SMTL ID : 8zng.1

Cryo-EM structure of W89F mutated Glutamate dehydrogenase from Thermococcus profundus in complex with NADPH and AKG in the steady stage of reaction

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 19 residues within 4Å: Chain A: T.188, Q.215, G.216, Y.217, G.218, N.219, A.220, D.241, S.242, K.261, N.278, A.292, A.293, I.294, V.314, A.315, N.316, N.341 Ligands: AKG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.188, A:Y.217, A:Y.217, A:N.219, A:N.219, A:A.220, A:S.242, A:S.242, A:S.242, A:A.293, A:N.316 Salt bridges: A:K.261

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 12 residues within 4Å: Chain A: K.66, G.67, M.87, K.90, A.140, P.141, D.142, N.316, G.344, V.345, S.348 Ligands: NDP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.316, A:G.344, A:S.348 Salt bridges: A:K.66, A:K.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wakabayashi, T. et al., Mechanism for drastic reduction in catalytic activity of Trp89Phe-mutated glutamate dehydrogenase revealed by crystal structure and cryoEM-sampling of metastable conformation in action. To Be Published

Release Date

2024-06-12

Peptides

Glutamate dehydrogenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glutamate dehydrogenase

Related Entries With Identical Sequence