MolNFT v1 · #181696 · protein

CDC34A-ubiquitin-2AB inhibitor complex

7M2K · Ubiquitin-conjugating enzyme E2 R1: “CDC34A-ubiquitin-2AB inhibitor complex”. X-ray diffraction, 1 ligand (GZM), 12 pockets (best druggability 0.75). MolNFT v1 #181696 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7M2K
Type: protein
Length: 950 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-conjugating enzyme E2 R1; Ubiquitin
EC: 2.3.2.23, 2.3.2.24
UniProt: P49427, P0CG47
Ligands: GZM
Pockets: 12 · best druggability 0.75

Structure

x-ray diffraction · 7 distinct chains · 33% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin-conjugating enzyme E2 R1 (EC 2.3.2.23, 2.3.2.24)	protein	169	36% helix, 15% strand	P49427
B, D	Ubiquitin	protein	75	19% helix, 36% strand	P0CG47
C	Ubiquitin-conjugating enzyme E2 R1 (EC 2.3.2.23, 2.3.2.24)	protein	169	37% helix, 15% strand	P49427
E	Ubiquitin-conjugating enzyme E2 R1 (EC 2.3.2.23, 2.3.2.24)	protein	160	38% helix, 16% strand	P49427
F	Ubiquitin	protein	71	21% helix, 32% strand	P0CG47
G	Ubiquitin-conjugating enzyme E2 R1 (EC 2.3.2.23, 2.3.2.24)	protein	158	38% helix, 16% strand	P49427
H	Ubiquitin	protein	73	16% helix, 34% strand	P0CG47

Ligands and binding sites

GZM · 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide · ligand · 4 copies · chains A, B, C, D, E, F, G, H

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1185	0.75	0.77	127	GZM
2	324	0.67	0.81	41	GZM
3	607	0.66	0.76	53	empty
4	738	0.66	0.74	61	empty
5	298	0.64	0.80	44	GZM

Interfaces

11 interfaces between chains.

A–B · 839 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 706 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 562 Å² buried · 12 hydrogen bonds · protein-protein
C–G · 552 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 495 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

7M2K · CDC34A-Ubiquitin-2ab inhibitor complex · the same entry in another collection · chain H against H, TM-score 1.00
P49427 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 R1 (P49427) · a predicted model of the same protein · chain G against A, TM-score 0.97

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 P49427
Every structure of UniProt P0CG47
Elsewhere: RCSB PDB 7M2K · PDBe 7M2K · UniProt P49427 · UniProt P0CG47

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