SMTL ID : 8kar.1

Glutamate dehydrogenase-AKG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-hexamer

Ligands

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

AKG.1: 15 residues within 4Å: Chain A: K.72, G.73, G.74, M.93, K.96, K.108, A.146, D.148, T.176, R.188, N.319, G.347, V.348, S.351 Ligands: NAD.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.146 Hydrogen bonds: A:G.74, A:K.108, A:D.148, A:T.176, A:N.319, A:S.351 Water bridges: A:K.96 Salt bridges: A:K.72, A:K.96, A:K.108, A:R.188 AKG.8: 15 residues within 4Å: Chain B: K.72, G.73, G.74, M.93, K.96, K.108, A.146, D.148, T.176, R.188, N.319, G.347, V.348, S.351 Ligands: NAD.9 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.146 Hydrogen bonds: B:G.74, B:D.148, B:T.176, B:N.319, B:S.351 Water bridges: B:K.96, B:K.108, B:K.108, B:K.108 Salt bridges: B:K.72, B:K.96, B:K.108, B:R.188 AKG.14: 15 residues within 4Å: Chain C: K.72, G.73, G.74, M.93, K.96, K.108, A.146, D.148, T.176, R.188, N.319, G.347, V.348, S.351 Ligands: NAD.15 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:A.146 Hydrogen bonds: C:G.74, C:D.148, C:N.319, C:S.351 Water bridges: C:K.96, C:K.108, C:K.108, C:K.108, C:N.344 Salt bridges: C:K.72, C:K.96, C:K.108, C:R.188 AKG.20: 15 residues within 4Å: Chain D: K.72, G.73, G.74, M.93, K.96, K.108, A.146, D.148, T.176, R.188, N.319, G.347, V.348, S.351 Ligands: NAD.21 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:A.146 Hydrogen bonds: D:G.74, D:K.108, D:D.148, D:D.148, D:N.319, D:S.351 Water bridges: D:K.96 Salt bridges: D:K.72, D:K.96, D:K.108, D:R.188 AKG.27: 15 residues within 4Å: Chain E: K.72, G.73, G.74, M.93, K.96, K.108, A.146, D.148, T.176, R.188, N.319, G.347, V.348, S.351 Ligands: NAD.28 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:A.146 Hydrogen bonds: E:G.74, E:D.148, E:D.148, E:N.319, E:S.351 Water bridges: E:K.96, E:K.108, E:K.108, E:K.108 Salt bridges: E:K.72, E:K.96, E:K.108, E:R.188 AKG.33: 15 residues within 4Å: Chain F: K.72, G.73, G.74, M.93, K.96, K.108, A.146, D.148, T.176, R.188, N.319, G.347, V.348, S.351 Ligands: NAD.34 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:A.146 Hydrogen bonds: F:G.74, F:T.176, F:N.319, F:S.351 Water bridges: F:K.96, F:K.108, F:K.108, F:K.108, F:N.344 Salt bridges: F:K.72, F:K.96, F:K.108, F:R.188

