Resolution 1.85 Å R-free 0.214
5HKY Crystal structure of c-Cbl TKBD domain in complex with SPRY2 peptide (36-60, pY55) Refined to 1.8A Resolution (P6 form) Deposited 2016-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 47–351（305 aa） Fragment：Tyrosine kinase binding domain (TKBD), residues 47-351
Not recorded CL CHLORIDE ION × 2 NA SODIUM ION × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；30% (v/v) PEG 400, 0.1M HEPES, 200 mM MgCl2
Resolution 1.80 Å R-free 0.180
5HKZ Crystal Structure of c-Cbl TKBD in complex with SPRY2 peptide (36-60, pY55) Refined to 1.8 A Resolution (P21 form) Deposited 2016-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 47–351（305 aa） Fragment：Tyrosine kinase binding domain (TKBD), residues 47-351
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% (w/v) PEG 2000 MME, 0.1M HEPES
Resolution 1.80 Å R-free 0.213
5HL0 Crystal Structure of c-Cbl TKBD in complex with SPRY2 peptide (54-60, pY55) Refined to 2.2A Resolution Deposited 2016-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 47–351（305 aa）
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；16% (w/v) PEG 8000, 0.04M Potassium phosphate (monobasic), 20% (v/v) glycerol
Resolution 2.20 Å R-free 0.237
5J3X Structure of c-CBL Y371F Deposited 2016-03-31 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 47–435（389 aa） Fragment：UNP residues 47-435
Mutation：Y371F ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；281.15 K；Equal volume protein at 10 mg/mL + well containing 3.0-3.1 M sodium formate 0.1 M Tris-HCl, pH 8.5 5 mM DTT
Resolution 2.82 Å R-free 0.254
5J3X Structure of c-CBL Y371F Deposited 2016-03-31 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 47–435（389 aa） Fragment：UNP residues 47-435
Mutation：Y371F ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；281.15 K；Equal volume protein at 10 mg/mL + well containing 3.0-3.1 M sodium formate 0.1 M Tris-HCl, pH 8.5 5 mM DTT
Resolution 2.82 Å R-free 0.254
5J3X Structure of c-CBL Y371F Deposited 2016-03-31 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 47–435（389 aa） Fragment：UNP residues 47-435
Mutation：Y371F ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；281.15 K；Equal volume protein at 10 mg/mL + well containing 3.0-3.1 M sodium formate 0.1 M Tris-HCl, pH 8.5 5 mM DTT
Resolution 2.82 Å R-free 0.254
5J3X Structure of c-CBL Y371F Deposited 2016-03-31 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 47–435（389 aa） Fragment：UNP residues 47-435
Mutation：Y371F ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；281.15 K；Equal volume protein at 10 mg/mL + well containing 3.0-3.1 M sodium formate 0.1 M Tris-HCl, pH 8.5 5 mM DTT
Resolution 2.82 Å R-free 0.254
5J3X Structure of c-CBL Y371F Deposited 2016-03-31 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 47–435（389 aa） Fragment：UNP residues 47-435
Mutation：Y371F ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；281.15 K；Equal volume protein at 10 mg/mL + well containing 3.0-3.1 M sodium formate 0.1 M Tris-HCl, pH 8.5 5 mM DTT
Resolution 2.82 Å R-free 0.254
5J3X Structure of c-CBL Y371F Deposited 2016-03-31 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 47–435（389 aa） Fragment：UNP residues 47-435
Mutation：Y371F ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；281.15 K；Equal volume protein at 10 mg/mL + well containing 3.0-3.1 M sodium formate 0.1 M Tris-HCl, pH 8.5 5 mM DTT
Resolution 2.82 Å R-free 0.254
5O76 Structure of phosphoY371 c-CBL in complex with ZAP70-peptide and UbV.pCBL ubiquitin variant Deposited 2017-06-08 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 47–435（389 aa）
Mutation：Y368F Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M monosaccharides, 0.1 M Buffer 1 pH 6.5, 50% Precipitant 2, Morpheus screen
Resolution 2.47 Å R-free 0.248
5O76 Structure of phosphoY371 c-CBL in complex with ZAP70-peptide and UbV.pCBL ubiquitin variant Deposited 2017-06-08 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 47–435（389 aa）
Mutation：Y368F Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M monosaccharides, 0.1 M Buffer 1 pH 6.5, 50% Precipitant 2, Morpheus screen
Resolution 2.47 Å R-free 0.248
6O02 Monobody (MC3) bound to tyrosine kinase binding domain of E3 ubiquitin ligase CBL Deposited 2019-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 47–353（307 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.12M Alcohols, 0.1M Buffer system 3 at PH 8.5 and 50% v/v Precipitant mix 2
Resolution 2.95 Å R-free 0.258
6O03 Monobody (MC17) bound to tyrosine kinase binding domain of E3 ubiquitin ligase CBL Deposited 2019-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 47–353（307 aa）
Mutation：G306E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (w/v) PEG 3000, 100mM tris base/hydrochloric acid pH 7, 200mM calcium acetate
Resolution 3.30 Å R-free 0.330
6O03 Monobody (MC17) bound to tyrosine kinase binding domain of E3 ubiquitin ligase CBL Deposited 2019-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 47–353（307 aa）
Mutation：G306E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (w/v) PEG 3000, 100mM tris base/hydrochloric acid pH 7, 200mM calcium acetate
Resolution 3.30 Å R-free 0.330
6XAR Structure of CBL tyrosine kinase binding domain (TKBD) with C-terminal tail of Src-like kinase protein 2 (SLAP2) Deposited 2020-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 25–357（333 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；CBL/SLAP2 complex mixed in hanging drop with equal volume (200 nL) of 0.1 M Hepes pH 7.5, 10% (w/v) PEG8000
Resolution 2.50 Å R-free 0.293
6XAR Structure of CBL tyrosine kinase binding domain (TKBD) with C-terminal tail of Src-like kinase protein 2 (SLAP2) Deposited 2020-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 25–357（333 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；CBL/SLAP2 complex mixed in hanging drop with equal volume (200 nL) of 0.1 M Hepes pH 7.5, 10% (w/v) PEG8000
Resolution 2.50 Å R-free 0.293
7SIY cCBL TKB domain in complex with pZAP70 peptide Deposited 2021-10-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 48–351（304 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Ammonium formate, 20% PEG3350
Resolution 1.48 Å R-free 0.221
9ERZ Structure of CBL-TKBD bound to Ubiquitin-fused CBLock peptide Deposited 2024-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 47–355（309 aa）
Chain C 47–355（309 aa）
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Bis-Tris Propane, pH 6.0, 0.2 M sodium fluoride, and 20% (v/v) PEG 3350
Resolution 2.02 Å R-free 0.229

