MolNFT v1 · #54837 · protein

Structure of native C-cbl

2Y1M · E3 ubiquitin-protein ligase: “Structure of native C-cbl”. X-ray diffraction, 2 ligands (ZN, CA), 20 pockets (best druggability 0.84). MolNFT v1 #54837 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2Y1M
Type: protein
Length: 2,306 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase
EC: 6.3.2.-
UniProt: P22681
Ligands: ZN, CA
Pockets: 20 · best druggability 0.84

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	E3 ubiquitin-protein ligase (EC 6.3.2.-)	protein	384	49% helix, 10% strand	P22681
B	E3 ubiquitin-protein ligase (EC 6.3.2.-)	protein	385	51% helix, 11% strand	P22681
C, D	E3 ubiquitin-protein ligase (EC 6.3.2.-)	protein	385	50% helix, 11% strand	P22681
E	E3 ubiquitin-protein ligase (EC 6.3.2.-)	protein	383	50% helix, 10% 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, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1159	0.84	0.85	104	empty
2	1186	0.83	0.84	116	empty
3	1091	0.83	0.84	107	empty
4	1100	0.83	0.84	96	empty
5	653	0.82	0.86	86	empty

Interfaces

8 interfaces between chains.

A–E · 1495 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 1468 Å² buried · 14 hydrogen bonds · protein-protein
A–F · 1444 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1438 Å² buried · 16 hydrogen bonds · protein-protein
D–F · 526 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2Y1M · Structure of native c-Cbl · 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 E 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 2Y1M · PDBe 2Y1M · UniProt P22681

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