SMTL ID : 6dhm.1

Bovine glutamate dehydrogenase complexed with zinc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-hexamer

Ligands

6 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 14 residues within 4Å: Chain A: K.171, G.172, G.173, M.192, K.195, K.207, A.247, P.248, D.249, R.292, N.430, V.459, S.462 Ligands: NDP.2 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:V.459 Hydrogen bonds: A:G.172, A:G.173, A:P.248, A:D.249, A:N.430, A:S.462 Salt bridges: A:K.171, A:K.195, A:K.207, A:R.292 GLU.6: 15 residues within 4Å: Chain B: K.171, G.172, G.173, M.192, K.195, K.207, A.247, P.248, D.249, R.292, N.430, G.458, V.459, S.462 Ligands: NDP.7 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:A.247, B:V.459 Hydrogen bonds: B:G.172, B:G.173, B:K.207, B:P.248, B:D.249, B:T.280, B:N.430, B:G.458, B:S.462 Salt bridges: B:K.171, B:K.195, B:K.207, B:R.292 GLU.11: 15 residues within 4Å: Chain C: K.171, G.172, G.173, M.192, K.195, K.207, A.247, P.248, D.249, T.280, R.292, N.430, V.459, S.462 Ligands: NDP.12 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:A.247, C:V.459 Hydrogen bonds: C:G.172, C:G.173, C:K.207, C:P.248, C:D.249, C:T.280, C:N.430, C:N.455, C:S.462 Salt bridges: C:K.171, C:K.195, C:K.207, C:R.292 GLU.16: 16 residues within 4Å: Chain D: K.171, G.172, G.173, M.192, K.195, K.207, A.247, P.248, D.249, T.280, R.292, N.430, G.458, V.459, S.462 Ligands: NDP.17 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:A.247, D:V.459 Hydrogen bonds: D:G.173, D:K.195, D:P.248, D:D.249, D:N.430, D:V.459, D:S.462, D:S.462 Salt bridges: D:K.171, D:K.195, D:K.207, D:R.292 GLU.21: 15 residues within 4Å: Chain E: K.171, G.172, G.173, M.192, K.195, K.207, A.247, P.248, D.249, R.292, N.430, G.458, V.459, S.462 Ligands: NDP.22 12 PLIP interactions: 10 interactions with chain E, 2 Ligand-Ligand interactions Hydrophobic interactions: E:A.247 Hydrogen bonds: E:G.172, E:G.173, E:P.248, E:N.430, E:S.462, E.21, E.21 Salt bridges: E:K.171, E:K.195, E:K.207, E:R.292 GLU.27: 14 residues within 4Å: Chain F: K.171, G.172, M.192, K.195, K.207, A.247, P.248, D.249, T.280, R.292, N.430, V.459, S.462 Ligands: NDP.28 12 PLIP interactions: 10 interactions with chain F, 2 Ligand-Ligand interactions Hydrogen bonds: F:K.207, F:P.248, F:T.280, F:N.430, F:G.458, F:S.462, E.27, E.27 Salt bridges: F:K.171, F:K.195, F:K.207, F:R.292

