SMTL ID : 2eb5.1

Crystal structure of HpcG complexed with oxalate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-10-mer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: K.61, E.106, E.108, E.139 Ligands: OXL.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.106, A:E.108, A:E.139, H2O.1 MG.5: 5 residues within 4Å: Chain B: K.61, E.106, E.108, E.139 Ligands: OXL.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.106, B:E.108, B:E.139, H2O.7 MG.8: 4 residues within 4Å: Chain C: E.106, E.108, E.139 Ligands: OXL.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.106, C:E.108, C:E.139, H2O.13 MG.12: 5 residues within 4Å: Chain D: K.61, E.106, E.108, E.139 Ligands: OXL.13 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.106, D:E.108, D:E.139, H2O.20 MG.15: 4 residues within 4Å: Chain E: E.106, E.108, E.139 Ligands: OXL.16 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.106, E:E.108, E:E.139, H2O.24 MG.18: 5 residues within 4Å: Chain F: K.61, E.106, E.108, E.139 Ligands: OXL.19 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.106, F:E.108, F:E.139, H2O.30 MG.22: 5 residues within 4Å: Chain G: K.61, E.106, E.108, E.139 Ligands: OXL.23 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.106, G:E.108, G:E.139, H2O.36 MG.25: 4 residues within 4Å: Chain H: E.106, E.108, E.139 Ligands: OXL.26 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.106, H:E.108, H:E.139, H2O.42 MG.29: 5 residues within 4Å: Chain I: K.61, E.106, E.108, E.139 Ligands: OXL.30 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.106, I:E.108, I:E.139, H2O.49 MG.32: 4 residues within 4Å: Chain J: E.106, E.108, E.139 Ligands: OXL.33 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.106, J:E.108, J:E.139, H2O.53

10 x OXL: OXALATE ION(Non-covalent)

OXL.2: 10 residues within 4Å: Chain A: K.61, G.63, L.64, T.65, E.106, E.108, E.139, G.238, S.239 Ligands: MG.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:L.64, A:T.65, A:E.108, A:S.239 Water bridges: A:K.61, A:S.66, A:S.239 Salt bridges: A:K.61 OXL.6: 10 residues within 4Å: Chain B: K.61, G.63, L.64, T.65, E.106, E.108, E.139, G.238, S.239 Ligands: MG.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:L.64, B:T.65, B:E.106, B:S.239 Water bridges: B:K.61, B:S.239 Salt bridges: B:K.61 OXL.9: 10 residues within 4Å: Chain C: K.61, G.63, L.64, T.65, E.106, E.108, E.139, G.238, S.239 Ligands: MG.8 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:L.64, C:T.65, C:E.106, C:S.239 Water bridges: C:K.61, C:K.61, C:S.66, C:S.239 Salt bridges: C:K.61 OXL.13: 10 residues within 4Å: Chain D: K.61, G.63, L.64, T.65, E.106, E.108, E.139, G.238, S.239 Ligands: MG.12 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:L.64, D:T.65, D:E.106, D:S.239 Water bridges: D:K.61, D:S.66, D:S.239 Salt bridges: D:K.61 OXL.16: 10 residues within 4Å: Chain E: K.61, G.63, L.64, T.65, E.106, E.108, E.139, G.238, S.239 Ligands: MG.15 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:L.64, E:T.65, E:E.139, E:S.239 Water bridges: E:K.61, E:K.61, E:S.66, E:S.239 Salt bridges: E:K.61 OXL.19: 10 residues within 4Å: Chain F: K.61, G.63, L.64, T.65, E.106, E.108, E.139, G.238, S.239 Ligands: MG.18 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:L.64, F:T.65, F:E.108, F:S.239 Water bridges: F:K.61, F:T.65, F:S.66, F:S.239 Salt bridges: F:K.61 OXL.23: 10 residues within 4Å: Chain G: K.61, G.63, L.64, T.65, E.106, E.108, E.139, G.238, S.239 Ligands: MG.22 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:L.64, G:T.65, G:E.106, G:S.239 Water bridges: G:K.61, G:T.65, G:T.65, G:S.239 Salt bridges: G:K.61 OXL.26: 10 residues within 4Å: Chain H: K.61, G.63, L.64, T.65, E.106, E.108, E.139, G.238, S.239 Ligands: MG.25 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:L.64, H:T.65, H:E.106, H:S.239 Water bridges: H:K.61, H:K.61, H:T.65, H:S.66, H:S.239 Salt bridges: H:K.61 OXL.30: 10 residues within 4Å: Chain I: K.61, G.63, L.64, T.65, E.106, E.108, E.139, G.238, S.239 Ligands: MG.29 8 PLIP interactions: 8 interactions with chain I Hydrogen bonds: I:L.64, I:T.65, I:E.106, I:S.239 Water bridges: I:K.61, I:S.66, I:S.239 Salt bridges: I:K.61 OXL.33: 10 residues within 4Å: Chain J: K.61, G.63, L.64, T.65, E.106, E.108, E.139, G.238, S.239 Ligands: MG.32 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:L.64, J:T.65, J:E.106, J:S.239 Water bridges: J:K.61, J:K.61, J:T.65, J:S.66, J:S.239 Salt bridges: J:K.61

