MolNFT v1 · #139973 · protein

Crystal structure of aspergillus niger glutamate dehydrogenase complexed with alpha-ketoglutarate and NADPH

5XVX: “Crystal structure of aspergillus niger glutamate dehydrogenase complexed with alpha-ketoglutarate and NADPH”. X-ray diffraction, 2 ligands (NDP, AKG), 2 pockets (best druggability 0.79). MolNFT v1 #139973 on GenesisL1: 3D structure…

PDB: 5XVX
Type: protein
Length: 459 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate dehydrogenase
UniProt: B6V7E4
Ligands: NDP, AKG
Pockets: 2 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutamate dehydrogenase	protein	459	46% helix, 15% strand	B6V7E4

Ligands and binding sites

NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
AKG · 2-oxoglutaric acid · ligand · chains A
GOL · Glycerol · additive · 23 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A

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

Pockets

2 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	737	0.79	0.84	72	NDP, AKG, GOL
2	72	0.29	0.73	20	empty

Compared structures

5XVX · Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With… · the same entry in another collection · chain A against A, TM-score 1.00

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 B6V7E4
Elsewhere: RCSB PDB 5XVX · PDBe 5XVX · UniProt B6V7E4

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