32 other PDB entries and 60 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CBL_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–391； UniProt 47–435

TYROSINE-PROTEIN KINASE ZAP-70

OrganismNot specified

UniProt P43403

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 286–297 Fragment：ZAP-70 PEPTIDE, RESIDUES 286-297 Non-standard monomer：Yes (specific site not provided by mmCIF) E3 UBIQUITIN-PROTEIN LIGASE CBL × 1 （P22681） UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；31-35% PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH), 0.2 M KCL, 50 MM HEPES, PH 7.5 Resolution 2.79 Å R-free 0.267

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 4A4B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1M61 Crystal structure of the apo SH2 domains of ZAP-70 Deposited 2002-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–256（256 aa） Fragment：tandem SH2 domains (Residues 1-256)
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG3350, Sodium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.286
1U59 Crystal Structure of the ZAP-70 Kinase Domain in Complex with Staurosporine Deposited 2004-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 327–606（280 aa） Fragment：kinase domain
Not recorded STU STAUROSPORINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 3350, DL-malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.271
2OQ1 Tandem SH2 domains of ZAP-70 with 19-mer zeta1 peptide Deposited 2007-01-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 3–256（254 aa） Fragment：residues 3-256
Non-standard monomer：Yes (specific site not provided by mmCIF) PB LEAD (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；298 K；20%PEG 4000, 50mM sodium citrate,100 mM ammonium acetate, 20mM DTT, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.90 Å R-free 0.255
2OZO Autoinhibited intact human ZAP-70 Deposited 2007-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–606（606 aa） Fragment：Inactive ZAP-70 (residues 1-606)
Mutation：Y315F,Y319F,D461N MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.05 M NaSCN, 21% PEG3350, protein mixed with 9 mM n-decyl-beta-D-thiomaltopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.290
2Y1N Structure of c-Cbl-ZAP-70 peptide complex Deposited 2010-12-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 286–297（12 aa） Fragment：PEPTIDE, RESIDUES 286-297
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 18-20% (W/V) PEG 3350, 0.2 M AMMONIUM FORMATE
Resolution 2.00 Å R-free 0.180
2Y1N Structure of c-Cbl-ZAP-70 peptide complex Deposited 2010-12-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 286–297（12 aa） Fragment：PEPTIDE, RESIDUES 286-297
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 18-20% (W/V) PEG 3350, 0.2 M AMMONIUM FORMATE
Resolution 2.00 Å R-free 0.180
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 286–297（12 aa） Fragment：RESIDUES 286-297
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 286–297（12 aa） Fragment：RESIDUES 286-297
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 286–297（12 aa） Fragment：RESIDUES 286-297
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain N 286–297（12 aa） Fragment：RESIDUES 286-297
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
4A4C Structure of phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex Deposited 2011-10-08 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 286–297（12 aa） Fragment：ZAP-70 PEPTIDE, RESIDUES 286-297
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；50 MM HEPES, PH 7.5, 0.2 M KCL AND 31-35% (V/V) PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH) AT 4 DEGREES CELSIUS.
Resolution 2.70 Å R-free 0.268
4K2R Structural basis for activation of ZAP-70 by phosphorylation of the SH2-kinase linker Deposited 2013-04-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–606（606 aa）
Mutation：D461N MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1 M Bis-Tris pH 6.5, 20% Polyethylene glycol monomethyl ether 5,000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.00 Å R-free 0.287
4XZ0 ZAP-70-tSH2:compound-A complex Deposited 2015-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–259（259 aa）
Not recorded 4N5 1-(3-{5-[(3-chlorobenzyl)sulfonyl]-1H-tetrazol-1-yl}phenyl)ethanone × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG 3350, ammonium sulfate, TCEP
Resolution 2.00 Å R-free 0.245
4XZ1 ZAP-70-tSH2:Compound-B adduct Deposited 2015-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–259（259 aa）
Not recorded 4N6 2-[(7-chloro-4-nitro-2,1,3-benzoxadiazol-5-yl)amino]ethanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 6000, calcium chloride, MES, TCEP
Resolution 2.80 Å R-free 0.270
7SIY cCBL TKB domain in complex with pZAP70 peptide Deposited 2021-10-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Z 292–296（5 aa） Fragment：Residues 292-296
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Ammonium formate, 20% PEG3350
Resolution 1.48 Å R-free 0.221

