1yvh

Crystal Structure of the c-Cbl TKB Domain in Complex with the APS pTyr-618 Phosphopeptide

Method: X-RAY DIFFRACTION D_max: 68.8 Å Quality: GOOD

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

CBL E3 ubiquitin protein ligase

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 23–351	Fragment：Tyrosine kinase binding domain, residues 25-351	13-mer fragment of SH2 and PH domain-containing adapter protein APS × 1 （Q9Z200） 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

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 1YVH	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 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
2CBL N-TERMINAL DOMAIN OF CBL IN COMPLEX WITH ITS BINDING SITE ON ZAP-70 Deposited 1998-08-28	Different construct 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 1–329； UniProt 23–351

13-mer fragment of SH2 and PH domain-containing adapter protein APS

OrganismNot specified

UniProt Q9Z200

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 609–621	Fragment：pTyr-618 phosphopeptide Non-standard monomer：Yes (specific site not provided by mmCIF)	CBL E3 ubiquitin protein ligase × 1 （P22681） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1YVH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1RPY CRYSTAL STRUCTURE OF THE DIMERIC SH2 DOMAIN OF APS Deposited 2003-12-03	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 401–510（110 aa） Fragment：SH2 domain Chain B 401–510（110 aa） Fragment：SH2 domain	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；Ammonium sulfate/tris, pH 7.5, pH 7.50	Resolution 2.30 Å R-free 0.270
1RPY CRYSTAL STRUCTURE OF THE DIMERIC SH2 DOMAIN OF APS Deposited 2003-12-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 401–510（110 aa） Fragment：SH2 domain Chain B 401–510（110 aa） Fragment：SH2 domain	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；Ammonium sulfate/tris, pH 7.5, pH 7.50	Resolution 2.30 Å R-free 0.270
1RQQ Crystal Structure of the Insulin Receptor Kinase in Complex with the SH2 Domain of APS Deposited 2003-12-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 401–510（110 aa） Fragment：SH2 domain Chain D 401–510（110 aa） Fragment：SH2 domain	Not recorded	MN MANGANESE (II) ION × 2 112 THIOPHOSPHORIC ACID O-((ADENOSYL-PHOSPHO)PHOSPHO)-S-ACETAMIDYL-DIESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.60 Å R-free 0.277

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	APS_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–13； UniProt 609–621

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1yvh
Deposition date deposition_date	2005-02-15
Structure title title	Crystal Structure of the c-Cbl TKB Domain in Complex with the APS pTyr-618 Phosphopeptide
Keywords keywords	X-RAY CRYSTALLOGRAPHY; PHOSPHOTYROSINE; ADAPTER PROTEIN, LIGASE, SIGNALING PROTEIN, IMMUNE SYSTEM; LIGASE,SIGNALING PROTEIN,IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	21.33 Å
Radius of gyration Rg (electron density) rg_electron	20.25 Å
Forward intensity I(0) i0	21378900.00
Molecular weight molecular_weight	36391.0 kDa
Excluded volume excluded_volume	46040 Å³
Envelope volume envelope_volume	52832 Å³
Hydration-shell volume shell_volume	21641 Å³
Envelope diameter envelope_diameter	68.4 Å
Shell Rg shell_rg	26.77 Å
Envelope Rg envelope_rg	20.41 Å
Shape Rg shape_rg	20.24 Å
Total Rg total_rg	21.14 Å
Total atoms total_atoms	2566
Residues n_residues	312
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	68.8 Å
Rg (real space) rg_real	21.22 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	2.1380e+07
I(0) uncertainty (real space) i0_real_error	2.7800e+05
Rg (reciprocal space) rg_reciprocal	21.24 Å
I(0) (reciprocal space) i0_reciprocal	21380000.0000
Solution quality estimate total_estimate	0.8958
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.3 Å
Skewness Skewness skewness	0.179
Kurtosis Kurtosis kurtosis	-0.459
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6587000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.996

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	CBL E3 ubiquitin protein ligase
Molecular weight formula_weight	38192.1 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2754

GSLIGLMKDAFQPHHHHHHHLSPHPPGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYEENSQPRRNLTKLSLIFSHMLAELKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPWKSFRQALHEVHPISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLAVTHPGYMAFLTYDEVKARLQKFIHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNKPLFQALIDGFREGFYLFPDGRNQNPDLTG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	13-mer fragment of SH2 and PH domain-containing adapter protein APS
Molecular weight formula_weight	1642.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GRARAVENQYSFY

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	188

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1yvha1
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.7 — EF-hand modules in multidomain proteins

Domain ID domain_id	d1yvha2
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.1 — N-terminal domain of cbl (N-cbl)
Family Family family	a.48.1.1 — N-terminal domain of cbl (N-cbl)

Domain ID domain_id	d1yvha3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.1 — SH2 domain

CATH v4.4 (3 domains)

Domain ID domain_id	1yvhA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	20 — Adaptor protein Cbl, N-terminal domain

Domain ID domain_id	1yvhA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	1yvhA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

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8. Citations (1)

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Unit-cell length a length_a	122.257 Å
Unit-cell length b length_b	122.257 Å
Unit-cell length c length_c	55.131 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 6
Space-group number int_tables_number	168
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2091
R_work r_work	0.2090
R_free r_free	0.2470

fit	/app/data/saxs_computation/yv/1yvh/1yvh.fit
pddf	/app/data/pr_computation/yv/1yvh/1yvh.pr.out
profile	/app/data/saxs_computation/yv/1yvh/1yvh.dat

Crystal Structure of the c-Cbl TKB Domain in Complex with the APS pTyr-618 Phosphopeptide

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

CBL E3 ubiquitin protein ligase

State in the Current Structure

Other States of the Same Protein in the Database

13-mer fragment of SH2 and PH domain-containing adapter protein APS

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)