MolNFT v1 · #146739 · protein

Human glutamate dehydrogenase, H454Y mutant

6DQG · Glutamate dehydrogenase 1, mitochondrial: “Human glutamate dehydrogenase, H454Y mutant”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.91). MolNFT v1 #146739 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6DQG
Type: protein
Length: 2,976 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate dehydrogenase 1, mitochondrial
EC: 1.4.1.3
UniProt: P00367
Ligands: PO4
Pockets: 20 · best druggability 0.91

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Glutamate dehydrogenase 1, mitochondrial (EC 1.4.1.3)	protein	496	47% helix, 14% strand	P00367

Ligands and binding sites

PO4 · Phosphate ion · ion · 15 copies · chains A, B, C, E, D, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	955	0.91	0.94	143	PO4
2	828	0.87	0.90	110	PO4
3	645	0.87	0.92	47	empty
4	654	0.87	0.91	47	empty
5	497	0.87	0.93	74	PO4

Interfaces

15 interfaces between chains.

D–E · 1992 Å² buried · 25 hydrogen bonds · protein-protein
A–F · 1958 Å² buried · 24 hydrogen bonds · protein-protein
B–F · 1944 Å² buried · 23 hydrogen bonds · protein-protein
C–E · 1940 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1932 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

6DQG · Human glutamate dehydrogenase, H454Y mutant · the same entry in another collection · chain F against F, TM-score 1.00
P00367 · AlphaFold monomer V2.0 prediction for glutamate dehydrogenase 1, mitochondrial (P00367) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 P00367
Elsewhere: RCSB PDB 6DQG · PDBe 6DQG · UniProt P00367

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