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Structure of glutamate dehydrogenase

Analyse Structure of glutamate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1GTM
Type: protein
Length: 1,251 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate dehydrogenase
EC: 1.4.1.3
UniProt: P80319
Ligands: SO4
Pockets: 12 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Glutamate dehydrogenase (EC 1.4.1.3)	protein	417	49% helix, 18% strand	P80319

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, C

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	560	0.74	0.82	52	empty
2	844	0.73	0.78	69	SO4
3	63	0.72	0.98	20	empty
4	865	0.72	0.77	70	SO4
5	812	0.72	0.77	66	empty

Interfaces

3 interfaces between chains.

A–C · 1011 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 996 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 993 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

1GTM · Structure of glutamate dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
P80319 · AlphaFold monomer V2.0 prediction for glutamate dehydrogenase (P80319) · a predicted model of the same protein · chain C 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 P80319
Elsewhere: RCSB PDB 1GTM · PDBe 1GTM · UniProt P80319

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