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

View Construct and Data Evidence
UniProt name ZAP70_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–12； UniProt 286–297

UBIQUITIN-CONJUGATING ENZYME E2 D2

HOMO SAPIENS

UniProt P62837

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 1–147 Not recorded E3 UBIQUITIN-PROTEIN LIGASE CBL × 1 （P22681） TYROSINE-PROTEIN KINASE ZAP-70 × 1 （P43403） ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；31-35% PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH), 0.2 M KCL, 50 MM HEPES, PH 7.5 Resolution 2.79 Å R-free 0.267

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 4A4B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2CLW Crystal structure of human ubiquitin-conjugating enzyme UbcH5B Deposited 2006-05-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–147（147 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；150 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME 2000
Resolution 1.95 Å R-free 0.255
2CLW Crystal structure of human ubiquitin-conjugating enzyme UbcH5B Deposited 2006-05-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；150 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME 2000
Resolution 1.95 Å R-free 0.255
2CLW Crystal structure of human ubiquitin-conjugating enzyme UbcH5B Deposited 2006-05-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；150 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME 2000
Resolution 1.95 Å R-free 0.255
2CLW Crystal structure of human ubiquitin-conjugating enzyme UbcH5B Deposited 2006-05-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–147（147 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；150 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME 2000
Resolution 1.95 Å R-free 0.255
2ESK Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type Deposited 2005-10-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；294 K；NaCl, PEG 6000, Sodium Acetate, temperature 294K, pH 4.5, VAPOR DIFFUSION, HANGING DROP
Resolution 1.36 Å R-free 0.224
2ESO Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala Deposited 2005-10-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–147（147 aa）
Mutation：I37A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；294 K；NaCl, PEG 6000, Sodium Acetate, temperature 294K, pH 4.5, VAPOR DIFFUSION, HANGING DROP
Resolution 1.50 Å R-free 0.219
2ESP Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala Deposited 2005-10-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–147（147 aa）
Mutation：I88A CL CHLORIDE ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；294 K；NaCl, PEG 6000, Sodium Acetate, temperature 294K, pH 4.5, VAPOR DIFFUSION, HANGING DROP
Resolution 1.52 Å R-free 0.233
2ESQ Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly Deposited 2005-10-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–147（147 aa）
Mutation：S94G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；294 K；NaCl, PEG 6000, Sodium Acetate, temperature 294K, pH 4.5, VAPOR DIFFUSION, HANGING DROP
Resolution 1.44 Å R-free 0.205
3A33 UbcH5b~Ubiquitin Conjugate Deposited 2009-06-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–147（147 aa）
Mutation：C85S 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
3JVZ E2~Ubiquitin-HECT Deposited 2009-09-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–147（146 aa）
Mutation：L3S, C85S, T98K 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 construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–147（146 aa）
Mutation：L3S, C85S, T98K 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 construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–147（146 aa）
Mutation：L3S, C85S, T98K 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 construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–147（146 aa）
Mutation：L3S, C85S, T98K 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
3L1Y Crystal structure of human UBC4 E2 conjugating enzyme Deposited 2009-12-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–147（147 aa） Fragment：residues 1-147
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；2M sodium formate, 0.1M sodium acetate trihydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.60 Å R-free 0.229
3TGD Crystal structure of the human ubiquitin-conjugating enzyme (E2) UbcH5b Deposited 2011-08-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.8M potassium phosphate, 0.8M sodium phosphate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.80 Å R-free 0.203
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 2–147（146 aa） Fragment：RESIDUES 2-147
Mutation：YES ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 2–147（146 aa） Fragment：RESIDUES 2-147
Mutation：YES ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain K 2–147（146 aa） Fragment：RESIDUES 2-147
Mutation：YES ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain O 2–147（146 aa） Fragment：RESIDUES 2-147
Mutation：YES ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
4A49 Structure of phosphoTyr371-c-Cbl-UbcH5B complex Deposited 2011-10-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–147（147 aa）
Not recorded ZN ZINC ION × 2 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 291 K；20% (W/V) PEG 3350 AND 0.2 M POTASSIUM THIOCYANATE AT 18 DEGREES CELSIUS.
