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2do6

Solution structure of RSGI RUH-065, a UBA domain from human cDNA

Method: SOLUTION NMR Dmax: 49.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase CBL-B

Homo sapiens

UniProt Q13191

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 931–970 Chain B； UniProt 931–970 Fragment：UBA domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure AMBIENT NMR sample composition：1.1mM UBA domain U-15N,13C, 20mM d-Tris-HCl buffer (pH 7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：1.0mM UBA domain U-15N,13C, 1.0mM UBA domain, 20mM d-Tris-HCl buffer (pH 7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 100% D2O | 100% D2O Resolution not provided

Other States of the Same Protein in the Database

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

Other PDB Difference from Current Entry 2DO6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2AK5 beta PIX-SH3 complexed with a Cbl-b peptide Deposited 2005-08-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 904–911（8 aa） Fragment：residues 904-911
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；PEG 3000, SODIUM CITRATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 6.50
Resolution 1.85 Å R-free 0.269
2BZ8 N-terminal Sh3 domain of CIN85 bound to Cbl-b peptide Deposited 2005-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 902–912（11 aa） Fragment：POLYPROLINE RICH REGION RESIDUES 902-912
Not recorded NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.8 M NA CITRATE, 0.1 M BIS-TRIS PH 7.5, 0.2 M NACL
Resolution 2.00 Å R-free 0.271
2J6F N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) BOUND TO CBL-B PEPTIDE Deposited 2006-09-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 902–912（11 aa） Fragment：PEPTIDE, RESIDUES 902-912
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；20% PEG3000, 0.1M ACETATE PH 5.5
Resolution 1.70 Å R-free 0.218
2JNH Solution Structure of the UBA Domain from Cbl-b Deposited 2007-01-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 926–971（46 aa） Fragment：UBA domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 1 mM [U-13C; U-15N] entity, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 0.01 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LDR Solution structure of Helix-RING domain of Cbl-b in the Tyr363 phosphorylated form Deposited 2011-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 351–426（76 aa） Fragment：Helix-RING domain, residues 345-426
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 150；Pressure ambient
NMR sample composition 20mM MES-1, 2mM DTT-2, 150mM sodium chloride-3, 0.4mM [U-99% 13C; U-99% 15N] protein-4, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2OOA crystal structure of the UBA domain from Cbl-b ubiquitin ligase Deposited 2007-01-25 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 924–973（50 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 8.2；293 K；1.2M sodium/potassium phosphate, 12% glycerol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.56 Å R-free 0.240
2OOA crystal structure of the UBA domain from Cbl-b ubiquitin ligase Deposited 2007-01-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 924–973（50 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 8.2；293 K；1.2M sodium/potassium phosphate, 12% glycerol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.56 Å R-free 0.240
2OOB crystal structure of the UBA domain from Cbl-b ubiquitin ligase in complex with ubiquitin Deposited 2007-01-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 924–973（50 aa） Fragment：UBA domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.2M calcium chloride, 0.1M sodium acetate, 20% PEG6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.256
3PFV Crystal structure of Cbl-b TKB domain in complex with EGFR pY1069 peptide Deposited 2010-10-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 38–344（307 aa） Fragment：N-terminal TKB domain (UNP residues 38-344)
Not recorded NA SODIUM ION × 1 CL CHLORIDE ION × 2 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；30% PEG 3350, 0.3M Ammonium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.27 Å R-free 0.262
3PFV Crystal structure of Cbl-b TKB domain in complex with EGFR pY1069 peptide Deposited 2010-10-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 38–344（307 aa） Fragment：N-terminal TKB domain (UNP residues 38-344)
Not recorded NA SODIUM ION × 1 SO4 SULFATE ION × 3 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；30% PEG 3350, 0.3M Ammonium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.27 Å R-free 0.262
