MolNFT v1 · #122918 · protein

Structure of C-cbl Y371F

5J3X · E3 ubiquitin-protein ligase cbl: “Structure of C-cbl Y371F”. X-ray diffraction, 2 ligands (ZN, CA), 20 pockets (best druggability 0.85). MolNFT v1 #122918 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5J3X
Type: protein
Length: 2,318 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase cbl
EC: 6.3.2.-
UniProt: P22681
Ligands: ZN, CA
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase cbl (EC 6.3.2.-)	protein	386	49% helix, 10% strand	P22681
B, C, D	E3 ubiquitin-protein ligase cbl (EC 6.3.2.-)	protein	389	48% helix, 11% strand	P22681
E	E3 ubiquitin-protein ligase cbl (EC 6.3.2.-)	protein	381	51% helix, 10% strand	P22681
F	E3 ubiquitin-protein ligase cbl (EC 6.3.2.-)	protein	384	50% helix, 11% strand	P22681

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	984	0.85	0.86	105	empty
2	1104	0.84	0.84	98	empty
3	958	0.84	0.85	81	empty
4	1191	0.83	0.84	108	empty
5	480	0.82	0.89	70	empty

Interfaces

7 interfaces between chains.

A–F · 1464 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1414 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 1401 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1313 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 478 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5J3X · Structure of c-CBL Y371F · the same entry in another collection · chain F against F, TM-score 1.00
P22681 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase cbl (P22681) · a predicted model of the same protein · chain F against A, TM-score 0.80

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 P22681
Elsewhere: RCSB PDB 5J3X · PDBe 5J3X · UniProt P22681

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