SMTL ID : 6dhd.1

Bovine glutamate dehydrogenase complexed with NADH, GTP, glutamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

6 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 15 residues within 4Å: Chain A: K.90, G.91, G.92, M.111, K.114, K.126, A.166, P.167, D.168, R.211, N.349, G.377, V.378, S.381 Ligands: NAI.2 12 PLIP interactions: 11 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:A.166 Hydrogen bonds: A:G.92, A:D.168, A:D.168, A:N.349, A:S.381, E.1 Water bridges: A:K.114 Salt bridges: A:K.90, A:K.114, A:K.126, A:R.211 GLU.5: 15 residues within 4Å: Chain B: K.90, G.91, G.92, M.111, K.114, K.126, A.166, P.167, D.168, R.211, N.349, G.377, V.378, S.381 Ligands: NAI.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.166 Hydrogen bonds: B:G.92, B:D.168, B:D.168, B:N.349, B:S.381 Water bridges: B:K.114, B:K.114 Salt bridges: B:K.90, B:K.114, B:K.126, B:R.211 GLU.9: 14 residues within 4Å: Chain C: K.90, G.92, M.111, K.114, K.126, A.166, P.167, D.168, R.211, N.349, G.377, V.378, S.381 Ligands: NAI.11 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:A.166 Hydrogen bonds: C:G.92, C:D.168, C:D.168, C:N.349, C:S.381 Salt bridges: C:K.90, C:K.114, C:K.126, C:R.211 GLU.13: 14 residues within 4Å: Chain D: K.90, G.92, M.111, K.114, K.126, A.166, P.167, D.168, R.211, N.349, G.377, V.378, S.381 Ligands: NAI.14 10 PLIP interactions: 10 interactions with chain D, Hydrophobic interactions: D:A.166 Hydrogen bonds: D:G.92, D:D.168, D:D.168, D:N.349, D:S.381 Salt bridges: D:K.90, D:K.114, D:K.126, D:R.211 GLU.17: 15 residues within 4Å: Chain E: K.90, G.91, G.92, M.111, K.114, K.126, A.166, P.167, D.168, R.211, N.349, G.377, V.378, S.381 Ligands: NAI.18 11 PLIP interactions: 10 interactions with chain E, 1 Ligand-Ligand interactions Hydrogen bonds: E:G.92, E:D.168, E:D.168, E:N.349, E:G.377, E:S.381, E.17 Salt bridges: E:K.90, E:K.114, E:K.126, E:R.211 GLU.21: 14 residues within 4Å: Chain F: K.90, G.92, M.111, K.114, K.126, A.166, P.167, D.168, R.211, N.349, G.377, V.378, S.381 Ligands: NAI.23 10 PLIP interactions: 10 interactions with chain F, Hydrophobic interactions: F:A.166 Hydrogen bonds: F:G.92, F:D.168, F:D.168, F:N.349, F:S.381 Salt bridges: F:K.90, F:K.114, F:K.126, F:R.211