3VGO Crystal structure of the N-terminal fragment of Cbl-b Deposited 2011-08-18 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 39–426（388 aa） Fragment：N-terminal fragment, UNP residues 39-426
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；25% PEG 3350, 0.1M bicine, 0.8M KNO3, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.10 Å R-free 0.328
3VGO Crystal structure of the N-terminal fragment of Cbl-b Deposited 2011-08-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 39–426（388 aa） Fragment：N-terminal fragment, UNP residues 39-426
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；25% PEG 3350, 0.1M bicine, 0.8M KNO3, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.10 Å R-free 0.328
3VGO Crystal structure of the N-terminal fragment of Cbl-b Deposited 2011-08-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 39–426（388 aa） Fragment：N-terminal fragment, UNP residues 39-426
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；25% PEG 3350, 0.1M bicine, 0.8M KNO3, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.10 Å R-free 0.328
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 36–427（392 aa） Fragment：RESIDUES 36-427
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 36–427（392 aa） Fragment：RESIDUES 36-427
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 36–427（392 aa） Fragment：RESIDUES 36-427
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain M 36–427（392 aa） Fragment：RESIDUES 36-427
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
8GCY Co-crystal structure of CBL-B in complex with N-Aryl isoindolin-1-one inhibitor Deposited 2023-03-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 38–427（390 aa）
Not recorded ZN ZINC ION × 2 Z3N 2-{3-[(1s,3R)-3-methyl-1-(4-methyl-4H-1,2,4-triazol-3-yl)cyclobutyl]phenyl}-6-{[(3S)-3-methylpiperidin-1-yl]methyl}-4-(trifluoromethyl)-2,3-dihydro-1H-isoindol-1-one × 1 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M Imidazole, 0.1 M MES monohydrate pH 6.5 0.09 M Sodium nitrate, 0.09 M Sodium phosphate dibasic, 0.09M Ammonium sulfate 12.5% v/v MPD; 12.5% PEG1000; 12.5% w/v PEG 3350
Resolution 1.81 Å R-free 0.230
8QNG Crystal structure of the E3 ubiquitin ligase Cbl-b with an allosteric inhibitor (benzodiazepine HTS hit compound 1) Deposited 2023-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–427（392 aa）
Not recorded W89 2-(morpholin-4-ylmethyl)-~{N}-[(3~{S})-2-oxidanylidene-5-phenyl-1,3-dihydro-1,4-benzodiazepin-3-yl]benzamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；9 % PEG8000, 0.05 M MgAcetate, 0.05 M PCTP pH 7.5
Resolution 2.20 Å R-free 0.295
8QNH Crystal structure of the E3 ubiquitin ligase Cbl-b with an allosteric inhibitor (WO2020264398 Ex23) Deposited 2023-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–427（392 aa）
Not recorded Z3N 2-{3-[(1s,3R)-3-methyl-1-(4-methyl-4H-1,2,4-triazol-3-yl)cyclobutyl]phenyl}-6-{[(3S)-3-methylpiperidin-1-yl]methyl}-4-(trifluoromethyl)-2,3-dihydro-1H-isoindol-1-one × 1 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；9 % PEG8000, 5 % MPD, 0.05 M MgAcetate, 0.05 M PCTP pH 8
Resolution 2.00 Å R-free 0.248
8QNI Crystal structure of the E3 ubiquitin ligase Cbl-b with an allosteric inhibitor (benzodiazepine compound 25) Deposited 2023-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–427（392 aa）
Not recorded W7R 2-[[(2~{S})-2-methylmorpholin-4-yl]methyl]-~{N}-[(3~{S})-2-oxidanylidene-5-phenyl-1,3-dihydropyrido[3,4-e][1,4]diazepin-3-yl]benzamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；11 % PEG8000, 5 % MPD, 0.05 M MgAcetate, 0.05 M PCPT pH 8.0
Resolution 2.48 Å R-free 0.286
8QTG Crystal structure of CBL-b in complex with an allosteric inhibitor (compound 9) Deposited 2023-10-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–427（392 aa）
Not recorded WUQ 3-[3-[3-methyl-1-(4-methyl-1,2,4-triazol-3-yl)cyclobutyl]phenyl]-5-(trifluoromethyl)-1~{H}-pyridin-2-one × 1 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；8-11 % PEG8000, 5 % MPD, 0.05 M MgAcetate, 0.05 M PCTP pH 8
Resolution 1.42 Å R-free 0.243
8QTH Crystal structure of CBL-b in complex with an allosteric inhibitor (compound 8) Deposited 2023-10-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–427（392 aa）
Not recorded WX0 1-methyl-5-[3-[3-methyl-1-(4-methyl-1,2,4-triazol-3-yl)cyclobutyl]phenyl]-3-(trifluoromethyl)-7H-pyrrolo[2,3-b]pyridin-6-one × 1 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；8-11 % PEG8000, 2.5 % MPD, 0.05 M MgAcetate, 0.05 M PCTP pH 8
Resolution 2.20 Å R-free 0.260
8QTJ Crystal structure of Cbl-b in complex with an allosteric inhibitor (compound 30) Deposited 2023-10-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–427（392 aa）
