Research workbench

Glutamate dehydrogenase from thermococcus litoralis

Analyse Glutamate dehydrogenase from thermococcus litoralis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1BVU
Type: protein
Length: 2,496 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (glutamate dehydrogenase)
EC: 1.4.1.3
UniProt: Q56304
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Protein (glutamate dehydrogenase) (EC 1.4.1.3)	protein	416	50% helix, 16% strand	Q56304

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	1138	0.89	0.91	124	empty
2	816	0.89	0.92	59	empty
3	829	0.89	0.92	58	empty
4	893	0.74	0.78	75	empty
5	760	0.74	0.79	58	empty

Interfaces

15 interfaces between chains.

B–E · 1058 Å² buried · 10 hydrogen bonds · protein-protein
A–F · 1056 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1051 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 968 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 949 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

1BVU · Glutamate dehydrogenase from thermococcus litoralis · the same entry in another collection · chain A against A, TM-score 1.00
Q56304 · AlphaFold monomer V2.0 prediction for glutamate dehydrogenase (Q56304) · 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 Q56304
Elsewhere: RCSB PDB 1BVU · PDBe 1BVU · UniProt Q56304

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.