Resolution 2.21 Å R-free 0.205
4A4C Structure of phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex Deposited 2011-10-08 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–147（147 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；50 MM HEPES, PH 7.5, 0.2 M KCL AND 31-35% (V/V) PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH) AT 4 DEGREES CELSIUS.
Resolution 2.70 Å R-free 0.268
4AUQ Structure of BIRC7-UbcH5b-Ub complex. Deposited 2012-05-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–147（147 aa） Fragment：UBCH5B, RESIDUES 1-147
Chain D 1–147（147 aa） Fragment：UBCH5B, RESIDUES 1-147
Mutation：YES Mutation：YES ZN ZINC ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.18 Å R-free 0.249
4DDG Crystal structure of human OTUB1/UbcH5b~Ub/Ub Deposited 2012-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–147（147 aa）
Chain B 1–147（147 aa）
Chain C 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG1500, 0.1 M SPG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.30 Å R-free 0.280
4DDG Crystal structure of human OTUB1/UbcH5b~Ub/Ub Deposited 2012-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain J 1–147（147 aa）
Chain K 1–147（147 aa）
Chain L 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG1500, 0.1 M SPG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.30 Å R-free 0.280
4DDI Crystal structure of human OTUB1/UbcH5b~Ub/Ub Deposited 2012-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–147（147 aa）
Chain B 1–147（147 aa）
Chain C 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；25% PEG1500, 0.1 M SPG, pH 8.0, VAPOR DIFFUSION, temperature 293K
Resolution 3.80 Å R-free 0.273
4LDT The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub Deposited 2013-06-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–147（147 aa）
Mutation：C85S EDO 1,2-ETHANEDIOL × 4 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；1:1 mix of 12 mg/mL purified complex and well solution (100 mM Bis-Tris, pH 6.0, 200 mM magnesium chloride, 22% PEG3350), crystals appeared in about 2 to 3 days, cryoprotection with well solution + 10% ethylene glycol, flash frozen in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 1.90 Å R-free 0.223
4V3K RNF38-UbcH5B-UB complex Deposited 2014-10-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 2–147（146 aa） Fragment：RESIDUES 2-147
Mutation：YES CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 50 MM TRIS-HCL, PH 8.5 AND 2.3 M AMMONIUM SULFATE
Resolution 2.04 Å R-free 0.223
4V3K RNF38-UbcH5B-UB complex Deposited 2014-10-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–147（146 aa） Fragment：RESIDUES 2-147
Mutation：YES CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 50 MM TRIS-HCL, PH 8.5 AND 2.3 M AMMONIUM SULFATE
Resolution 2.04 Å R-free 0.223
4V3L RNF38-UB-UbcH5B-Ub complex Deposited 2014-10-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–147（146 aa） Fragment：RESIDUES 2-147
Mutation：YES EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 50 MM HEPES, PH 7.5, 0.2 M MAGNESIUM ACETATE AND 13% (W/V) PEG 8K
Resolution 1.53 Å R-free 0.193
4WZ3 Crystal structure of the complex between LubX/LegU2/Lpp2887 U-box 1 and Homo sapiens UBE2D2 Deposited 2014-11-18 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Mutation：C85S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；15 mg/ml of E2D2.(C85S)-Ub conjugate and an equimolar concentration of LubX (1-186), 0.2 M sodium tartrate, 0.1 M Tris-Cl (pH 8.5) and 25% PEG3350
Resolution 2.70 Å R-free 0.223
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–147（147 aa）
Mutation：C21S, C85K, C107S, C111S ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–147（147 aa）
Mutation：C21S, C85K, C107S, C111S ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–147（147 aa）
Mutation：C21S, C85K, C107S, C111S ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–147（147 aa）
Mutation：C21S, C85K, C107S, C111S ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0M Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–147（147 aa）
Mutation：C21S, S22R, C85K, C107S, C111S PO4 PHOSPHATE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；SPG buffer, PEG 1500
Resolution 1.91 Å R-free 0.213
5D1K Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 Deposited 2015-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 OXL OXALATE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；20% PEG-10000, 8% ethylene glycol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.78 Å R-free 0.202
5D1L Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (Y165A) Deposited 2015-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 OXL OXALATE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；15% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.62 Å R-free 0.200
5D1M Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A) Deposited 2015-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Not recorded OXL OXALATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；20% PEG 10000, 8% Ethylene glycol, 0.1M HEPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.58 Å R-free 0.223
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 2–147（146 aa）