14 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.3: 10 residues within 4Å: Chain A: Y.193, R.194, N.195, G.196, T.251, F.252, H.253 Chain G: T.251, H.253, S.263 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:S.263, A:G.196 SCN.4: 3 residues within 4Å: Chain A: P.96, D.98, R.99 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.99 SCN.7: 10 residues within 4Å: Chain B: Y.193, R.194, N.195, G.196, T.251, F.252, H.253 Chain F: T.251, H.253, S.263 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:G.196, F:H.253 SCN.10: 10 residues within 4Å: Chain C: Y.193, R.194, N.195, G.196, T.251, F.252, H.253 Chain J: T.251, H.253, S.263 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain J Hydrogen bonds: C:G.196, J:H.253, J:S.263 SCN.11: 4 residues within 4Å: Chain C: F.2, Y.31, P.32, E.33 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.33 SCN.14: 10 residues within 4Å: Chain D: Y.193, R.194, N.195, G.196, T.251, F.252, H.253 Chain I: T.251, H.253, S.263 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain D Hydrogen bonds: I:H.253, I:S.263, D:G.196 SCN.17: 10 residues within 4Å: Chain E: Y.193, R.194, N.195, G.196, T.251, F.252, H.253 Chain H: T.251, H.253, S.263 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain E Hydrogen bonds: H:H.253, H:S.263, E:G.196 SCN.20: 10 residues within 4Å: Chain B: T.251, H.253, S.263 Chain F: Y.193, R.194, N.195, G.196, T.251, F.252, H.253 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:G.196, B:H.253, B:S.263 SCN.21: 3 residues within 4Å: Chain F: P.96, D.98, R.99 1 PLIP interactions: 1 interactions with chain F Water bridges: F:R.99 SCN.24: 10 residues within 4Å: Chain A: T.251, H.253, S.263 Chain G: Y.193, R.194, N.195, G.196, T.251, F.252, H.253 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.196 SCN.27: 10 residues within 4Å: Chain E: T.251, H.253, S.263 Chain H: Y.193, R.194, N.195, G.196, T.251, F.252, H.253 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain H Hydrogen bonds: E:S.263, H:G.196 SCN.28: 4 residues within 4Å: Chain H: F.2, Y.31, P.32, E.33 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:E.33 SCN.31: 10 residues within 4Å: Chain D: T.251, H.253, S.263 Chain I: Y.193, R.194, N.195, G.196, T.251, F.252, H.253 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain I Hydrogen bonds: D:S.263, I:G.196 SCN.34: 10 residues within 4Å: Chain C: T.251, H.253, S.263 Chain J: Y.193, R.194, N.195, G.196, T.251, F.252, H.253 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain C Hydrogen bonds: J:G.196, C:S.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Izumi, A. et al., Structure and Mechanism of HpcG, a Hydratase in the Homoprotocatechuate Degradation Pathway of Escherichia coli. J.Mol.Biol. (2007)

Release Date

2007-07-17

Peptides

2-oxo-hept-3-ene-1,7-dioate hydratase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

2-oxo-hept-3-ene-1,7-dioate hydratase

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