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

NAI.2: 23 residues within 4Å: Chain A: R.94, P.167, D.168, M.169, S.170, R.211, T.215, Q.250, G.251, F.252, G.253, N.254, V.255, E.275, S.276, A.325, A.326, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.255, A:N.374 Hydrogen bonds: A:R.94, A:D.168, A:S.170, A:R.211, A:R.211, A:Q.250, A:F.252, A:F.252, A:N.254, A:V.255, A:S.276, A:A.326, A:Q.330, A:N.349, A:N.349 Water bridges: A:G.253, A:G.256 pi-Cation interactions: A:K.126 NAI.3: 20 residues within 4Å: Chain A: H.195, Q.205, G.206, K.387, N.388, H.391, V.392, S.393 Chain B: H.85, R.86, T.87, C.115, A.116, D.119, V.120, P.121, F.122, K.488, R.491, V.492 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:N.388, A:N.388, A:H.391, A:S.393, A:S.393, B:R.86, B:T.87, B:T.87, B:V.120, B:R.491 Salt bridges: A:K.387, A:K.387 Water bridges: B:A.116, B:A.116 pi-Cation interactions: B:R.86, B:R.86 NAI.6: 22 residues within 4Å: Chain B: R.94, D.168, M.169, S.170, R.211, T.215, Q.250, G.251, F.252, G.253, N.254, V.255, E.275, S.276, A.325, A.326, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.5 19 PLIP interactions: 18 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:T.215, B:V.255, B:N.374, E.5 Hydrogen bonds: B:R.94, B:D.168, B:D.168, B:S.170, B:R.211, B:R.211, B:Q.250, B:F.252, B:F.252, B:N.254, B:V.255, B:A.326, B:Q.330, B:N.349, B:N.349 NAI.8: 21 residues within 4Å: Chain B: H.195, Q.205, G.206, K.387, N.388, H.391, V.392, S.393, E.445 Chain C: H.85, R.86, T.87, C.115, A.116, D.119, V.120, P.121, F.122, K.488, R.491, V.492 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:K.387, B:N.388, B:H.391, B:V.392, B:S.393, B:S.393, C:R.86, C:T.87, C:T.87, C:V.120, C:R.491 Salt bridges: B:K.387, B:K.387 pi-Cation interactions: C:R.86, C:R.86 NAI.11: 22 residues within 4Å: Chain C: R.94, P.167, D.168, M.169, S.170, R.211, T.215, Q.250, G.251, G.253, N.254, V.255, E.275, S.276, A.325, A.326, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.9 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:T.215, C:V.255, C:N.374 Hydrogen bonds: C:R.94, C:D.168, C:S.170, C:R.211, C:R.211, C:Q.250, C:N.254, C:V.255, C:A.326, C:N.349, C:N.349 Water bridges: C:N.254 pi-Cation interactions: C:K.126 NAI.12: 20 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, R.491 Chain C: H.195, S.204, Q.205, G.206, K.387, N.388, H.391, V.392, S.393 18 PLIP interactions: 9 interactions with chain A, 9 interactions with chain C Hydrogen bonds: A:R.86, A:R.86, A:T.87, A:T.87, A:V.120, A:F.122, A:R.491, C:N.388, C:N.388, C:H.391, C:S.393, C:S.393 pi-Cation interactions: A:R.86, A:R.86 Water bridges: C:S.393, C:R.396 Salt bridges: C:K.387, C:K.387 NAI.14: 22 residues within 4Å: Chain D: R.94, P.167, D.168, M.169, S.170, R.211, T.215, Q.250, G.251, G.253, N.254, V.255, E.275, S.276, A.325, A.326, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.13 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:V.255, D:N.374 Hydrogen bonds: D:R.94, D:D.168, D:D.168, D:S.170, D:R.211, D:R.211, D:Q.250, D:N.254, D:V.255, D:K.295, D:A.326, D:Q.330, D:N.349, D:N.349 pi-Cation interactions: D:K.126 NAI.15: 20 residues within 4Å: Chain D: H.195, S.204, Q.205, G.206, K.387, N.388, 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, R.491 13 PLIP interactions: 8 interactions with chain F, 5 interactions with chain D Hydrogen bonds: F:R.86, F:T.87, F:T.87, F:D.119, F:V.120, F:R.491, D:N.388, D:H.391, D:S.393 pi-Cation interactions: F:R.86, F:R.86 Salt bridges: D:K.387, D:K.387 NAI.18: 23 residues within 4Å: Chain E: R.94, P.167, D.168, M.169, S.170, R.211, T.215, Q.250, G.251, F.252, G.253, N.254, V.255, E.275, S.276, A.325, A.326, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.17 18 PLIP interactions: 18 interactions with chain E Hydrophobic interactions: E:T.215, E:V.255, E:N.374 Hydrogen bonds: E:R.94, E:D.168, E:S.170, E:R.211, E:R.211, E:Q.250, E:F.252, E:N.254, E:V.255, E:S.276, E:K.295, E:A.326, E:Q.330, E:N.349, E:N.349 NAI.19: 20 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, R.491, V.492 Chain E: H.195, Q.205, G.206, K.387, N.388, H.391, V.392, S.393 17 PLIP interactions: 9 interactions with chain E, 8 interactions with chain D Hydrogen bonds: E:K.387, E:N.388, E:H.391, E:V.392, E:S.393, E:S.393, D:R.86, D:T.87, D:T.87, D:D.119, D:V.120, D:R.491 Salt bridges: E:K.387, E:K.387 pi-Stacking: E:H.195 pi-Cation interactions: D:R.86, D:R.86 NAI.22: 20 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, K.387, N.388, H.391, V.392, S.393, E.445 14 PLIP interactions: 7 interactions with chain F, 7 interactions with chain E Hydrogen bonds: F:K.387, F:N.388, F:H.391, F:S.393, F:S.393, E:R.86, E:T.87, E:T.87, E:V.120 Salt bridges: F:K.387, F:K.387 Water bridges: E:A.116, E:Y.382 pi-Cation interactions: E:R.86 NAI.23: 23 residues within 4Å: Chain F: R.94, P.167, D.168, M.169, S.170, R.211, T.215, Q.250, G.251, F.252, G.253, N.254, V.255, E.275, S.276, A.325, A.326, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.21 22 PLIP interactions: 22 interactions with chain F Hydrophobic interactions: F:V.255, F:N.374 Hydrogen bonds: F:R.94, F:D.168, F:D.168, F:S.170, F:R.211, F:R.211, F:Q.250, F:F.252, F:N.254, F:S.276, F:K.295, F:A.326, F:Q.330, F:N.349, F:N.349 Water bridges: F:R.94, F:N.254, F:V.255, F:G.256 pi-Cation interactions: F:K.126