6 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 23 residues within 4Å: Chain A: R.175, D.249, M.250, S.251, R.292, T.296, Q.331, G.332, F.333, G.334, N.335, V.336, E.356, S.357, A.406, A.407, S.408, Q.411, G.428, A.429, N.430, N.455 Ligands: GLU.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.336, A:N.455 Hydrogen bonds: A:R.175, A:D.249, A:S.251, A:R.292, A:R.292, A:Q.331, A:F.333, A:N.335, A:N.335, A:V.336, A:E.356, A:S.357, A:S.357, A:A.407, A:S.408, A:S.408, A:N.430, A:N.430 NDP.7: 22 residues within 4Å: Chain B: R.175, D.249, M.250, S.251, R.292, T.296, Q.331, G.332, F.333, G.334, N.335, V.336, E.356, S.357, A.406, A.407, Q.411, G.428, A.429, N.430, N.455 Ligands: GLU.6 20 PLIP interactions: 19 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:V.336, B:N.455, E.6 Hydrogen bonds: B:R.175, B:D.249, B:S.251, B:R.292, B:R.292, B:F.333, B:N.335, B:N.335, B:V.336, B:S.357, B:S.357, B:A.407, B:Q.411, B:Q.411, B:N.430, B:N.430 Salt bridges: B:K.215 NDP.12: 25 residues within 4Å: Chain C: R.175, K.215, D.249, M.250, S.251, R.292, T.296, Q.331, G.332, F.333, G.334, N.335, V.336, G.337, E.356, S.357, A.406, A.407, S.408, Q.411, G.428, A.429, N.430, N.455 Ligands: GLU.11 23 PLIP interactions: 22 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:N.455, E.11 Hydrogen bonds: C:R.175, C:D.249, C:S.251, C:R.292, C:R.292, C:Q.331, C:F.333, C:N.335, C:N.335, C:V.336, C:G.337, C:E.356, C:S.357, C:S.357, C:A.407, C:S.408, C:S.408, C:N.430, C:N.430 Salt bridges: C:K.215, C:K.376 NDP.17: 26 residues within 4Å: Chain D: A.82, K.195, K.215, D.249, M.250, S.251, R.292, T.296, Q.331, G.332, F.333, G.334, N.335, V.336, E.356, S.357, A.406, A.407, S.408, Q.411, G.428, A.429, N.430, N.455, G.458 Ligands: GLU.16 22 PLIP interactions: 21 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:V.336, D:N.455, E.16 Hydrogen bonds: D:R.175, D:D.249, D:S.251, D:R.292, D:R.292, D:Q.331, D:F.333, D:N.335, D:N.335, D:V.336, D:E.356, D:S.357, D:S.357, D:A.407, D:S.408, D:S.408, D:N.430, D:N.430 Salt bridges: D:K.215 NDP.22: 25 residues within 4Å: Chain E: R.175, K.195, K.215, P.248, D.249, M.250, S.251, R.292, T.296, Q.331, G.332, F.333, G.334, N.335, V.336, E.356, S.357, A.406, A.407, Q.411, G.428, A.429, N.430, N.455 Ligands: GLU.21 23 PLIP interactions: 22 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: E:V.336, E:N.455, E.21 Hydrogen bonds: E:R.175, E:D.249, E:S.251, E:R.292, E:R.292, E:T.296, E:T.296, E:F.333, E:G.334, E:N.335, E:N.335, E:V.336, E:E.356, E:S.357, E:A.407, E:Q.411, E:N.430, E:N.430 Salt bridges: E:K.215, E:K.376 NDP.28: 24 residues within 4Å: Chain F: R.175, K.215, P.248, D.249, M.250, S.251, R.292, T.296, Q.331, G.332, F.333, G.334, N.335, V.336, E.356, S.357, A.406, A.407, Q.411, G.428, A.429, N.430, N.455 Ligands: GLU.27 22 PLIP interactions: 21 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: F:V.336, F:N.455 Hydrogen bonds: F:R.175, F:D.249, F:S.251, F:R.292, F:R.292, F:Q.331, F:F.333, F:G.334, F:N.335, F:N.335, F:V.336, F:S.357, F:S.357, F:A.407, F:Q.411, F:Q.411, F:N.430, F:N.430, E.27 Salt bridges: F:K.215

