SMTL ID : 1pmm.1

Crystal structure of Escherichia coli GadB (low pH)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

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

PLP.1: 15 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 Chain B: F.317, S.318 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Q.163, A:T.208, A:T.212, A:K.276 Hydrogen bonds: A:S.126, A:S.127, A:S.273, A:K.276, B:F.317, B:S.318 Water bridges: A:Q.163, A:S.246 Salt bridges: A:H.275, A:K.276 PLP.2: 15 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 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Q.163, B:T.208, B:T.212, B:K.276 Hydrogen bonds: B:S.126, B:S.127, B:S.273, A:F.317, A:S.318 Water bridges: B:Q.163, B:G.210, B:S.246, B:K.276 Salt bridges: B:H.275, B:K.276 PLP.3: 15 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 Chain D: F.317, S.318 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Q.163, C:Q.163, C:T.208, C:T.212, C:K.276 Hydrogen bonds: C:S.126, C:S.127, C:S.273, D:F.317, D:S.318 Water bridges: C:Q.163, C:G.210, C:S.246, C:K.276 Salt bridges: C:H.275, C:K.276 PLP.4: 15 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 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Q.163, D:Q.163, D:T.208, D:T.212, D:K.276 Hydrogen bonds: D:S.126, D:S.127, D:S.273, C:F.317, C:S.318 Water bridges: D:Q.163, D:G.210, D:S.246 Salt bridges: D:H.275, D:K.276 PLP.5: 15 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 Chain F: F.317, S.318 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:Q.163, E:Q.163, E:T.208, E:T.212, E:K.276 Hydrogen bonds: E:S.126, E:S.127, E:S.273, E:K.276, F:F.317, F:S.318 Water bridges: E:Q.163, E:G.210, E:S.246 Salt bridges: E:H.275, E:K.276 PLP.6: 15 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 15 PLIP interactions: 13 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:Q.163, F:T.208, F:T.212, F:K.276 Hydrogen bonds: F:S.126, F:S.127, F:S.273, F:K.276, E:F.317, E:S.318 Water bridges: F:Q.163, F:G.210, F:S.246 Salt bridges: F:H.275, F:K.276

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

ACY.7: 7 residues within 4Å: Chain A: N.83, D.86, F.317, S.318 Chain B: T.62, F.63, C.64 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.62, B:F.63, B:C.64, A:N.83, A:D.86 Water bridges: B:K.276 Salt bridges: B:K.276 Hydrophobic interactions: A:F.317 ACY.8: 7 residues within 4Å: Chain A: T.62, F.63, C.64 Chain B: N.83, D.86, F.317, S.318 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.62, A:F.63, A:C.64, B:N.83 Water bridges: A:K.276, B:D.86 Salt bridges: A:K.276 Hydrophobic interactions: B:F.317 ACY.9: 7 residues within 4Å: Chain C: N.83, D.86, F.317, S.318 Chain D: T.62, F.63, C.64 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:F.63, D:C.64, C:N.83, C:D.86 Water bridges: D:T.62 Salt bridges: D:K.276 Hydrophobic interactions: C:F.317 ACY.10: 7 residues within 4Å: Chain C: T.62, F.63, C.64 Chain D: N.83, D.86, F.317, S.318 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:F.317 Hydrogen bonds: D:N.83, C:F.63, C:C.64 Water bridges: C:T.62, C:K.276, C:K.276 Salt bridges: C:K.276 ACY.11: 7 residues within 4Å: Chain E: N.83, D.86, F.317, S.318 Chain F: T.62, F.63, C.64 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:F.317 Hydrogen bonds: E:N.83, E:D.86, F:T.62, F:F.63, F:C.64 Water bridges: E:D.86 Salt bridges: F:K.276 ACY.12: 7 residues within 4Å: Chain E: T.62, F.63, C.64 Chain F: N.83, D.86, F.317, S.318 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:F.63, E:C.64, F:N.83 Water bridges: E:T.62, E:K.276 Salt bridges: E:K.276 Hydrophobic interactions: F:F.317

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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