Mutation：S22R, C85K ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 2–147（146 aa）
Chain D 2–147（146 aa）
Mutation：S22R, C85K Mutation：S22R, C85K ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 2–147（146 aa）
Mutation：S22R, C85K ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain I 2–147（146 aa）
Mutation：S22R, C85K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5MNJ Structure of MDM2-MDMX-UbcH5B-ubiquitin complex Deposited 2016-12-13 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–147（147 aa）
Mutation：S22R, C85K ZN ZINC ION × 4 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Tris-HCl, pH 8.5, 0.175 M Li2SO4 and 16-20 %(v/v) PEG 3350
Resolution 2.16 Å R-free 0.231
5MNJ Structure of MDM2-MDMX-UbcH5B-ubiquitin complex Deposited 2016-12-13 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–147（147 aa）
Mutation：S22R, C85K ZN ZINC ION × 4 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Tris-HCl, pH 8.5, 0.175 M Li2SO4 and 16-20 %(v/v) PEG 3350
Resolution 2.16 Å R-free 0.231
5ULF Crystal Structure of a UbcH5b~Ub conjugate Deposited 2017-01-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Mutation：C21S, S22R, C85K, C107S, C111S GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；100 mM bis-Tris pH 5.5, 150 mM ammonium sulfate, 20% PEG 3350
Resolution 1.80 Å R-free 0.261
5ULF Crystal Structure of a UbcH5b~Ub conjugate Deposited 2017-01-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–147（147 aa）
Mutation：C21S, S22R, C85K, C107S, C111S GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；100 mM bis-Tris pH 5.5, 150 mM ammonium sulfate, 20% PEG 3350
Resolution 1.80 Å R-free 0.261
5ULH Structure of RNF165 in complex with a UbcH5b~Ub conjugate Deposited 2017-01-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–147（147 aa）
Mutation：C21S, C85K, C107S, C111S GOL GLYCEROL × 2 SCN THIOCYANATE ION × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；200 mM potassium thiocyanate, 20% PEG 3350
Resolution 1.95 Å R-free 0.217
5ULK Crystal Structure of RNF165 in complex with a UbcH5b~Ub conjugate Deposited 2017-01-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–147（147 aa）
Mutation：C21S, C85K, C107S, C111S ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；200 mM ammonium nitrate, 20% PEG 3350
Resolution 2.38 Å R-free 0.267
5VZW TRIM23 RING domain in complex with UbcH5-Ub Deposited 2017-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–147（147 aa）
Chain B 1–147（147 aa）
Mutation：S22R,C85K Mutation：S22R,C85K ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；0.1 M Bis-Tris, pH 5.5, 0.2 M calcium chloride, 17% w/v PEG3350
Resolution 2.28 Å R-free 0.237
5ZBU Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub Deposited 2018-02-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–147（147 aa）
Mutation：C85K ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES monohydrate, 14% PEG 4000
Resolution 3.20 Å R-free 0.262
5ZBU Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub Deposited 2018-02-12 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–147（147 aa）
Mutation：C85K ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES monohydrate, 14% PEG 4000
Resolution 3.20 Å R-free 0.262
6HPR Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub Deposited 2018-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–147（147 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M ammonium fluoride and 15% (w/v) PEG 3350
Resolution 1.70 Å R-free 0.197
6M2C Distinct mechanism of MUL1-RING domain simultaneously recruiting E2 enzyme and the substrate p53-TAD domain Deposited 2020-02-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；4% v/v Tacsimate pH 6.0, 12% w/v Polyethylene glycol 3350
Resolution 2.70 Å R-free 0.258
6M2C Distinct mechanism of MUL1-RING domain simultaneously recruiting E2 enzyme and the substrate p53-TAD domain Deposited 2020-02-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–147（147 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；4% v/v Tacsimate pH 6.0, 12% w/v Polyethylene glycol 3350
Resolution 2.70 Å R-free 0.258
6M2C Distinct mechanism of MUL1-RING domain simultaneously recruiting E2 enzyme and the substrate p53-TAD domain Deposited 2020-02-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–147（147 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；4% v/v Tacsimate pH 6.0, 12% w/v Polyethylene glycol 3350
Resolution 2.70 Å R-free 0.258
6M2C Distinct mechanism of MUL1-RING domain simultaneously recruiting E2 enzyme and the substrate p53-TAD domain Deposited 2020-02-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–147（147 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；4% v/v Tacsimate pH 6.0, 12% w/v Polyethylene glycol 3350
Resolution 2.70 Å R-free 0.258
6SQO Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2019-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 2–147（146 aa）
Chain E 2–147（146 aa）
Mutation：S22R, C85K Mutation：S22R, C85K ZN ZINC ION × 4 CL CHLORIDE ION × 4 NO3 NITRATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；292 K；0.1 M SPG, pH 7.0, 10% (w/v) PEG Smear Broad, 0.15 M NH4NO3
Resolution 1.41 Å R-free 0.173
6SQR Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub Deposited 2019-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 2–147（146 aa）
