MolNFT v1 · #134927 · protein

Hugdh A136M substitution

5TJH · Udp-glucose 6-dehydrogenase: “Hugdh A136M substitution”. X-ray diffraction, 3 ligands (POP, UPG, CL), 20 pockets (best druggability 0.79). MolNFT v1 #134927 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5TJH
Type: protein
Length: 2,765 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Udp-glucose 6-dehydrogenase
EC: 1.1.1.22
UniProt: O60701
Ligands: POP, UPG, CL
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 6 distinct chains · 46% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Udp-glucose 6-dehydrogenase (EC 1.1.1.22)	protein	460	46% helix, 15% strand	O60701
B	Udp-glucose 6-dehydrogenase (EC 1.1.1.22)	protein	460	45% helix, 14% strand	O60701
C	Udp-glucose 6-dehydrogenase (EC 1.1.1.22)	protein	462	45% helix, 14% strand	O60701
D	Udp-glucose 6-dehydrogenase (EC 1.1.1.22)	protein	459	46% helix, 14% strand	O60701
E	Udp-glucose 6-dehydrogenase (EC 1.1.1.22)	protein	461	46% helix, 14% strand	O60701
F	Udp-glucose 6-dehydrogenase (EC 1.1.1.22)	protein	463	46% helix, 15% strand	O60701

Ligands and binding sites

POP · Pyrophosphate 2- · ligand · 5 copies · chains A, B, D, E, F
UPG · Uridine-5'-diphosphate-glucose · ligand · chains C, D
CL · Chloride ion · ion · 2 copies · chains A, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	858	0.79	0.81	88	POP
2	902	0.77	0.80	84	POP
3	925	0.77	0.80	99	UPG
4	712	0.76	0.81	78	POP
5	808	0.76	0.80	77	POP

Interfaces

12 interfaces between chains.

B–E · 2858 Å² buried · 30 hydrogen bonds · protein-protein
A–F · 2846 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 2828 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 697 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 677 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5TJH · hUGDH A136M Substitution · the same entry in another collection · chain F against F, TM-score 1.00
O60701 · AlphaFold monomer V2.0 prediction for udp-glucose 6-dehydrogenase (O60701) · a predicted model of the same protein · chain F 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 O60701
Elsewhere: RCSB PDB 5TJH · PDBe 5TJH · UniProt O60701

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