SMTL ID : 3ete.1

Crystal structure of bovine glutamate dehydrogenase complexed with hexachlorophene

Coordinates

PDB Format Compare

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.90, G.91, G.92, M.111, K.114, K.126, A.166, P.167, D.168, R.211, N.349, V.378, S.381 Ligands: NDP.2 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:V.378 Hydrogen bonds: A:G.92, A:K.114, A:K.126, A:P.167, A:T.199, 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.92, M.111, K.114, K.126, A.166, P.167, D.168, T.199, R.211, N.349, G.377, V.378, S.381 Ligands: NDP.6 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:A.166, B:V.378 Hydrogen bonds: B:G.92, B:K.126, B:P.167, B:D.168, B:N.349, B:S.381 Salt bridges: B:K.90, 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: NDP.10 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:V.378 Hydrogen bonds: C:G.91, C:G.92, C:P.167, C:D.168, C:S.381 Salt bridges: C:K.90, C:R.211 GLU.14: 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: NDP.15 8 PLIP interactions: 8 interactions with chain D, Hydrophobic interactions: D:A.166 Hydrogen bonds: D:G.92, D:K.126, D:P.167, D:N.349, D:S.381 Salt bridges: D:K.90, D:R.211 GLU.18: 15 residues within 4Å: Chain E: K.90, G.92, M.111, K.114, K.126, A.166, P.167, D.168, T.199, R.211, N.349, G.377, V.378, S.381 Ligands: NDP.19 11 PLIP interactions: 11 interactions with chain E, Hydrophobic interactions: E:V.378 Hydrogen bonds: E:G.92, E:K.126, E:P.167, E:D.168, E:T.199, E:N.349, E:G.377, E:S.381 Salt bridges: E:K.90, E:R.211 GLU.21: 16 residues within 4Å: Chain F: K.90, G.91, G.92, M.111, K.114, K.126, A.166, P.167, D.168, T.199, R.211, N.349, G.377, V.378, S.381 Ligands: NDP.22 9 PLIP interactions: 9 interactions with chain F, Hydrophobic interactions: F:A.166 Hydrogen bonds: F:G.92, F:K.126, F:D.168, F:T.199, F:N.349, F:S.381 Salt bridges: F:K.90, F:R.211

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

NDP.2: 26 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, D.277, A.325, A.326, S.327, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.1 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:T.215, E.1 Hydrogen bonds: A:R.94, A:S.170, A:R.211, A:R.211, A:T.215, A:F.252, A:F.252, A:N.254, A:V.255, A:E.275, A:E.275, A:S.276, A:S.276, A:A.326, A:S.327, A:Q.330, A:N.349 Water bridges: A:G.253, A:G.256 Salt bridges: A:K.134, A:K.295 NDP.6: 25 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.325, A.326, S.327, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.5 22 PLIP interactions: 21 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:T.215, B:Q.250, B:F.252, B:F.252, B:N.254, B:V.255, B:S.276, B:S.276, B:A.326, B:Q.330, B:N.349 Water bridges: B:G.253, B:G.256 Salt bridges: B:K.134, B:K.295 NDP.10: 25 residues within 4Å: Chain C: R.94, K.134, P.167, D.168, M.169, S.170, R.211, T.215, G.251, F.252, G.253, N.254, V.255, E.275, S.276, D.277, A.325, A.326, S.327, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.9 28 PLIP interactions: 26 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:T.215, C:N.374 Hydrogen bonds: C:S.170, C:R.211, C:R.211, C:F.252, C:F.252, C:N.254, C:V.255, C:E.275, C:S.276, C:S.276, C:D.277, C:A.326, C:S.327, C:Q.330, C:N.349, E.9, E.9 Water bridges: C:R.94, C:D.168, C:D.168, C:T.171, C:G.253, C:N.254, C:G.256 Salt bridges: C:K.134, C:K.295 NDP.15: 26 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, G.274, E.275, S.276, A.325, A.326, S.327, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.14 26 PLIP interactions: 25 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:T.215, E.14 Hydrogen bonds: D:R.94, D:S.170, D:R.211, D:R.211, D:Q.250, D:F.252, D:F.252, D:N.254, D:V.255, D:E.275, D:E.275, D:S.276, D:S.276, D:D.277, D:A.326, D:S.327, D:Q.330, D:N.349 Water bridges: D:D.168, D:D.168, D:G.253, D:N.254 Salt bridges: D:K.134, D:K.295 NDP.19: 25 residues within 4Å: Chain E: 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.325, A.326, S.327, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.18 20 PLIP interactions: 19 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: E:T.215, E.18 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:S.276, E:S.276, E:A.326, E:S.327, E:Q.330, E:N.349 Water bridges: E:N.254 Salt bridges: E:K.134, E:K.295 NDP.22: 24 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.325, A.326, S.327, Q.330, G.347, A.348, N.349, N.374 Ligands: GLU.21 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:T.215 Hydrogen bonds: F:R.94, F:S.170, F:R.211, F:R.211, F:T.215, F:T.215, F:Q.250, F:F.252, 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 Salt bridges: F:K.134

