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2oo9

crystal structure of the UBA domain from human c-Cbl ubiquitin ligase

Method: X-RAY DIFFRACTION Dmax: 55.0 Å Quality: GOOD
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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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 856–895 Chain B； UniProt 856–895 Fragment：UBA domain Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer 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
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 856–895 Fragment：UBA domain Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer 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

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 2OO9 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 oligomeric state 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 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
2Y1M Structure of native c-Cbl Deposited 2010-12-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
4A4B Structure of modified phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex Deposited 2011-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 47–435（389 aa） Fragment：TKB DOMAIN, LINKER HELIX REGION, AND RING DOMAIN, RESIDUES 47-435
Mutation：YES 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 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
4A4C Structure of phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex Deposited 2011-10-08 Different construct Different oligomeric state Different ligand/ion 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 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 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 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：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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 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 59 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 3–42； UniProt 856–895 Author chain B； PDBConstruct 3–42； UniProt 856–895 Author chain C； PDBConstruct 3–42； UniProt 856–895

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 2oo9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2oo9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2oo9
Deposition date deposition_date2007-01-25
Structure title titlecrystal structure of the UBA domain from human c-Cbl ubiquitin ligase
Keywords keywordsalpha-helical domain, homodimer, LIGASE; LIGASE
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_guinier16.57 Å
Radius of gyration Rg (electron density) rg_electron15.45 Å
Forward intensity I(0) i04733010.00
Molecular weight molecular_weight14841.0 kDa
Excluded volume excluded_volume18168 ų
Envelope volume envelope_volume21602 ų
Hydration-shell volume shell_volume12290 ų
Envelope diameter envelope_diameter55.1 Å
Shell Rg shell_rg20.57 Å
Envelope Rg envelope_rg15.84 Å
Shape Rg shape_rg15.42 Å
Total Rg total_rg16.46 Å
Total atoms total_atoms1019
Residues n_residues125
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 dmax55.0 Å
Rg (real space) rg_real16.52 Å
Rg uncertainty (real space) rg_real_error0.31 Å
I(0) (real space) i0_real4.7330e+06
I(0) uncertainty (real space) i0_real_error4.9450e+04
Rg (reciprocal space) rg_reciprocal16.53 Å
I(0) (reciprocal space) i0_reciprocal4733000.0000
Solution quality estimate total_estimate0.8871
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.9 Å
Skewness Skewness skewness0.225
Kurtosis Kurtosis kurtosis-0.459
Angular range angular_range— – 0.4800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha809200.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.851; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.983
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id2oo9A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2oo9B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2oo9C00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
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8. Citations (1)

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9. Files and Curves (10)