Not recorded ZN ZINC ION × 2 NA SODIUM ION × 1 WUI 3-[3-[3-methyl-1-(4-methyl-1,2,4-triazol-3-yl)cyclobutyl]phenyl]-1-[(1~{R})-1-(1-methylpyrazol-4-yl)ethyl]-5-(trifluoromethyl)pyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；8-11 % PEG8000, 2.5 % MPD, 0.05 M MgAcetate, 0.05 M PCTP pH 8
Resolution 1.52 Å R-free 0.232
8QTK Crystal structure of CBL-b in complex with an allosteric inhibitor (compound 31) Deposited 2023-10-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–427（392 aa）
Not recorded ZN ZINC ION × 2 NA SODIUM ION × 1 WX9 3-[3-[3-methyl-1-(4-methyl-1,2,4-triazol-3-yl)cyclobutyl]phenyl]-1-[(1S)-1-(1-methylpyrazol-4-yl)ethyl]-5-(trifluoromethyl)pyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；8-11 % PEG8000, 2.5 % MPD, 0.05 M MgAcetate, 0.05 M PCTP pH 8
Resolution 1.87 Å R-free 0.268
8VW4 Crystal structure of Cbl-b TKB bound to compound 26 Deposited 2024-01-31 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 36–343（308 aa） Fragment：Cbl-PTB domain, residues 36-343
Not recorded MG MAGNESIUM ION × 1 A1AEG (7-methoxy-2-{2-[(1S,3S,4S)-3-(3-methoxy-2-methyl-5-nitrophenyl)-1-methyl-5-oxo-1,5-dihydroimidazo[1,5-a]pyridin-2(3H)-yl]-2-oxoethoxy}quinolin-8-yl)acetic acid × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M NaCitrate, 20% PEG3350
Resolution 2.40 Å R-free 0.253
8VW4 Crystal structure of Cbl-b TKB bound to compound 26 Deposited 2024-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 36–343（308 aa） Fragment：Cbl-PTB domain, residues 36-343
Not recorded MG MAGNESIUM ION × 1 A1AEG (7-methoxy-2-{2-[(1S,3S,4S)-3-(3-methoxy-2-methyl-5-nitrophenyl)-1-methyl-5-oxo-1,5-dihydroimidazo[1,5-a]pyridin-2(3H)-yl]-2-oxoethoxy}quinolin-8-yl)acetic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M NaCitrate, 20% PEG3350
Resolution 2.40 Å R-free 0.253
8VW5 Crystal structure of Cbl-b TKB bound to compound 2 Deposited 2024-01-31 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 36–343（308 aa） Fragment：Cbl-PTB domain, residues 36-343
Not recorded MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 A1AD4 [5-(2-{(2R,5S)-2-[2-(carboxymethoxy)-3-methoxy-5-nitrophenyl]-3,5-dimethyl-4-oxoimidazolidin-1-yl}-2-oxoethyl)-3,6-dimethoxy-9,9-dimethyl-9H-xanthen-4-yl]acetic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Ca(OAc)2, 0.1 M NaCacodylate pH 6.5, 18% PEG8000
Resolution 1.76 Å R-free 0.204
8VW5 Crystal structure of Cbl-b TKB bound to compound 2 Deposited 2024-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 36–343（308 aa） Fragment：Cbl-PTB domain, residues 36-343
Not recorded CA CALCIUM ION × 1 A1AD4 [5-(2-{(2R,5S)-2-[2-(carboxymethoxy)-3-methoxy-5-nitrophenyl]-3,5-dimethyl-4-oxoimidazolidin-1-yl}-2-oxoethyl)-3,6-dimethoxy-9,9-dimethyl-9H-xanthen-4-yl]acetic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Ca(OAc)2, 0.1 M NaCacodylate pH 6.5, 18% PEG8000
Resolution 1.76 Å R-free 0.204
9FQH E3 ligase Cbl-b in complex with a triazolone core inhibitor (compound 1) Deposited 2024-06-17 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 36–427（392 aa）
Not recorded A1IEW 8-[3-[3-methyl-1-(4-methyl-1,2,4-triazol-3-yl)cyclobutyl]phenyl]-3-[[(3~{S})-3-methylpiperidin-1-yl]methyl]-5-(trifluoromethyl)-1$l^{4},7,8-triazabicyclo[4.3.0]nona-1(6),2,4-trien-9-one × 1 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；9 % PEG8000, 5 % MPD, 0.05 M MgAcetate, 0.05 M PCTP pH 8
Resolution 1.79 Å R-free 0.249
9FQI E3 ligase Cbl-b in complex with a lactam scaffold inhibitor (compound 7) Deposited 2024-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–427（392 aa）
Not recorded A1IEV 8-[3-[(4~{R})-4-methyl-2-oxidanylidene-piperidin-4-yl]phenyl]-3-[[(3~{S})-3-methylpiperidin-1-yl]methyl]-5-(trifluoromethyl)-1$l^{4},7,8-triazabicyclo[4.3.0]nona-1(6),2,4-trien-9-one × 1 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；11 % PEG8000, 0.05 M Mg Acetate, 5 % MPD, 0.05 M PCPT pH 8.0
Resolution 1.95 Å R-free 0.291
9FQJ E3 ligase Cbl-b in complex with a carbamate scaffold inhibitor (compound 12) Deposited 2024-06-17 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 36–427（392 aa）
Mutation：EC:2.3.2.27 A1IE5 2-cyclopropyl-6-methyl-~{N}-[3-[(6~{S})-6-methyl-2-oxidanylidene-1,3-oxazinan-6-yl]phenyl]pyrimidine-4-carboxamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；11 % PEG8000, 0.05 M Mg Acetate, 5 % MPD, 0.05 M PCPT pH 8.0
Resolution 1.56 Å R-free 0.222
9FQJ E3 ligase Cbl-b in complex with a carbamate scaffold inhibitor (compound 12) Deposited 2024-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 36–427（392 aa）
Mutation：EC:2.3.2.27 A1IE5 2-cyclopropyl-6-methyl-~{N}-[3-[(6~{S})-6-methyl-2-oxidanylidene-1,3-oxazinan-6-yl]phenyl]pyrimidine-4-carboxamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；11 % PEG8000, 0.05 M Mg Acetate, 5 % MPD, 0.05 M PCPT pH 8.0
Resolution 1.56 Å R-free 0.222

