SMTL ID : 1pmo.1

Crystal structure of Escherichia coli GadB (neutral pH)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

6 x PLR: (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE(Non-covalent)

PLR.1: 17 residues within 4Å: Chain A: G.125, S.126, S.127, Q.163, C.165, T.208, G.210, T.212, D.243, A.245, S.273, H.275, K.276, H.465, T.466 Chain B: F.317, S.318 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Q.163, A:T.208, A:A.245 Hydrogen bonds: A:S.126, A:S.127, A:T.212, A:S.273, B:F.317, B:S.318, B:S.318 Water bridges: A:K.276, A:T.466 Salt bridges: A:H.275, A:K.276 PLR.5: 17 residues within 4Å: Chain A: F.317, S.318 Chain B: G.125, S.126, S.127, Q.163, C.165, T.208, G.210, T.212, D.243, A.245, S.273, H.275, K.276, H.465, T.466 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Q.163, B:T.208, B:A.245 Hydrogen bonds: B:S.126, B:S.127, B:T.212, B:S.273, A:S.318, A:S.318 Water bridges: B:Q.163, B:K.276, A:F.317, A:F.317, A:S.318 Salt bridges: B:H.275, B:K.276 PLR.8: 17 residues within 4Å: Chain C: G.125, S.126, S.127, Q.163, C.165, T.208, G.210, T.212, D.243, A.245, S.273, H.275, K.276, H.465, T.466 Chain D: F.317, S.318 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:Q.163, C:T.208, C:A.245 Hydrogen bonds: C:S.126, C:S.127, C:T.212, C:S.273, D:S.318 Water bridges: C:T.466, D:F.317, D:F.317, D:S.318 Salt bridges: C:H.275, C:K.276 PLR.12: 17 residues within 4Å: Chain C: F.317, S.318 Chain D: G.125, S.126, S.127, Q.163, C.165, T.208, G.210, T.212, D.243, A.245, S.273, H.275, K.276, H.465, T.466 14 PLIP interactions: 11 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Q.163, D:T.208, D:A.245 Hydrogen bonds: D:S.126, D:S.127, D:T.212, D:S.273, C:S.318 Water bridges: D:K.276, D:T.466, C:F.317, C:F.317 Salt bridges: D:H.275, D:K.276 PLR.16: 17 residues within 4Å: Chain E: G.125, S.126, S.127, Q.163, C.165, T.208, G.210, T.212, D.243, A.245, S.273, H.275, K.276, H.465, T.466 Chain F: F.317, S.318 14 PLIP interactions: 11 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:Q.163, E:T.208, E:A.245 Hydrogen bonds: E:S.126, E:S.127, E:S.273, F:F.317, F:S.318, F:S.318 Water bridges: E:G.210, E:K.276, E:T.466 Salt bridges: E:H.275, E:K.276 PLR.21: 17 residues within 4Å: Chain E: F.317, S.318 Chain F: G.125, S.126, S.127, Q.163, C.165, T.208, G.210, T.212, D.243, A.245, S.273, H.275, K.276, H.465, T.466 14 PLIP interactions: 9 interactions with chain F, 5 interactions with chain E Hydrophobic interactions: F:Q.163, F:T.208, F:A.245 Hydrogen bonds: F:S.126, F:S.127, F:T.212, F:S.273, E:S.318, E:S.318 Salt bridges: F:H.275, F:K.276 Water bridges: E:F.317, E:F.317, E:S.318

18 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 12 residues within 4Å: Chain A: Q.65, T.66, W.67, D.69, V.72, L.279, A.280, P.281, E.330, R.427 Chain B: I.80, N.81 Ligand excluded by PLIP TRS.3: 10 residues within 4Å: Chain A: A.118, V.119, G.120, T.121, L.295, V.300, G.311, T.312, F.313 Ligands: TRS.4 Ligand excluded by PLIP TRS.4: 9 residues within 4Å: Chain A: W.84, D.97, L.98, V.101, G.120, T.121, N.122, G.311 Ligands: TRS.3 Ligand excluded by PLIP TRS.6: 11 residues within 4Å: Chain A: I.80, N.81 Chain B: Q.65, W.67, D.68, V.72, L.279, A.280, P.281, E.330, R.427 Ligand excluded by PLIP TRS.7: 9 residues within 4Å: Chain B: W.84, K.87, D.97, L.98, V.101, G.120, T.121, N.122, G.311 Ligand excluded by PLIP TRS.9: 9 residues within 4Å: Chain C: W.84, K.87, D.97, L.98, V.101, G.120, T.121, N.122, T.312 Ligand excluded by PLIP TRS.10: 11 residues within 4Å: Chain C: Q.65, W.67, D.68, D.69, V.72, L.279, A.280, P.281, E.330 Chain D: I.80, N.81 Ligand excluded by PLIP TRS.11: 7 residues within 4Å: Chain A: P.91, Q.92 Chain B: L.52 Chain C: Q.58, R.402, L.436, D.440 Ligand excluded by PLIP TRS.13: 12 residues within 4Å: Chain C: I.80, N.81 Chain D: Q.65, T.66, W.67, D.69, V.72, L.279, A.280, P.281, E.330, R.427 Ligand excluded by PLIP TRS.14: 10 residues within 4Å: Chain D: W.84, K.87, D.97, L.98, V.101, G.120, T.121, N.122, T.312 Ligands: TRS.15 Ligand excluded by PLIP TRS.15: 9 residues within 4Å: Chain D: V.119, G.120, T.121, L.295, V.300, G.311, T.312, F.313 Ligands: TRS.14 Ligand excluded by PLIP TRS.17: 12 residues within 4Å: Chain E: Q.65, T.66, W.67, D.69, V.72, L.279, A.280, P.281, E.330, R.427 Chain F: I.80, N.81 Ligand excluded by PLIP TRS.18: 10 residues within 4Å: Chain E: W.84, K.87, D.97, L.98, V.101, G.120, T.121, N.122, T.312 Ligands: TRS.19 Ligand excluded by PLIP TRS.19: 9 residues within 4Å: Chain E: A.118, V.119, G.120, L.295, V.300, G.311, T.312, F.313 Ligands: TRS.18 Ligand excluded by PLIP TRS.20: 7 residues within 4Å: Chain E: P.184, G.185, L.187, E.364, K.381, D.384, I.418 Ligand excluded by PLIP TRS.22: 10 residues within 4Å: Chain E: N.81 Chain F: Q.65, T.66, W.67, V.72, L.279, A.280, P.281, E.330, R.427 Ligand excluded by PLIP TRS.23: 12 residues within 4Å: Chain F: W.84, K.87, D.97, L.98, V.101, G.120, T.121, N.122, I.310, G.311, T.312 Ligands: TRS.24 Ligand excluded by PLIP TRS.24: 11 residues within 4Å: Chain F: A.118, V.119, G.120, T.121, W.289, L.295, V.300, G.311, T.312, F.313 Ligands: TRS.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Capitani, G. et al., Crystal structure and functional analysis of escherichia coli glutamate decarboxylase. Embo J. (2003)

Release Date

2004-02-17

Peptides

Glutamate decarboxylase beta: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Glutamate decarboxylase beta

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