SMTL ID : 3jd1.1

Glutamate dehydrogenase in complex with NADH, closed conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

12 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 19 residues within 4Å: Chain A: R.94, D.168, M.169, S.170, Q.250, G.251, F.252, G.253, N.254, V.255, G.274, E.275, S.276, A.325, A.326, S.327, Q.330, G.347, N.349 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.94, A:D.168, A:S.170, A:Q.250, A:F.252, A:F.252, A:F.252, A:N.254, A:A.326, A:Q.330, A:N.349 NAI.2: 18 residues within 4Å: Chain A: H.195, Q.205, G.206, N.387, H.391, V.392, S.393 Chain C: H.85, R.86, T.87, C.115, A.116, D.119, V.120, P.121, F.122, K.488, V.492 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:H.85, C:R.86, C:R.86, C:T.87, C:V.120, A:H.391, A:V.392, A:S.393 pi-Cation interactions: C:R.86, C:R.86, C:R.86, C:K.488 NAI.3: 19 residues within 4Å: Chain B: R.94, D.168, M.169, S.170, Q.250, G.251, F.252, G.253, N.254, V.255, G.274, E.275, S.276, A.325, A.326, S.327, Q.330, G.347, N.349 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.94, B:D.168, B:S.170, B:Q.250, B:F.252, B:F.252, B:F.252, B:N.254, B:A.326, B:Q.330, B:N.349 NAI.4: 18 residues within 4Å: Chain A: H.85, R.86, T.87, C.115, A.116, D.119, V.120, P.121, F.122, K.488, V.492 Chain B: H.195, Q.205, G.206, N.387, H.391, V.392, S.393 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:H.391, B:V.392, B:S.393, A:H.85, A:R.86, A:R.86, A:T.87, A:V.120 pi-Cation interactions: A:R.86, A:R.86, A:R.86, A:K.488 NAI.5: 19 residues within 4Å: Chain C: R.94, D.168, M.169, S.170, Q.250, G.251, F.252, G.253, N.254, V.255, G.274, E.275, S.276, A.325, A.326, S.327, Q.330, G.347, N.349 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:R.94, C:D.168, C:S.170, C:Q.250, C:F.252, C:F.252, C:F.252, C:N.254, C:A.326, C:Q.330, C:N.349 NAI.6: 18 residues within 4Å: Chain B: H.85, R.86, T.87, C.115, A.116, D.119, V.120, P.121, F.122, K.488, V.492 Chain C: H.195, Q.205, G.206, N.387, H.391, V.392, S.393 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:H.391, C:V.392, C:S.393, B:H.85, B:R.86, B:R.86, B:T.87, B:V.120 pi-Cation interactions: B:R.86, B:R.86, B:R.86, B:K.488 NAI.7: 19 residues within 4Å: Chain D: R.94, D.168, M.169, S.170, Q.250, G.251, F.252, G.253, N.254, V.255, G.274, E.275, S.276, A.325, A.326, S.327, Q.330, G.347, N.349 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:R.94, D:D.168, D:D.168, D:S.170, D:Q.250, D:F.252, D:F.252, D:F.252, D:N.254, D:A.326, D:Q.330, D:N.349 NAI.8: 18 residues within 4Å: Chain D: H.195, Q.205, G.206, N.387, H.391, V.392, S.393 Chain F: H.85, R.86, T.87, C.115, A.116, D.119, V.120, P.121, F.122, K.488, V.492 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:H.85, F:R.86, F:R.86, F:T.87, F:V.120, D:H.391, D:V.392, D:S.393 pi-Cation interactions: F:R.86, F:R.86, F:R.86, F:K.488 NAI.9: 19 residues within 4Å: Chain E: R.94, D.168, M.169, S.170, Q.250, G.251, F.252, G.253, N.254, V.255, G.274, E.275, S.276, A.325, A.326, S.327, Q.330, G.347, N.349 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:R.94, E:D.168, E:D.168, E:S.170, E:Q.250, E:F.252, E:F.252, E:F.252, E:N.254, E:A.326, E:Q.330, E:N.349 NAI.10: 18 residues within 4Å: Chain D: H.85, R.86, T.87, C.115, A.116, D.119, V.120, P.121, F.122, K.488, V.492 Chain E: H.195, Q.205, G.206, N.387, H.391, V.392, S.393 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:H.85, D:R.86, D:R.86, D:T.87, D:V.120, E:H.391, E:V.392, E:S.393 pi-Cation interactions: D:R.86, D:R.86, D:R.86, D:K.488 NAI.11: 19 residues within 4Å: Chain F: R.94, D.168, M.169, S.170, Q.250, G.251, F.252, G.253, N.254, V.255, G.274, E.275, S.276, A.325, A.326, S.327, Q.330, G.347, N.349 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:R.94, F:D.168, F:D.168, F:S.170, F:Q.250, F:F.252, F:F.252, F:F.252, F:N.254, F:A.326, F:Q.330, F:N.349 NAI.12: 18 residues within 4Å: Chain E: H.85, R.86, T.87, C.115, A.116, D.119, V.120, P.121, F.122, K.488, V.492 Chain F: H.195, Q.205, G.206, N.387, H.391, V.392, S.393 12 PLIP interactions: 3 interactions with chain F, 9 interactions with chain E Hydrogen bonds: F:H.391, F:V.392, F:S.393, E:H.85, E:R.86, E:R.86, E:T.87, E:V.120 pi-Cation interactions: E:R.86, E:R.86, E:R.86, E:K.488

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borgnia, M.J. et al., Using Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with Glutamate Dehydrogenase. Mol.Pharmacol. (2016)

Release Date

2016-04-27

Peptides

Glutamate dehydrogenase 1, mitochondrial: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Glutamate dehydrogenase 1, mitochondrial

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