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Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus

Analyse Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JNC
Type: protein
Length: 419 residues
Chains: 1
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.7
Source: Thermococcus profundus
Molecule: Glutamate dehydrogenase
EC: 1.4.1.3
UniProt: O74024
Pockets: 1 · best druggability 0.73

Structure

electron microscopy · resolution 3.7 · 1 distinct chain · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutamate dehydrogenase (EC 1.4.1.3)	protein	419	41% helix, 16% strand	O74024

Ligands and binding sites

TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	803	0.73	0.78	70	TRS

Compared structures

6JNC · Cryo-EM structure of glutamate dehydrogenase from thermococcus profundus · the same entry in another collection · chain A against A, TM-score 1.00
O74024 · AlphaFold monomer V2.0 prediction for glutamate dehydrogenase (O74024) · 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 O74024
Elsewhere: RCSB PDB 6JNC · PDBe 6JNC · UniProt O74024

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