› 8xd6

Electron Microscopy
2.79Å resolution

Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus in complex with NADPH, AKG and NH4 in the steady stage of reaction

Released:
DOI: 10.2210/pdb8xd6/pdb
PDB entry 8xd6 coloured by chain, front view.
PDB entry 8xd6 coloured by chain, side view.
PDB entry 8xd6 coloured by chain, top view.
Source organism: Thermococcus profundus
Primary publication:
CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase.
Wakabayashi T, Oide M, Nakasako M
OpenAccess logo Sci Rep 14 11165 (2024)
PMID: 38750092
Related structures: EMD-38267

Function and Biology Details

Reaction catalysed: 
L-glutamate + H(2)O + NAD(P)(+) = 2-oxoglutarate + NH(3) + NAD(P)H
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130751 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glutamate dehydrogenase Chain: A
Molecule details ›
Chain: A
Length: 419 amino acids
Theoretical weight: 46.76 KDa
Source organism: Thermococcus profundus
Expression system: Escherichia coli
UniProt:
  • Canonical: O74024 (Residues: 1-419; Coverage: 100%)
Gene names: gdh, gdhA
Sequence domains:

Ligands and Environments


Cofactor: Ligand NDP 1 x NDP
2 bound ligands:
Ligand AKG 2 x AKG
Ligand NH4 1 x NH4
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.79Å
Relevant EMDB volumes: EMD-38267
Expression system: Escherichia coli

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