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

GTP.3: 11 residues within 4Å: Chain A: I.212, S.213, R.217, L.257, H.258, R.261, Y.262, R.265, E.292, K.446, H.450 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.213, A:R.217, A:Y.262, A:Y.262 Water bridges: A:H.258 Salt bridges: A:R.217, A:R.261, A:R.265, A:E.292, A:K.446, A:H.450, A:H.450 GTP.7: 9 residues within 4Å: Chain B: H.209, R.217, L.257, H.258, R.261, Y.262, R.265, E.292, H.450 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Y.262, B:H.450 Water bridges: B:S.213, B:R.261 Salt bridges: B:H.209, B:H.209, B:R.217, B:R.261, B:R.265, B:E.292 GTP.11: 10 residues within 4Å: Chain C: H.209, R.217, L.257, H.258, R.261, Y.262, R.265, K.289, E.292, H.450 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:H.258, C:H.258, C:K.289 Water bridges: C:S.213, C:R.261 Salt bridges: C:H.209, C:H.209, C:R.217, C:R.261, C:R.265, C:H.450, C:H.450 pi-Cation interactions: C:R.261 GTP.16: 10 residues within 4Å: Chain D: H.209, R.217, L.257, H.258, R.261, Y.262, R.265, E.292, K.446, H.450 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Y.262, D:Y.262 Water bridges: D:S.213, D:S.213, D:S.213, D:S.213, D:H.258, D:E.292 Salt bridges: D:H.209, D:H.209, D:R.217, D:R.261, D:R.265, D:E.292, D:H.450 GTP.20: 9 residues within 4Å: Chain E: H.209, R.217, L.257, H.258, R.261, Y.262, R.265, E.292, H.450 8 PLIP interactions: 8 interactions with chain E 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 GTP.23: 9 residues within 4Å: Chain F: H.209, R.217, H.258, R.261, Y.262, R.265, E.292, K.446, H.450 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:Y.262, F:Y.262 Salt bridges: F:H.209, F:H.209, F:R.217, F:R.261, F:R.265, F:E.292, F:H.450

6 x H3P: 2,2'-methanediylbis(3,4,6-trichlorophenol)(Non-covalent)

H3P.4: 10 residues within 4Å: Chain A: T.186, I.187, Y.190 Chain E: M.150, K.154, T.186, I.187, H.189, Y.190 Ligands: H3P.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.187 Water bridges: A:T.186 H3P.8: 9 residues within 4Å: Chain A: Y.190 Chain B: A.153, I.158, Y.183, I.187 Chain C: Y.190 Chain E: A.153, K.154 Ligands: H3P.4 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Halogen bonds: E:A.153, E:K.154, B:A.153 pi-Stacking: C:Y.190, A:Y.190 H3P.12: 10 residues within 4Å: Chain B: Y.190 Chain C: A.153, K.154, G.156 Chain D: Y.190 Chain F: A.153, K.154, G.156, I.158 Ligands: H3P.13 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: D:Y.190, B:Y.190 Halogen bonds: F:K.154, C:A.153, C:K.154 H3P.13: 9 residues within 4Å: Chain B: T.186, I.187, Y.190 Chain C: M.150, T.186, I.187, H.189, Y.190 Ligands: H3P.12 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.187 H3P.17: 7 residues within 4Å: Chain A: A.153, I.158 Chain D: A.153, K.154 Chain E: Y.190 Chain F: Y.190 Ligands: H3P.24 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F, 1 interactions with chain E Halogen bonds: D:A.153, D:K.154 pi-Stacking: F:Y.190 Hydrophobic interactions: E:Y.190 H3P.24: 10 residues within 4Å: Chain D: M.150, K.154, T.186, I.187, H.189 Chain F: K.154, T.186, I.187, Y.190 Ligands: H3P.17 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.187

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

Related Entries With Identical Sequence