SMTL ID : 3etd.1

Structure of glutamate dehydrogenase complexed with bithionol

Coordinates

PDB Format

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: NDP.2 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:A.166 Hydrogen bonds: A:G.92, A:K.126, A:D.168, A:N.349, A:S.381 Salt bridges: A:K.90, 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: NDP.6 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:A.166 Hydrogen bonds: B:G.92, B:K.126, B:D.168, B:D.168, B:N.349, B:S.381 Salt bridges: B:K.90, B:R.211 GLU.9: 15 residues within 4Å: Chain C: 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: NDP.10 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:A.166 Hydrogen bonds: C:G.92, C:K.126, C:P.167, C:D.168, C:N.349, C:S.381 Salt bridges: C:K.90, C:R.211 GLU.13: 15 residues within 4Å: Chain D: 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: NDP.14 10 PLIP interactions: 10 interactions with chain D, Hydrophobic interactions: D:A.166, D:V.378 Hydrogen bonds: D:G.92, D:K.126, D:D.168, D:N.349, D:G.377, D:S.381 Salt bridges: D:K.90, 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: NDP.18 9 PLIP interactions: 9 interactions with chain E, Hydrophobic interactions: E:A.166 Hydrogen bonds: E:G.92, E:K.126, E:D.168, E:D.168, E:N.349, E:S.381 Salt bridges: E:K.90, E:R.211 GLU.21: 15 residues within 4Å: Chain F: 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: NDP.22 8 PLIP interactions: 8 interactions with chain F, Hydrogen bonds: F:G.92, F:K.126, F:P.167, F:N.349, F:G.377, F:S.381 Salt bridges: F:K.90, F:R.211

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

NDP.2: 23 residues within 4Å: Chain A: R.94, K.134, 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.326, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.215 Hydrogen bonds: A:S.170, A:R.211, A:R.211, A:T.215, A:Q.250, A:F.252, A:N.254, A:V.255, A:S.276, A:S.276, A:A.326, A:Q.330, A:N.349 Salt bridges: A:K.134 NDP.6: 24 residues within 4Å: Chain B: R.94, K.134, 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.326, S.327, G.347, A.348, N.349, N.374, G.377 Ligands: GLU.5 20 PLIP interactions: 19 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:T.215, E.5 Hydrogen bonds: B:R.94, B:S.170, B:R.211, B:R.211, B:T.215, B:Q.250, B:F.252, B:F.252, B:N.254, B:V.255, B:E.275, B:S.276, B:S.276, B:A.326, B:S.327, B:N.349, B:N.349 Salt bridges: B:K.134 NDP.10: 23 residues within 4Å: Chain C: R.94, K.134, 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.326, S.327, G.347, A.348, N.349, N.374 Ligands: GLU.9 21 PLIP interactions: 20 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:T.215, E.9 Hydrogen bonds: C:S.170, C:R.211, C:R.211, C:T.215, C:Q.250, C:F.252, C:F.252, C:N.254, C:V.255, C:E.275, C:S.276, C:S.276, C:A.326, C:Q.330, C:N.349 Water bridges: C:D.168, C:N.254 Salt bridges: C:K.134, C:K.295 NDP.14: 23 residues within 4Å: Chain D: R.94, K.134, 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.326, S.327, G.347, A.348, N.349, N.374 Ligands: GLU.13 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:T.215 Hydrogen bonds: D:R.94, D:S.170, D:R.211, D:R.211, D:Q.250, D:F.252, D:N.254, D:V.255, D:S.276, D:S.276, D:A.326, D:S.327, D:N.349, D:N.349 Water bridges: D:G.253, D:G.253 Salt bridges: D:K.134 NDP.18: 21 residues within 4Å: Chain E: R.94, K.134, P.167, D.168, M.169, S.170, R.211, T.215, Q.250, F.252, G.253, N.254, V.255, E.275, S.276, A.326, G.347, A.348, N.349, N.374 Ligands: GLU.17 20 PLIP interactions: 19 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: E:T.215, E.17 Hydrogen bonds: E:R.94, E:S.170, E:R.211, E:R.211, E:Q.250, E:F.252, E:F.252, E:N.254, E:V.255, E:E.275, E:S.276, E:S.276, E:A.326, E:N.349, E:N.349, E:N.349 Water bridges: E:G.253 Salt bridges: E:K.134 NDP.22: 21 residues within 4Å: Chain F: R.94, K.134, D.168, M.169, S.170, R.211, T.215, Q.250, F.252, G.253, N.254, V.255, E.275, S.276, D.277, A.326, G.347, A.348, N.349, N.374 Ligands: GLU.21 21 PLIP interactions: 20 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: F:T.215, F:N.374, E.21 Hydrogen bonds: F:S.170, F:R.211, F:R.211, F:T.215, F:Q.250, F:F.252, F:N.254, F:V.255, F:S.276, F:S.276, F:D.277, F:A.326, F:Q.330, F:N.349 Water bridges: F:D.168, F:N.254 Salt bridges: F:K.134, F:K.295

