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Dimeric hugdh, K94E

Analyse Dimeric hugdh, K94E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4EDF
Type: protein
Length: 1,711 residues
Chains: 4
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: UPG
Pockets: 11 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Udp-glucose 6-dehydrogenase (EC 1.1.1.22)	protein	431	47% helix, 15% strand	O60701
C	Udp-glucose 6-dehydrogenase (EC 1.1.1.22)	protein	424	47% helix, 15% strand	O60701
D	Udp-glucose 6-dehydrogenase (EC 1.1.1.22)	protein	425	47% helix, 15% strand	O60701

Ligands and binding sites

UPG · Uridine-5'-diphosphate-glucose · ligand · 4 copies · chains A, D, 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1177	0.80	0.82	90	empty
2	638	0.78	0.84	68	UPG
3	618	0.77	0.83	70	UPG
4	613	0.77	0.83	67	UPG
5	640	0.76	0.82	73	UPG

Interfaces

6 interfaces between chains.

B–C · 2759 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 2754 Å² buried · 29 hydrogen bonds · protein-protein
B–D · 457 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 418 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 367 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4EDF · Dimeric hUGDH, K94E · 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 D against A, TM-score 0.99

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 4EDF · PDBe 4EDF · UniProt O60701

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