SMTL ID : 1xey.1

Crystal structure of the complex of Escherichia coli GADA with glutarate at 2.05 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-hexamer

Ligands

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 8 residues within 4Å: Chain A: W.67, L.279, E.330, L.334, V.342, R.427 Chain F: S.16, F.18 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:L.279, A:L.334, A:V.342 Salt bridges: A:R.427 Hydrogen bonds: F:S.16 Water bridges: F:R.17 ACT.2: 6 residues within 4Å: Chain A: S.16, R.17, F.18 Chain F: W.67, V.342, R.427 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain F Hydrophobic interactions: A:F.18, F:W.67 Hydrogen bonds: A:S.16 Water bridges: F:R.333, F:R.427 Salt bridges: F:R.427 ACT.7: 8 residues within 4Å: Chain B: S.16, F.18 Chain C: W.67, L.279, E.330, L.334, V.342, R.427 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:S.16 Water bridges: B:R.17 Hydrophobic interactions: C:L.279, C:L.334, C:V.342 Salt bridges: C:R.427 ACT.8: 6 residues within 4Å: Chain B: W.67, V.342, R.427 Chain C: S.16, R.17, F.18 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:W.67, C:F.18 Water bridges: B:R.333, B:R.427 Salt bridges: B:R.427 Hydrogen bonds: C:S.16 ACT.13: 8 residues within 4Å: Chain D: S.16, F.18 Chain E: W.67, L.279, E.330, L.334, V.342, R.427 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:L.279, E:L.334, E:V.342 Salt bridges: E:R.427 Hydrogen bonds: D:S.16 Water bridges: D:R.17 ACT.14: 6 residues within 4Å: Chain D: W.67, V.342, R.427 Chain E: S.16, R.17, F.18 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:W.67, E:F.18 Water bridges: D:R.333, D:R.427 Salt bridges: D:R.427 Hydrogen bonds: E:S.16

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

PLP.3: 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 16 PLIP interactions: 3 interactions with chain B, 13 interactions with chain A Hydrogen bonds: B:F.317, B:S.318, A:S.126, A:S.127, A:S.273, A:K.276, A:K.276 Water bridges: B:S.318, A:Q.163, A:S.246, A:K.276 Hydrophobic interactions: A:Q.163, A:T.208, A:K.276 Salt bridges: A:H.275, A:K.276 PLP.5: 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 13 PLIP interactions: 11 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:S.318 Water bridges: B:Q.163, B:S.246, A:F.317 Salt bridges: B:H.275, B:K.276 PLP.9: 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: 13 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Q.163, C:T.208, C:K.276 Hydrogen bonds: C:S.126, C:S.127, C:S.273, C:K.276, C:K.276, D:F.317, D:S.318 Water bridges: C:Q.163, C:S.246, C:K.276, D:S.318 Salt bridges: C:H.275, C:K.276 PLP.11: 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 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Q.163, D:T.208, D:T.212, D:K.276 Hydrogen bonds: D:S.126, D:S.127, D:S.273, D:K.276, C:S.318 Water bridges: D:Q.163, D:S.246, C:F.317 Salt bridges: D:H.275, D:K.276 PLP.15: 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 15 PLIP interactions: 3 interactions with chain F, 12 interactions with chain E Hydrogen bonds: F:F.317, F:S.318, E:S.126, E:S.127, E:S.273, E:K.276 Water bridges: F:S.318, E:Q.163, E:S.246, E:K.276 Hydrophobic interactions: E:Q.163, E:T.208, E:K.276 Salt bridges: E:H.275, E:K.276 PLP.17: 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 14 PLIP interactions: 12 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, E:S.318 Water bridges: F:Q.163, F:S.246, F:S.246, E:F.317 Salt bridges: F:H.275, F:K.276

6 x GUA: GLUTARIC ACID(Non-covalent)

GUA.4: 8 residues within 4Å: Chain A: N.83, D.86, E.89 Chain B: A.61, T.62, F.63, C.64, R.422 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.63 Hydrogen bonds: B:T.62, B:F.63, B:C.64, A:N.83, A:D.86 Water bridges: B:R.422 Salt bridges: B:R.422 GUA.6: 9 residues within 4Å: Chain A: A.61, T.62, F.63, C.64, R.422 Chain B: N.83, D.86, E.89, F.317 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:F.63, A:C.64, B:N.83, B:D.86 Water bridges: A:T.62, A:R.422 Salt bridges: A:R.422 Hydrophobic interactions: B:F.317 GUA.10: 8 residues within 4Å: Chain C: N.83, D.86, E.89 Chain D: A.61, T.62, F.63, C.64, R.422 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.63 Hydrogen bonds: D:T.62, D:F.63, D:C.64, C:N.83, C:D.86 Water bridges: D:R.422 Salt bridges: D:R.422 GUA.12: 9 residues within 4Å: Chain C: A.61, T.62, F.63, C.64, R.422 Chain D: N.83, D.86, E.89, F.317 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:F.63, C:C.64, D:N.83, D:D.86 Water bridges: C:T.62, C:R.422 Salt bridges: C:R.422 Hydrophobic interactions: D:F.317 GUA.16: 8 residues within 4Å: Chain E: N.83, D.86, E.89 Chain F: A.61, T.62, F.63, C.64, R.422 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:F.63 Hydrogen bonds: F:T.62, F:F.63, F:C.64, E:N.83, E:D.86 Water bridges: F:R.422 Salt bridges: F:R.422 GUA.18: 9 residues within 4Å: Chain E: A.61, T.62, F.63, C.64, R.422 Chain F: N.83, D.86, E.89, F.317 9 PLIP interactions: 3 interactions with chain F, 6 interactions with chain E Hydrophobic interactions: F:F.317 Hydrogen bonds: F:N.83, F:D.86, E:F.63, E:C.64 Water bridges: E:T.62, E:K.276, E:R.422 Salt bridges: E:R.422

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dutyshev, D.I. et al., Structure of Escherichia coli glutamate decarboxylase (GADalpha) in complex with glutarate at 2.05 angstroms resolution. Acta Crystallogr.,Sect.D (2005)

Release Date

2004-10-05

Peptides

Glutamate decarboxylase alpha: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Glutamate decarboxylase alpha