6 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.4: 12 residues within 4Å: Chain A: H.209, G.210, S.213, R.217, L.257, H.258, R.261, Y.262, R.265, E.292, K.446, H.450 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:S.213, A:H.258, A:R.261, A:R.261, A:Y.262, A:Y.262 Water bridges: A:H.209, A:G.210, A:E.292, A:E.292 Salt bridges: A:H.209, A:H.209, A:R.217, A:R.261, A:R.265, A:E.292, A:K.446, A:K.446, A:H.450 pi-Cation interactions: A:R.261, A:R.261 GTP.7: 13 residues within 4Å: Chain B: H.209, G.210, S.213, R.217, L.257, H.258, R.261, Y.262, R.265, K.289, E.292, K.446, H.450 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:S.213, B:R.217, B:H.258, B:R.261, B:R.261, B:Y.262, B:Y.262, B:Y.262, B:K.289 Water bridges: B:H.258 Salt bridges: B:H.209, B:H.209, B:R.217, B:R.261, B:R.265, B:E.292, B:K.446, B:K.446, B:H.450 pi-Cation interactions: B:R.261, B:R.261 GTP.10: 12 residues within 4Å: Chain C: H.209, G.210, S.213, R.217, L.257, H.258, R.261, Y.262, R.265, E.292, K.446, H.450 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:S.213, C:H.258, C:R.261, C:Y.262, C:Y.262 Salt bridges: C:H.209, C:H.209, C:R.217, C:R.261, C:R.265, C:E.292, C:K.446, C:K.446, C:H.450 pi-Cation interactions: C:R.261, C:R.261 GTP.16: 13 residues within 4Å: Chain D: H.209, G.210, S.213, R.217, L.257, H.258, R.261, Y.262, R.265, K.289, E.292, K.446, H.450 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:S.213, D:R.261, D:R.261, D:Y.262, D:Y.262, D:Y.262, D:K.289 Salt bridges: D:H.209, D:H.209, D:R.217, D:R.261, D:R.265, D:E.292, D:K.446, D:K.446, D:H.450 pi-Cation interactions: D:R.261, D:R.261 GTP.20: 13 residues within 4Å: Chain E: H.209, G.210, S.213, R.217, L.257, H.258, R.261, Y.262, R.265, K.289, E.292, K.446, H.450 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:S.213, E:H.258, E:R.261, E:R.261, E:Y.262, E:Y.262, E:Y.262, E:K.289 Salt bridges: E:H.209, E:H.209, E:R.217, E:R.261, E:R.265, E:E.292, E:K.446, E:H.450 pi-Cation interactions: E:R.261, E:R.261 GTP.24: 13 residues within 4Å: Chain F: H.209, G.210, S.213, R.217, L.257, H.258, R.261, Y.262, R.265, K.289, E.292, K.446, H.450 21 PLIP interactions: 21 interactions with chain F Hydrogen bonds: F:S.213, F:H.258, F:R.261, F:R.261, F:Y.262, F:Y.262, F:Y.262, F:K.289 Water bridges: F:H.258, F:R.265, F:R.265 Salt bridges: F:H.209, F:H.209, F:R.217, F:R.261, F:R.265, F:E.292, F:K.446, F:H.450 pi-Cation interactions: F:R.261, F:R.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, T.J. et al., Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation. J. Mol. Biol. (2001)

Release Date

2018-07-25

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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