MolNFT v1 · #82245 · protein

Crystal structure of the N-terminal fragment of cbl-B

3VGO · E3 ubiquitin-protein ligase cbl-B: “Crystal structure of the N-terminal fragment of cbl-B”. X-ray diffraction, 14 pockets (best druggability 0.74). MolNFT v1 #82245 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VGO
Type: protein
Length: 873 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase cbl-B
EC: 6.3.2.-
UniProt: Q13191
Pockets: 14 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 60% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase cbl-B (EC 6.3.2.-)	protein	287	60% helix, 7% strand	Q13191
B	E3 ubiquitin-protein ligase cbl-B (EC 6.3.2.-)	protein	294	61% helix, 10% strand	Q13191
C	E3 ubiquitin-protein ligase cbl-B (EC 6.3.2.-)	protein	292	60% helix, 9% strand	Q13191

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	69	0.74	0.98	16	empty
2	84	0.74	0.96	25	empty
3	65	0.73	0.97	19	empty
4	163	0.70	0.88	27	empty
5	371	0.62	0.77	51	empty

Interfaces

2 interfaces between chains.

A–B · 253 Å² buried · 1 hydrogen bond · protein-protein
A–C · 64 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3VGO · Crystal structure of the N-terminal fragment of Cbl-b · the same entry in another collection · chain A against A, TM-score 1.00
Q13191 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase cbl-B (Q13191) · a predicted model of the same protein · chain A against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q13191
Elsewhere: RCSB PDB 3VGO · PDBe 3VGO · UniProt Q13191

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