23 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CBLB_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–47； UniProt 931–970 Author chain B； PDBConstruct 8–47； UniProt 931–970

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 2do6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2do6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2do6
Deposition date deposition_date2006-04-27
Structure title titleSolution structure of RSGI RUH-065, a UBA domain from human cDNA
Keywords keywords;UBA domain, dimer, protein binding, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, LIGASE ;; LIGASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.35 Å
Radius of gyration Rg (electron density) rg_electron13.91 Å
Forward intensity I(0) i0752253000.00
Molecular weight molecular_weight219880.0 kDa
Excluded volume excluded_volume270680 ų
Envelope volume envelope_volume31927 ų
Hydration-shell volume shell_volume16159 ų
Envelope diameter envelope_diameter54.4 Å
Shell Rg shell_rg22.65 Å
Envelope Rg envelope_rg16.87 Å
Shape Rg shape_rg13.89 Å
Total Rg total_rg14.15 Å
Total atoms total_atoms30640
Residues n_residues2120
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 dmax49.5 Å
Rg (real space) rg_real14.29 Å
Rg uncertainty (real space) rg_real_error0.40 Å
I(0) (real space) i0_real7.5230e+08
I(0) uncertainty (real space) i0_real_error8.6980e+06
Rg (reciprocal space) rg_reciprocal14.30 Å
I(0) (reciprocal space) i0_reciprocal752300000.0000
Solution quality estimate total_estimate0.8256
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary14.4 Å
Skewness Skewness skewness0.186
Kurtosis Kurtosis kurtosis-0.434
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha780600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.588; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.995
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)