SMTL ID : 8znc.1

Cryo-EM structure of W89F mutated Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH, 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, G.221, D.241, S.242, R.243, K.261, N.278, A.292, A.293, I.294, V.314, A.315, N.316 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.188 Hydrogen bonds: A:T.188, A:Y.217, A:N.219, A:N.219, A:A.220, A:G.221, A:D.241, A:S.242, A:S.242, A:N.316, A:N.316 Salt bridges: A:K.261

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

AKG.2: 11 residues within 4Å: Chain A: K.66, G.67, G.68, M.87, K.90, K.102, A.140, D.142, V.345, S.348 Ligands: NH4.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.140 Hydrogen bonds: A:G.68, A:S.348 Water bridges: A:K.102, A:K.102 Salt bridges: A:K.66, A:K.90, A:K.102

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.3: 5 residues within 4Å: Chain A: K.90, N.341, G.344, V.345 Ligands: AKG.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.90, A:K.90, A:G.344, A:V.345

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

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