MolNFT v1 · #189376 · protein

2.26 a structure of the glutamate dehydrogenase

7VDA · Glutamate dehydrogenase 1, mitochondrial: “2.26 a structure of the glutamate dehydrogenase”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #189376 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7VDA
Type: protein
Length: 2,976 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate dehydrogenase 1, mitochondrial
EC: 1.4.1.3
UniProt: P00366
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 1 distinct chain · 50% 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	50% helix, 14% strand	P00366

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	804	0.88	0.91	48	empty
2	806	0.88	0.91	49	empty
3	844	0.86	0.89	99	empty
4	825	0.85	0.88	99	empty
5	776	0.84	0.87	75	empty

Interfaces

15 interfaces between chains.

A–F · 1915 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1904 Å² buried · 21 hydrogen bonds · protein-protein
B–F · 1899 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1896 Å² buried · 21 hydrogen bonds · protein-protein
C–E · 1895 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

7VDA · 2.26 A structure of the glutamate dehydrogenase · the same entry in another collection · chain F against F, TM-score 1.00
P00366 · AlphaFold monomer V2.0 prediction for glutamate dehydrogenase 1, mitochondrial (P00366) · a predicted model of the same protein · chain E against A, TM-score 0.94

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 P00366
Elsewhere: RCSB PDB 7VDA · PDBe 7VDA · UniProt P00366

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