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

NAD.2: 22 residues within 4Å: Chain A: R.76, D.148, I.149, N.150, R.188, T.192, 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, N.344 Ligands: AKG.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:T.192, A:V.224, A:N.344 Hydrogen bonds: A:R.76, A:D.148, A:N.150, A:R.188, A:R.188, A:F.221, A:F.221, A:N.223, A:N.223, A:V.224, A:I.245, A:A.296, A:N.319, A:N.319 Water bridges: A:R.76, A:G.222, A:G.225 NAD.9: 23 residues within 4Å: Chain B: R.76, D.148, I.149, N.150, R.188, T.192, 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, N.344, G.347 Ligands: AKG.8 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:T.192, B:V.224, B:N.344 Hydrogen bonds: B:R.76, B:D.148, B:N.150, B:R.188, B:R.188, B:F.221, B:N.223, B:N.223, B:V.224, B:I.245, B:A.296, B:N.319, B:N.319 Water bridges: B:D.148, B:T.192, B:G.222, B:G.225, B:D.244 pi-Cation interactions: B:K.108 NAD.15: 24 residues within 4Å: Chain C: R.76, 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, N.344, G.347 Ligands: AKG.14 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:T.192, C:V.224, C:N.344 Hydrogen bonds: C:R.76, C:K.108, C:D.148, C:N.150, C:R.188, C:R.188, C:T.192, 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:D.148, C:T.192, C:Q.219, C:G.222, C:G.225, C:D.244 pi-Cation interactions: C:K.108 NAD.21: 22 residues within 4Å: Chain D: R.76, D.148, I.149, N.150, R.188, T.192, 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, N.344 Ligands: AKG.20 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:T.192, D:V.224, D:N.344 Hydrogen bonds: D:R.76, D:D.148, D:N.150, D:R.188, D:R.188, D:T.192, D:F.221, D:F.221, D:N.223, D:N.223, D:V.224, D:I.245, D:A.296, D:N.319, D:N.319 Water bridges: D:R.76, D:G.222, D:G.225, D:D.244 NAD.28: 23 residues within 4Å: Chain E: R.76, D.148, I.149, N.150, R.188, T.192, 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, N.344, G.347 Ligands: AKG.27 24 PLIP interactions: 24 interactions with chain E Hydrophobic interactions: E:T.192, E:V.224, E:N.344 Hydrogen bonds: E:R.76, E:D.148, E:N.150, E:R.188, E:R.188, E:T.192, E:F.221, E:N.223, E:N.223, E:V.224, E:I.245, E:A.296, E:N.319, E:N.319 Water bridges: E:D.148, E:T.192, E:G.222, E:G.225, E:D.244, E:D.244 pi-Cation interactions: E:K.108 NAD.34: 24 residues within 4Å: Chain F: R.76, 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, N.344, G.347 Ligands: AKG.33 22 PLIP interactions: 22 interactions with chain F Hydrophobic interactions: F:T.192, F:V.224, F:N.344 Hydrogen bonds: F:R.76, F:K.108, F:D.148, F:N.150, F:R.188, F:R.188, 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:Q.219, F:G.222, F:N.223, F:G.225 pi-Cation interactions: F:K.108

26 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: Q.13, K.16, D.340, I.341, R.398, M.402 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: V.40, Q.42, W.60, Q.83 Chain C: V.40, Q.42, W.60, Q.83 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: E.38, R.39, Y.71 Chain C: Q.132, L.133 Ligands: EDO.6, EDO.7 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: R.39, Y.71 Chain B: I.164, G.168, V.170 Ligands: EDO.5 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: E.38, S.66, A.67, M.413, R.416, L.418 Ligands: EDO.5 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain B: E.38, S.66, R.416, L.418 Ligands: EDO.12 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain B: Q.13, K.16, D.340, I.341, R.398, M.402 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain B: E.38, R.39, Y.71 Chain E: L.133 Chain F: I.164 Ligands: EDO.10 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: R.359 Chain B: F.172, N.357, N.358, G.361, G.362 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: K.165 Chain C: D.125, K.129, E.162, K.165 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain C: Q.13, K.16, D.340, I.341, R.398, M.402 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain C: E.38, S.66, A.67, M.413, R.416, L.418 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain C: H.135, K.136, L.138, Y.163, T.167 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain D: Q.13, K.16, D.340, I.341, R.398, M.402 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain D: V.40, Q.42, W.60, Q.83 Chain F: V.40, Q.42, W.60, Q.83 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain D: E.38, R.39, Y.71 Chain F: Q.132, L.133 Ligands: EDO.25, EDO.26 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain D: R.39, Y.71 Chain E: I.164, G.168, V.170 Ligands: EDO.24 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain D: E.38, S.66, A.67, M.413, R.416, L.418 Ligands: EDO.24 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain E: E.38, S.66, R.416, L.418 Ligands: EDO.31 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain E: Q.13, K.16, D.340, I.341, R.398, M.402 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain B: L.133 Chain C: I.164 Chain E: E.38, R.39, Y.71 Ligands: EDO.29 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain D: R.359 Chain E: F.172, N.357, N.358, G.361, G.362 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain E: K.165 Chain F: D.125, K.129, E.162, K.165 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain F: Q.13, K.16, D.340, I.341, R.398, M.402 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain F: E.38, S.66, A.67, M.413, R.416, L.418 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain F: H.135, K.136, L.138, Y.163, T.167 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakuraba, H. et al., Structure of glutamate dehydrogenase-AKG. 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

Related Entries With Identical Sequence