MolNFT v1 · #31781 · protein

Crystal structure of glucose dehydrogenase from haloferax mediterranei

2B5V: “Crystal structure of glucose dehydrogenase from haloferax mediterranei”. X-ray diffraction, 1 ligand (NAP), 3 pockets (best druggability 0.68). MolNFT v1 #31781 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2B5V
Type: protein
Length: 355 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucose dehydrogenase
EC: 1.1.1.47
UniProt: Q977U7
Ligands: NAP
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucose dehydrogenase (EC 1.1.1.47)	protein	355	33% helix, 28% strand	Q977U7

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	595	0.68	0.78	50	NAP
2	185	0.45	0.74	26	empty
3	70	0.31	0.74	15	empty

Compared structures

2B5V · Crystal structure of glucose dehydrogenase from Haloferax mediterranei · the same entry in another collection · chain A against A, TM-score 1.00
Q977U7 · AlphaFold monomer V2.0 prediction for glucose 1-dehydrogenase (Q977U7) · a predicted model of the same protein · chain A 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 Q977U7
Elsewhere: RCSB PDB 2B5V · PDBe 2B5V · UniProt Q977U7

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