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

GTP.3: 9 residues within 4Å: Chain A: H.209, G.210, I.212, R.217, R.261, Y.262, R.265, E.292, H.450 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.210 Water bridges: A:I.212 Salt bridges: A:H.209, A:H.209, A:R.217, A:R.265, A:E.292, A:H.450, A:H.450 pi-Stacking: A:H.258, A:H.258 GTP.7: 8 residues within 4Å: Chain B: H.209, L.257, H.258, R.261, Y.262, R.265, E.292, K.446 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.262 Salt bridges: B:H.209, B:R.261, B:R.265, B:E.292 pi-Stacking: B:H.258 GTP.11: 10 residues within 4Å: Chain C: I.212, S.213, R.217, L.257, R.261, Y.262, R.265, E.292, K.446, H.450 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:I.212, C:S.213, C:S.213, C:S.213, C:R.217, C:R.261 Salt bridges: C:R.261, C:R.265, C:E.292, C:K.446, C:H.450, C:H.450 pi-Cation interactions: C:R.261 GTP.15: 8 residues within 4Å: Chain D: H.209, G.210, R.217, R.261, Y.262, R.265, E.292, H.450 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.210, D:R.261, D:Y.262, D:Y.262 Salt bridges: D:H.209, D:R.217, D:R.265, D:E.292, D:H.450, D:H.450 pi-Cation interactions: D:H.258 GTP.19: 13 residues within 4Å: Chain E: H.209, G.210, I.212, S.213, R.217, L.257, H.258, R.261, Y.262, R.265, E.292, K.446, H.450 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.210, E:R.217, E:R.261, E:K.289 Salt bridges: E:H.209, E:R.265, E:E.292, E:K.446, E:H.450 GTP.23: 12 residues within 4Å: Chain F: G.210, I.212, S.213, R.217, H.258, R.261, Y.262, R.265, K.289, E.292, K.446, H.450 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:S.213, F:S.213, F:Y.262, F:K.289 Salt bridges: F:R.217, F:R.265, F:E.292, F:H.450

6 x B1T: 2,2'-sulfanediylbis(4,6-dichlorophenol)(Non-covalent)

B1T.4: 7 residues within 4Å: Chain A: E.142, R.146, D.181, S.185 Chain E: R.146, R.147 Ligands: B1T.20 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:R.146 B1T.8: 7 residues within 4Å: Chain B: R.146, R.147, M.150 Chain C: E.142, R.146, D.181 Ligands: B1T.12 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.146 Hydrogen bonds: B:R.147, B:R.147 B1T.12: 7 residues within 4Å: Chain B: K.143, R.146, T.186 Chain C: R.146, R.147, M.150 Ligands: B1T.8 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:R.146 B1T.16: 8 residues within 4Å: Chain A: V.498 Chain D: K.143, R.146, R.147, M.150 Chain F: R.146, T.186 Ligands: B1T.24 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:R.146 B1T.20: 7 residues within 4Å: Chain A: K.143, R.146, R.147 Chain D: V.498 Chain E: E.142, R.146 Ligands: B1T.4 No protein-ligand interaction detected (PLIP) B1T.24: 6 residues within 4Å: Chain D: E.142, R.146 Chain F: R.146, R.147, M.150 Ligands: B1T.16 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:R.146 Hydrogen bonds: F:R.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, M. et al., Novel Inhibitors Complexed with Glutamate Dehydrogenase: ALLOSTERIC REGULATION BY CONTROL OF PROTEIN DYNAMICS. J.Biol.Chem. (2009)

Release Date

2009-06-09

Peptides

GLUD1 protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

GLUD1 protein

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