Chain E 2–147（146 aa）
Chain H 2–147（146 aa）
Chain K 2–147（146 aa）
Mutation：S22R, C85K Mutation：S22R, C85K Mutation：S22R, C85K Mutation：S22R, C85K EDO 1,2-ETHANEDIOL × 12 ZN ZINC ION × 8 NO3 NITRATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；292 K；0.1 M Tris-HCl, pH 8.5, 20% (v/v) PEG Smear High
Resolution 2.18 Å R-free 0.227
6SQS Crystal structure of cat phospho-Ser429 MDM2 RING domain bound to UbcH5B-Ub Deposited 2019-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 2–147（146 aa）
Chain E 2–147（146 aa）
Mutation：S22R, C85K Mutation：S22R, C85K ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；292 K；0.1 M Tris-HCl, pH 8.0, 15% (w/v) PEG 2000 MME and 0.1 M KCl
Resolution 1.83 Å R-free 0.242
6TTU Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 Deposited 2019-12-30 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 D 1–147（147 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.70 Å
6W7Z RNF12 RING domain in complex with Ube2d2 Deposited 2020-03-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Not recorded GOL GLYCEROL × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15-20% PEG 3350, 100-200 mM ammonium formate
Resolution 1.80 Å R-free 0.211
6W9D RNF12 RING domain in complex with a Ube2d2~Ub conjugate Deposited 2020-03-22 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–147（147 aa）
Mutation：C21S, S22R, C85K, C107S, C111S ZN ZINC ION × 2 IOD IODIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；15-20% PEG 3350, 200-400 mM NaI
Resolution 3.19 Å R-free 0.281
6W9D RNF12 RING domain in complex with a Ube2d2~Ub conjugate Deposited 2020-03-22 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–147（147 aa）
Mutation：C21S, S22R, C85K, C107S, C111S ZN ZINC ION × 2 IOD IODIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；15-20% PEG 3350, 200-400 mM NaI
Resolution 3.19 Å R-free 0.281
6W9D RNF12 RING domain in complex with a Ube2d2~Ub conjugate Deposited 2020-03-22 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–147（147 aa）
Mutation：C21S, S22R, C85K, C107S, C111S ZN ZINC ION × 2 IOD IODIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；15-20% PEG 3350, 200-400 mM NaI
Resolution 3.19 Å R-free 0.281
7AI0 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) Deposited 2020-09-25 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain BBB 1–147（147 aa）
Mutation：S22R, C85K CL CHLORIDE ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
Resolution 1.56 Å R-free 0.185
7AI0 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) Deposited 2020-09-25 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain EEE 1–147（147 aa）
Mutation：S22R, C85K CL CHLORIDE ION × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
Resolution 1.56 Å R-free 0.185
7AI1 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2) Deposited 2020-09-25 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain BBB 1–147（147 aa）
Mutation：S22R, C85K CL CHLORIDE ION × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
Resolution 2.07 Å R-free 0.266
7AI1 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2) Deposited 2020-09-25 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain EEE 1–147（147 aa）
Mutation：S22R, C85K CL CHLORIDE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
Resolution 2.07 Å R-free 0.266
7BOL ubiquitin-conjugating enzyme, Ube2D2 Deposited 2020-03-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.5 M Ammonium sulfate 0.1 M Sodium citrate pH 5.6 1.0 M Lithium sulfate
Resolution 1.80 Å R-free 0.219
7R71 Crystal Structure of the UbArk2C-UbcH5b~Ub complex Deposited 2021-06-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–147（147 aa）
Mutation：C21S, S22R, C85K, C107S, C111S ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.1 M MMT pH 6.0, 25% w/v PEG 1500
Resolution 2.80 Å R-free 0.271
8B3I CRL4CSA-E2-Ub (state 2) Deposited 2022-09-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–147（147 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8GBQ Structure of RNF125 in complex with UbcH5b Deposited 2023-02-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Not recorded GOL GLYCEROL × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；289 K；0.1 M CHES 9.5 20% PEG 8000
Resolution 1.74 Å R-free 0.201
8GCB Structure of RNF125 in complex with a UbcH5b~Ub conjugate Deposited 2023-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 9；289 K；0.1 M BICINE pH 9.0, 20% PEG 6000
Resolution 2.39 Å R-free 0.271
8JWJ PHD Finger Protein 7 (PHF7) in complex with UBE2D2 Deposited 2023-06-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–147（147 aa）
Mutation：S22R, C85K ZN ZINC ION × 7 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；277 K；MPD, Tris
Resolution 2.96 Å R-free 0.222
8JWJ PHD Finger Protein 7 (PHF7) in complex with UBE2D2 Deposited 2023-06-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–147（147 aa）
Mutation：S22R, C85K ZN ZINC ION × 7 SO4 SULFATE ION × 1 GOL GLYCEROL × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；277 K；MPD, Tris
Resolution 2.96 Å R-free 0.222
8JWU PHD Finger Protein 7 (PHF7) fused to UBE2D2 via a (GSGG)3 linker Deposited 2023-06-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–147（147 aa）