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

GTP.3: 13 residues within 4Å: Chain A: H.290, G.291, S.294, R.298, H.339, R.342, Y.343, R.346, K.370, E.373, K.527, H.531 Ligands: ZN.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.294, A:H.339, A:R.342, A:R.342, A:Y.343, A:K.370 Salt bridges: A:H.290, A:H.290, A:R.298, A:R.342, A:R.346, A:E.373, A:K.527, A:K.527, A:H.531 pi-Cation interactions: A:R.342 GTP.8: 14 residues within 4Å: Chain B: H.290, G.291, S.294, R.298, L.338, H.339, R.342, Y.343, R.346, K.370, E.373, K.527, H.531 Ligands: ZN.10 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:S.294, B:H.339, B:R.342, B:R.342, B:Y.343, B:K.370 Salt bridges: B:H.290, B:H.290, B:R.298, B:R.342, B:R.346, B:E.373, B:K.527, B:K.527, B:H.531 pi-Cation interactions: B:R.342, B:R.342 GTP.13: 12 residues within 4Å: Chain C: H.290, G.291, S.294, R.298, H.339, R.342, Y.343, R.346, K.370, E.373, H.531 Ligands: ZN.15 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:S.294, C:R.342, C:R.342, C:Y.343, C:Y.343, C:K.370, C:K.370 Salt bridges: C:H.290, C:H.290, C:R.298, C:R.342, C:R.346, C:E.373, C:K.527, C:K.527, C:H.531 pi-Cation interactions: C:R.342, C:R.342 GTP.18: 13 residues within 4Å: Chain D: H.290, G.291, S.294, R.298, L.338, H.339, R.342, Y.343, R.346, K.370, E.373, H.531 Ligands: ZN.20 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:S.294, D:R.298, D:H.339, D:R.342, D:R.342, D:Y.343, D:Y.343, D:Y.343, D:K.370 Salt bridges: D:H.290, D:H.290, D:R.298, D:R.342, D:R.346, D:E.373, D:H.531 pi-Cation interactions: D:R.342, D:R.342 GTP.23: 14 residues within 4Å: Chain E: H.290, G.291, S.294, R.298, L.338, H.339, R.342, Y.343, R.346, K.370, E.373, K.527, H.531 Ligands: ZN.25 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:G.291, E:S.294, E:H.339, E:R.342, E:R.342, E:Y.343, E:Y.343, E:K.370, E:K.370 Salt bridges: E:H.290, E:H.290, E:R.298, E:R.342, E:R.346, E:E.373, E:K.527, E:K.527, E:H.531 pi-Cation interactions: E:R.342, E:R.342 GTP.29: 14 residues within 4Å: Chain F: H.290, G.291, S.294, R.298, L.338, H.339, R.342, Y.343, R.346, K.370, E.373, K.527, H.531 Ligands: ZN.30 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:S.294, F:H.339, F:R.342, F:R.342, F:Y.343, F:Y.343, F:Y.343, F:K.370, F:K.370 Salt bridges: F:H.290, F:H.290, F:R.298, F:R.342, F:R.346, F:E.373, F:H.531 pi-Cation interactions: F:R.342

12 x ZN: ZINC ION(Non-covalent)

ZN.4: 3 residues within 4Å: Chain A: E.232 Chain D: H.138, Q.165 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Metal complexes: A:E.232, D:H.138 ZN.5: 4 residues within 4Å: Chain A: H.290, R.298, H.531 Ligands: GTP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.290, A:H.531 ZN.9: 3 residues within 4Å: Chain B: E.232 Chain E: H.138, Q.165 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E Metal complexes: B:E.232, B:E.232, E:H.138 ZN.10: 4 residues within 4Å: Chain B: H.290, R.298, H.531 Ligands: GTP.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.290, B:H.531 ZN.14: 3 residues within 4Å: Chain C: E.232, K.235 Chain F: H.138 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain C Metal complexes: F:H.138, C:E.232, C:E.232 ZN.15: 4 residues within 4Å: Chain C: H.290, R.298, H.531 Ligands: GTP.13 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.290, C:H.531 ZN.19: 4 residues within 4Å: Chain A: H.138, Q.165 Chain D: E.232, K.235 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Metal complexes: A:H.138, D:E.232, D:E.232 ZN.20: 4 residues within 4Å: Chain D: H.290, R.298, H.531 Ligands: GTP.18 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.290, D:H.531 ZN.24: 3 residues within 4Å: Chain B: H.138 Chain E: E.232, K.235 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B Metal complexes: E:E.232, E:E.232, B:H.138 ZN.25: 3 residues within 4Å: Chain E: H.290, H.531 Ligands: GTP.23 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.290, E:H.531 ZN.26: 3 residues within 4Å: Chain C: H.138 Chain F: E.232, K.235 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain F Metal complexes: C:H.138, F:E.232, F:E.232 ZN.30: 4 residues within 4Å: Chain F: H.290, R.298, H.531 Ligands: GTP.29 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.290, F:H.531

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bailey, J. et al., A novel mechanism of V-type zinc inhibition of glutamate dehydrogenase results from disruption of subunit interactions necessary for efficient catalysis. FEBS J. (2011)

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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