SMTL ID : 3etg.1

Glutamate dehydrogenase complexed with GW5074

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: 14 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, G.377, V.378, S.381 Ligands: NDP.2 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:A.166 Hydrogen bonds: A:G.92, A:K.126, A:P.167, A:S.381 Salt bridges: A:K.90, A:R.211 GLU.5: 14 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, G.377, V.378, S.381 Ligands: NDP.6 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:A.166, B:V.378 Hydrogen bonds: B:G.92, B:P.167, B:D.168, B:S.381 Water bridges: B:V.378 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 8 PLIP interactions: 8 interactions with chain C, Hydrogen bonds: C:G.92, C:D.168, C:D.168, C:N.349, C:G.377, 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 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:V.378 Hydrogen bonds: D:G.92, D:K.126, D:P.167, 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, T.199, R.211, N.349, V.378, S.381 Ligands: NDP.18 8 PLIP interactions: 8 interactions with chain E, Hydrogen bonds: E:P.167, E:D.168, E:T.199, E:N.349, E:S.381, 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, Hydrophobic interactions: F:A.166 Hydrogen bonds: F:G.92, 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: 22 residues within 4Å: Chain A: 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, A.326, S.327, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.1 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:T.215, A:V.255, A:N.374 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:S.327, A:Q.330, A:N.349 Water bridges: A:R.94, A:G.253, A:N.254, A:G.256, A:N.349 Salt bridges: A:K.134 NDP.6: 21 residues within 4Å: Chain B: 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, A.326, S.327, G.347, A.348, N.349, N.374 Ligands: GLU.5 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:T.215 Hydrogen bonds: B:S.170, B:R.211, B:R.211, B:T.215, 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:Q.330, B:N.349 Water bridges: B:G.253, B:G.253 Salt bridges: B:K.134, B:K.295 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, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.9 19 PLIP interactions: 18 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:T.215, E.9 Hydrogen bonds: C:R.94, C:S.170, C:R.211, C:R.211, C:T.215, C:Q.250, 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:N.254 Salt bridges: C:K.134 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, F.252, G.253, N.254, V.255, E.275, S.276, A.326, S.327, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.13 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:T.215, D:V.255 Hydrogen bonds: D:R.94, D:S.170, D:R.211, D:R.211, D:T.215, D:Q.250, D:F.252, D:N.254, D:V.255, D:S.276, D:S.276, D:D.277, D:A.326, D:S.327, D:Q.330, D:N.349, D:N.349 Water bridges: D:R.94, D:G.253, D:G.253, D:N.254 Salt bridges: D:K.134 NDP.18: 23 residues within 4Å: Chain E: R.94, K.134, 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, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.17 21 PLIP interactions: 21 interactions with chain E Hydrophobic interactions: E:T.215, E:V.255, E:N.374 Hydrogen bonds: E:R.94, E:S.170, E:R.211, E:R.211, E:T.215, E:Q.250, E:F.252, E:N.254, E:V.255, E:E.275, E:S.276, E:S.276, E:A.326, E:S.327, E:Q.330, E:N.349 Salt bridges: E:K.134, E:K.295 NDP.22: 23 residues within 4Å: Chain F: 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, S.327, Q.330, 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:V.255, F:N.374, E.21 Hydrogen bonds: F:S.170, F:R.211, F:R.211, F:T.215, F:T.215, F:Q.250, F:F.252, F:N.254, F:V.255, F:S.276, F:S.276, F:A.326, F:S.327, F:Q.330, F:N.349, F:N.349 Salt bridges: F:K.134

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

GTP.3: 12 residues within 4Å: Chain A: H.209, G.210, S.213, R.217, L.257, H.258, R.261, Y.262, R.265, K.289, E.292, H.450 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.210, A:S.213, A:S.213, A:R.261, A:Y.262, A:Y.262, A:K.289 Water bridges: A:H.209 Salt bridges: A:H.209, A:H.209, A:R.217, A:R.265, A:E.292, A:H.450, A:H.450 pi-Cation interactions: A:R.261, A:R.261 GTP.7: 10 residues within 4Å: Chain B: H.209, 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 B Hydrogen bonds: B:Y.262, B:K.289 Salt bridges: B:H.209, B:R.217, B:R.261, B:R.265, B:E.292, B:H.450 pi-Cation interactions: B:R.261 GTP.11: 13 residues within 4Å: Chain C: 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 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:S.213, C:S.213, C:H.258, C:R.261, C:Y.262, C:Y.262, C:K.289 Water bridges: C:H.209, C:R.265 Salt bridges: C:H.209, C:H.209, C:R.217, C:R.261, C:R.265, C:E.292, C:K.446, C:H.450, C:H.450 pi-Cation interactions: C:R.261, C:R.261 GTP.15: 12 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, H.450 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:G.210, D:S.213, D:S.213, D:H.258, D:R.261, D:Y.262, D:Y.262, D:K.289 Water bridges: D:H.209, D:H.209, D:R.265, D:R.265, D:E.292, D:E.292, D:H.450 Salt bridges: D:H.209, D:H.209, D:R.217, D:R.265, D:E.292, D:H.450, D:H.450 pi-Cation interactions: D:R.261, D:R.261 GTP.19: 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 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:S.213, E:H.258, 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, E:H.450 pi-Cation interactions: E:R.261 GTP.23: 10 residues within 4Å: Chain F: H.209, R.217, L.257, H.258, R.261, Y.262, R.265, K.289, E.292, H.450 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:R.261, F:K.289 Water bridges: F:H.258 Salt bridges: F:H.209, F:H.209, F:R.217, F:R.261, F:R.265, F:E.292 pi-Cation interactions: F:R.261

6 x GWD: (3E)-3-[(3,5-dibromo-4-hydroxyphenyl)methylidene]-5-iodo-1,3-dihydro-2H-indol-2-one(Non-covalent)

GWD.4: 7 residues within 4Å: Chain A: E.142, R.146, R.147, M.150, D.181, S.185 Ligands: GWD.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.147, A:D.181 pi-Cation interactions: A:R.146, A:R.146 GWD.8: 7 residues within 4Å: Chain B: E.142, R.146, R.147, M.150, S.185, T.186 Ligands: GWD.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.147, B:R.147, B:D.181 pi-Cation interactions: B:R.146 GWD.12: 8 residues within 4Å: Chain C: E.142, R.146, R.147, M.150, D.181, S.185, T.186 Ligands: GWD.8 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.147, C:D.181 pi-Cation interactions: C:R.146 GWD.16: 5 residues within 4Å: Chain D: R.146, R.147, M.150, T.186 Ligands: GWD.24 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.147, D:R.147 pi-Cation interactions: D:R.146 GWD.20: 8 residues within 4Å: Chain E: E.142, R.146, R.147, M.150, T.182, S.185, T.186 Ligands: GWD.4 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:T.182 Hydrogen bonds: E:R.147 pi-Cation interactions: E:R.146 GWD.24: 7 residues within 4Å: Chain F: E.142, R.146, R.147, M.150, S.185, T.186 Ligands: GWD.16 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.147 pi-Cation interactions: F:R.146

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

Glutamate dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Glutamate dehydrogenase

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