Mutation：S346R,C409K ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；PEG8000, DMSO, MOPS
Resolution 3.58 Å R-free 0.265
8JWU PHD Finger Protein 7 (PHF7) fused to UBE2D2 via a (GSGG)3 linker Deposited 2023-06-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–147（147 aa）
Mutation：S346R,C409K ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；PEG8000, DMSO, MOPS
Resolution 3.58 Å R-free 0.265
8JWU PHD Finger Protein 7 (PHF7) fused to UBE2D2 via a (GSGG)3 linker Deposited 2023-06-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–147（147 aa）
Mutation：S346R,C409K ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；PEG8000, DMSO, MOPS
Resolution 3.58 Å R-free 0.265
8V0D Ubch5B-RING3 of MIB1 fusion structure Deposited 2023-11-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Chain B 1–147（147 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；4% v/v TacsimateTM pH 6.0, 12% w/v Polyethylene glycol 3,350
Resolution 2.40 Å R-free 0.243
8VK8 Structure of UbV.d2.1 in complex with Ube2d2 Deposited 2024-01-08 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–147（147 aa）
Mutation：C21S, C107S, and C111S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；289 K；0.1 M Sodium citrate pH 5.6, 20% w/v PEG 4000, 20% v/v 2-Propanol
Resolution 2.99 Å R-free 0.295
8VK8 Structure of UbV.d2.1 in complex with Ube2d2 Deposited 2024-01-08 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–147（147 aa）
Mutation：C21S, C107S, and C111S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；289 K；0.1 M Sodium citrate pH 5.6, 20% w/v PEG 4000, 20% v/v 2-Propanol
Resolution 2.99 Å R-free 0.295
8VK8 Structure of UbV.d2.1 in complex with Ube2d2 Deposited 2024-01-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–147（147 aa）
Mutation：C21S, C107S, and C111S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；289 K；0.1 M Sodium citrate pH 5.6, 20% w/v PEG 4000, 20% v/v 2-Propanol
Resolution 2.99 Å R-free 0.295
8VK9 Structure of UbV.d2.3 in complex with Ube2d2-S22R Deposited 2024-01-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Mutation：C21S, S22R, C107S, C111S GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；0.1 M Sodium HEPES pH 7.0, 15% w/v PEG 20,000
Resolution 2.00 Å R-free 0.224
8VK9 Structure of UbV.d2.3 in complex with Ube2d2-S22R Deposited 2024-01-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–147（147 aa）
Mutation：C21S, S22R, C107S, C111S GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；0.1 M Sodium HEPES pH 7.0, 15% w/v PEG 20,000
Resolution 2.00 Å R-free 0.224
8VK9 Structure of UbV.d2.3 in complex with Ube2d2-S22R Deposited 2024-01-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–147（147 aa）
Mutation：C21S, S22R, C107S, C111S GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；0.1 M Sodium HEPES pH 7.0, 15% w/v PEG 20,000
Resolution 2.00 Å R-free 0.224
8VK9 Structure of UbV.d2.3 in complex with Ube2d2-S22R Deposited 2024-01-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–147（147 aa）
Mutation：C21S, S22R, C107S, C111S GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；0.1 M Sodium HEPES pH 7.0, 15% w/v PEG 20,000
Resolution 2.00 Å R-free 0.224
9DNS Cryo-EM structure of Tom1-UBE2D2-ubiquitin complex Deposited 2024-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–147（147 aa）
Chain E 1–147（147 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；30 mM HEPES pH 7.2, 200 mM NaCl, 0.5 mM TCEP, 0.2 mM CHAPSO
cryo-EM vitrification conditions Cryogen ETHANE；CHAPSO detergent added to final conc. of 0.2 mM. Sample applied twice.
Resolution 2.80 Å
9GLS Crystal Structure of Human UBCH5B C85E Deposited 2024-08-28 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 1–147（147 aa）
Mutation：C85E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；10% PEG 200, 0.1 M Bis-Tris propane, pH 9, 15% PEG 8000
Resolution 1.25 Å R-free 0.211
9Q8Y Structure of RNF38 RING with linchpin mutant R454Y in complex with Ubch5B-Ub Deposited 2025-02-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–147（146 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；0.2 M Sodium acetate trihydrate, 0.1 M Imidazole pH 8.0, 10% PEG 8000
Resolution 2.63 Å R-free 0.275
9Q8Y Structure of RNF38 RING with linchpin mutant R454Y in complex with Ubch5B-Ub Deposited 2025-02-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–147（146 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；0.2 M Sodium acetate trihydrate, 0.1 M Imidazole pH 8.0, 10% PEG 8000
Resolution 2.63 Å R-free 0.275
9YE9 Structure of UbcH5b in complex with the U-box domain of the E3 ubiquitin ligase CHIP Deposited 2025-09-23 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–147（147 aa）
Mutation：M1K, C85K BME BETA-MERCAPTOETHANOL × 5 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Magnesium chloride hexahydrate, 0.1 M Potassium chloride, 0.1 M PIPES, 20 % v/v PEG Smear Medium
Resolution 2.01 Å R-free 0.288
9YEA Structure of the isopeptide bond-linked UbcH5b~Ubiquitin conjugate complex for an M1K/C85K UbcH5b mutant Deposited 2025-09-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Mutation：M1K, C85K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1 M Sodium Citrate, 20 % (w/v) PEG 3000
Resolution 1.83 Å R-free 0.239

