MolNFT v1 · #137975 · protein

Truncated hugdh

5W4X · Udp-glucose 6-dehydrogenase: “Truncated hugdh”. X-ray diffraction, 11 pockets (best druggability 0.71). MolNFT v1 #137975 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5W4X
Type: protein
Length: 1,380 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Udp-glucose 6-dehydrogenase
EC: 1.1.1.22
UniProt: O60701
Pockets: 11 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Udp-glucose 6-dehydrogenase (EC 1.1.1.22)	protein	459	45% helix, 15% strand	O60701
B	Udp-glucose 6-dehydrogenase (EC 1.1.1.22)	protein	460	45% helix, 16% strand	O60701
C	Udp-glucose 6-dehydrogenase (EC 1.1.1.22)	protein	461	45% helix, 15% strand	O60701

Ligands and binding sites

PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · 3 copies · chains A, B, C

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

Pockets

11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	546	0.71	0.80	55	PG5
2	516	0.70	0.80	53	PG5
3	567	0.70	0.79	57	PG5
4	183	0.63	0.84	22	empty
5	191	0.63	0.84	24	empty

Interfaces

3 interfaces between chains.

A–B · 707 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 707 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 695 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5W4X · Truncated hUGDH · the same entry in another collection · chain A against A, TM-score 1.00
O60701 · AlphaFold monomer V2.0 prediction for udp-glucose 6-dehydrogenase (O60701) · a predicted model of the same protein · chain C 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 O60701
Elsewhere: RCSB PDB 5W4X · PDBe 5W4X · UniProt O60701

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