MolNFT v1 · #68221 · protein

Glutamate dehydrogenase in complex with GTP

3JD0 · Glutamate dehydrogenase 1, mitochondrial: “Glutamate dehydrogenase in complex with GTP”. Electron microscopy, 1 ligand (GTP), 20 pockets (best druggability 0.87). MolNFT v1 #68221 on GenesisL1: 3D structure, binding sites and…

PDB: 3JD0
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
Ligands: GTP
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 1 distinct chain · 49% helix, 10% 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	49% helix, 10% strand	P00366

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, 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	753	0.87	0.90	96	empty
2	1176	0.86	0.87	106	empty
3	552	0.86	0.91	39	empty
4	553	0.86	0.91	39	empty
5	595	0.85	0.90	72	empty

Interfaces

15 interfaces between chains.

E–F · 1995 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1993 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 1991 Å² buried · 14 hydrogen bonds · protein-protein
D–F · 1988 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 1987 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3JD0 · Glutamate dehydrogenase in complex with GTP · 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 D against A, TM-score 0.93

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 3JD0 · PDBe 3JD0 · UniProt P00366

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