57 other PDB entries and 92 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UB2D2_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–147； UniProt 1–147

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 4a4b

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4a4b
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4a4b
Deposition date deposition_date2011-10-08
Structure title titleStructure of modified phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex
Keywords keywordsLIGASE-TRANSFERASE COMPLEX; LIGASE/TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.91 Å
Radius of gyration Rg (electron density) rg_electron28.17 Å
Forward intensity I(0) i059797500.00
Molecular weight molecular_weight60756.0 kDa
Excluded volume excluded_volume75997 ų
Envelope volume envelope_volume96947 ų
Hydration-shell volume shell_volume29097 ų
Envelope diameter envelope_diameter91.1 Å
Shell Rg shell_rg35.03 Å
Envelope Rg envelope_rg27.87 Å
Shape Rg shape_rg28.18 Å
Total Rg total_rg28.80 Å
Total atoms total_atoms4267
Residues n_residues541
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 dmax91.9 Å
Rg (real space) rg_real28.88 Å
Rg uncertainty (real space) rg_real_error0.58 Å
I(0) (real space) i0_real5.9800e+07
I(0) uncertainty (real space) i0_real_error9.1330e+05
Rg (reciprocal space) rg_reciprocal28.90 Å
I(0) (reciprocal space) i0_reciprocal59800000.0000
Solution quality estimate total_estimate0.9088
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.1 Å
Skewness Skewness skewness0.228
Kurtosis Kurtosis kurtosis-0.614
Angular range angular_range— – 0.2750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13640000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.980
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4a4bc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.1 — UBC-related

CATH v4.4 (5 domains)

Domain ID domain_id4a4bA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily20 — Adaptor protein Cbl, N-terminal domain
Domain ID domain_id4a4bA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id4a4bA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain
Domain ID domain_id4a4bA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
Domain ID domain_id4a4bC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
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8. Citations (1)

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9. Files and Curves (10)