SMTL ID : 8kao.1

Glutamate dehydrogenase-69O

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-hexamer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 23 residues within 4Å: Chain C: R.76, P.147, D.148, I.149, N.150, R.188, T.192, Q.219, G.220, F.221, G.222, N.223, V.224, D.244, I.245, N.281, A.295, A.296, V.297, G.317, A.318, N.319 Ligands: 69O.2 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:R.76, C:D.148, C:N.150, C:R.188, C:R.188, C:F.221, C:N.223, C:N.223, C:V.224, C:I.245, C:A.296, C:N.319, C:N.319 Water bridges: C:R.76, C:N.223 NAD.3: 23 residues within 4Å: Chain F: R.76, P.147, D.148, I.149, N.150, R.188, T.192, Q.219, G.220, F.221, G.222, N.223, V.224, D.244, I.245, N.281, A.295, A.296, V.297, G.317, A.318, N.319 Ligands: 69O.4 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:R.76, F:D.148, F:N.150, F:R.188, F:R.188, F:T.192, F:F.221, F:N.223, F:N.223, F:V.224, F:I.245, F:A.296, F:N.319, F:N.319 Water bridges: F:R.76, F:N.223

2 x 69O: 2-oxopentanoic acid(Non-covalent)

69O.2: 12 residues within 4Å: Chain C: G.73, G.74, M.93, K.96, K.108, A.146, R.188, N.319, N.344, V.348, S.351 Ligands: NAD.1 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.146 Hydrogen bonds: C:G.74, C:K.108, C:N.319, C:N.344 Salt bridges: C:K.96, C:K.108 69O.4: 12 residues within 4Å: Chain F: G.73, G.74, M.93, K.96, K.108, A.146, R.188, N.319, N.344, V.348, S.351 Ligands: NAD.3 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:A.146 Hydrogen bonds: F:G.74, F:K.108, F:N.319, F:N.344 Salt bridges: F:K.96, F:K.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakuraba, H. et al., Structure of glutamate dehydrogenase-69O. To be published

Release Date

2024-08-07

Peptides

Glutamate dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Glutamate dehydrogenase

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