SMTL ID : 2dgl.1

Crystal structure of Escherichia coli GadB in complex with bromide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

homo-hexamer

Ligands

24 x BR: BROMIDE ION(Non-covalent)

BR.1: 3 residues within 4Å: Chain A: S.16 Chain F: V.342, R.427 Ligand excluded by PLIP BR.2: 1 residues within 4Å: Chain A: R.17 Ligand excluded by PLIP BR.3: 4 residues within 4Å: Chain A: W.67, D.68, H.73 Chain B: N.81 Ligand excluded by PLIP BR.4: 2 residues within 4Å: Chain A: G.185, I.418 Ligand excluded by PLIP BR.7: 2 residues within 4Å: Chain B: S.16 Chain C: R.427 Ligand excluded by PLIP BR.8: 1 residues within 4Å: Chain B: R.17 Ligand excluded by PLIP BR.9: 2 residues within 4Å: Chain B: R.427 Chain C: S.16 Ligand excluded by PLIP BR.10: 4 residues within 4Å: Chain A: N.81 Chain B: W.67, D.68, H.73 Ligand excluded by PLIP BR.11: 2 residues within 4Å: Chain B: K.381, I.418 Ligand excluded by PLIP BR.14: 4 residues within 4Å: Chain C: W.67, D.68, H.73 Chain D: N.81 Ligand excluded by PLIP BR.15: 1 residues within 4Å: Chain C: R.17 Ligand excluded by PLIP BR.16: 4 residues within 4Å: Chain C: N.81 Chain D: W.67, D.68, H.73 Ligand excluded by PLIP BR.17: 2 residues within 4Å: Chain C: K.381, I.418 Ligand excluded by PLIP BR.21: 2 residues within 4Å: Chain D: S.16 Chain E: R.427 Ligand excluded by PLIP BR.22: 1 residues within 4Å: Chain D: R.17 Ligand excluded by PLIP BR.23: 2 residues within 4Å: Chain D: K.381, I.418 Ligand excluded by PLIP BR.25: 4 residues within 4Å: Chain E: W.67, D.68, H.73 Chain F: N.81 Ligand excluded by PLIP BR.26: 2 residues within 4Å: Chain D: R.427 Chain E: S.16 Ligand excluded by PLIP BR.27: 1 residues within 4Å: Chain E: R.17 Ligand excluded by PLIP BR.28: 3 residues within 4Å: Chain E: G.185, K.381, I.418 Ligand excluded by PLIP BR.31: 4 residues within 4Å: Chain E: N.81 Chain F: W.67, D.68, H.73 Ligand excluded by PLIP BR.32: 2 residues within 4Å: Chain A: R.427 Chain F: S.16 Ligand excluded by PLIP BR.33: 1 residues within 4Å: Chain F: R.17 Ligand excluded by PLIP BR.34: 3 residues within 4Å: Chain F: G.185, K.381, I.418 Ligand excluded by PLIP

6 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.5: 15 residues within 4Å: Chain A: G.125, S.126, S.127, Q.163, C.165, T.208, T.212, D.243, A.245, S.246, S.273, H.275, K.276 Chain B: F.317, S.318 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Q.163, A:Q.163, A:T.208, A:A.245, A:K.276 Hydrogen bonds: A:S.126, A:S.127, A:S.246, A:S.273, B:S.318 Salt bridges: A:H.275, A:K.276 PLP.12: 14 residues within 4Å: Chain A: F.317, S.318 Chain B: G.125, S.126, S.127, Q.163, C.165, T.212, D.243, A.245, S.246, S.273, H.275, K.276 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Q.163, B:Q.163, B:A.245, B:K.276 Hydrogen bonds: B:S.126, B:S.127, B:S.246, B:S.273, B:S.273, A:S.318 Salt bridges: B:H.275, B:K.276 Water bridges: A:F.317, A:F.317 PLP.18: 14 residues within 4Å: Chain C: G.125, S.126, S.127, Q.163, C.165, T.212, D.243, A.245, S.246, S.273, H.275, K.276 Chain D: F.317, S.318 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Q.163, C:Q.163, C:A.245, C:K.276 Hydrogen bonds: C:S.126, C:S.127, C:S.246, C:S.273, C:K.276, D:S.318 Salt bridges: C:H.275, C:K.276 PLP.24: 14 residues within 4Å: Chain C: F.317, S.318 Chain D: G.125, S.126, S.127, Q.163, C.165, T.212, D.243, A.245, S.246, S.273, H.275, K.276 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Q.163, D:K.276 Hydrogen bonds: D:S.126, D:S.127, D:S.246, D:S.273, D:K.276, C:F.317, C:S.318 Salt bridges: D:H.275, D:K.276 PLP.29: 15 residues within 4Å: Chain E: G.125, S.126, S.127, Q.163, C.165, T.208, T.212, D.243, A.245, S.246, S.273, H.275, K.276 Chain F: F.317, S.318 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:Q.163, E:Q.163, E:T.208, E:K.276 Hydrogen bonds: E:S.126, E:S.127, E:S.246, E:S.273, E:K.276, F:S.318, F:S.318 Salt bridges: E:H.275, E:K.276 PLP.35: 14 residues within 4Å: Chain E: F.317, S.318 Chain F: G.125, S.126, S.127, Q.163, C.165, T.208, T.212, D.243, A.245, S.273, H.275, K.276 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:Q.163, F:Q.163, F:T.208, F:K.276 Hydrogen bonds: F:S.126, F:S.127, F:S.246, F:S.273, F:S.273, E:S.318 Salt bridges: F:H.275, F:K.276

6 x ACY: ACETIC ACID(Non-functional Binders)

ACY.6: 8 residues within 4Å: Chain A: N.83, D.86, F.317, S.318 Chain B: T.62, F.63, C.64, K.276 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.63, A:N.83 Salt bridges: B:K.276 Hydrophobic interactions: A:F.317 ACY.13: 7 residues within 4Å: Chain A: T.62, F.63, C.64, K.276 Chain B: N.83, D.86, S.318 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.83, B:D.86, B:S.318, A:F.63 Salt bridges: A:K.276 ACY.19: 8 residues within 4Å: Chain C: T.62, F.63, C.64, K.276 Chain D: N.83, D.86, F.317, S.318 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:T.62, C:F.63, D:N.83, D:D.86 Salt bridges: C:K.276 Hydrophobic interactions: D:F.317 ACY.20: 7 residues within 4Å: Chain C: N.83, D.86, F.317, S.318 Chain D: T.62, F.63, C.64 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.317 Hydrogen bonds: C:N.83, D:T.62, D:F.63 Salt bridges: D:K.276 ACY.30: 7 residues within 4Å: Chain E: T.62, F.63, C.64, K.276 Chain F: D.86, F.317, S.318 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:F.63, F:D.86 Salt bridges: E:K.276 Hydrophobic interactions: F:F.317 ACY.36: 6 residues within 4Å: Chain E: N.83, D.86, S.318 Chain F: T.62, F.63, C.64 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:N.83, F:F.63 Salt bridges: F:K.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gut, H. et al., Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB. Embo J. (2006)

Release Date

2006-06-20

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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