SMTL ID : 2rht.1

Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3-Cl HOPDA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain A: S.177 Ligands: MLI.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.177 NA.4: 2 residues within 4Å: Chain B: S.177 Ligands: MLI.6 No protein-ligand interaction detected (PLIP) NA.7: 2 residues within 4Å: Chain C: S.177 Ligands: MLI.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.177 NA.10: 2 residues within 4Å: Chain D: S.177 Ligands: MLI.12 No protein-ligand interaction detected (PLIP)

4 x C1E: (2Z,4E)-3-chloro-2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid(Non-covalent)

C1E.2: 18 residues within 4Å: Chain A: G.38, G.39, G.40, A.43, N.48, N.108, A.109, M.110, G.135, I.150, L.153, F.172, R.187, L.210, W.213, F.236, V.237, H.262 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.109, A:I.150, A:L.153, A:L.210, A:W.213, A:V.237 Hydrogen bonds: A:G.38, A:G.39, A:G.40, A:N.48, A:N.108, A:M.110, A:R.187, A:R.187 Salt bridges: A:R.187 C1E.5: 18 residues within 4Å: Chain B: G.38, G.39, G.40, A.43, N.48, N.108, A.109, M.110, G.135, I.150, L.153, F.172, R.187, L.210, W.213, F.236, V.237, H.262 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.109, B:I.150, B:L.153, B:L.210, B:W.213, B:V.237 Hydrogen bonds: B:G.38, B:G.39, B:G.40, B:N.48, B:N.108, B:M.110, B:R.187, B:R.187 Salt bridges: B:R.187 C1E.8: 18 residues within 4Å: Chain C: G.38, G.39, G.40, A.43, N.48, N.108, A.109, M.110, G.135, I.150, L.153, F.172, R.187, L.210, W.213, F.236, V.237, H.262 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:A.109, C:I.150, C:L.153, C:L.210, C:W.213, C:V.237 Hydrogen bonds: C:G.38, C:G.39, C:G.40, C:N.48, C:N.108, C:M.110, C:R.187, C:R.187 Salt bridges: C:R.187 C1E.11: 18 residues within 4Å: Chain D: G.38, G.39, G.40, A.43, N.48, N.108, A.109, M.110, G.135, I.150, L.153, F.172, R.187, L.210, W.213, F.236, V.237, H.262 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:A.109, D:I.150, D:L.153, D:L.210, D:W.213, D:V.237 Hydrogen bonds: D:G.38, D:G.39, D:G.40, D:N.48, D:N.108, D:M.110, D:R.187, D:R.187 Salt bridges: D:R.187

4 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 4 residues within 4Å: Chain A: Q.176, S.177, I.179 Ligands: NA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.179 Water bridges: A:I.179 MLI.6: 4 residues within 4Å: Chain B: Q.176, S.177, I.179 Ligands: NA.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.179 Water bridges: B:I.179 MLI.9: 4 residues within 4Å: Chain C: Q.176, S.177, I.179 Ligands: NA.7 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.179 Water bridges: C:I.179 MLI.12: 4 residues within 4Å: Chain D: Q.176, S.177, I.179 Ligands: NA.10 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.179 Water bridges: D:I.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhowmik, S. et al., The Molecular Basis for Inhibition of BphD, a C-C Bond Hydrolase Involved in Polychlorinated Biphenyls Degradation: LARGE 3-SUBSTITUENTS PREVENT TAUTOMERIZATION. J.Biol.Chem. (2007)

Release Date

2007-11-13

Peptides

2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase

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