SMTL ID : 2rhw.1

Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3,10-Di-Fluoro HOPDA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 1 residues within 4Å: Ligands: MLI.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.177 NA.5: 1 residues within 4Å: Ligands: MLI.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.177 NA.9: 1 residues within 4Å: Ligands: MLI.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.177 NA.13: 1 residues within 4Å: Ligands: MLI.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.177

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

MLI.2: 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:S.177 Water bridges: A:S.177 MLI.3: 10 residues within 4Å: Chain A: G.38, G.39, G.40, N.108, A.109, M.110, L.153, F.172, H.262 Ligands: C0E.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.153 Hydrogen bonds: A:G.39, A:G.40, A:M.110 Salt bridges: A:H.262, A:H.262 MLI.6: 4 residues within 4Å: Chain B: Q.176, S.177, I.179 Ligands: NA.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.177 Water bridges: B:S.177 MLI.7: 10 residues within 4Å: Chain B: G.38, G.39, G.40, N.108, A.109, M.110, L.153, F.172, H.262 Ligands: C0E.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.153 Hydrogen bonds: B:G.39, B:G.40, B:M.110 Salt bridges: B:H.262, B:H.262 MLI.10: 4 residues within 4Å: Chain C: Q.176, S.177, I.179 Ligands: NA.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.177 Water bridges: C:S.177 MLI.11: 10 residues within 4Å: Chain C: G.38, G.39, G.40, N.108, A.109, M.110, L.153, F.172, H.262 Ligands: C0E.12 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.153 Hydrogen bonds: C:G.39, C:G.40, C:M.110 Salt bridges: C:H.262, C:H.262 MLI.14: 4 residues within 4Å: Chain D: Q.176, S.177, I.179 Ligands: NA.13 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.177 Water bridges: D:S.177 MLI.15: 10 residues within 4Å: Chain D: G.38, G.39, G.40, N.108, A.109, M.110, L.153, F.172, H.262 Ligands: C0E.16 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.153 Hydrogen bonds: D:G.39, D:G.40, D:M.110 Salt bridges: D:H.262, D:H.262

4 x C0E: 3-fluoro-6-(4-fluorophenyl)-2-hydroxy-6-oxohexa-2,4-dienoic acid(Non-covalent)

C0E.4: 19 residues within 4Å: Chain A: G.38, G.39, G.40, A.43, N.48, N.108, A.109, M.110, G.135, G.136, I.150, L.153, F.172, L.210, W.213, F.236, V.237, H.262 Ligands: MLI.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.109, A:I.150, A:L.210, A:W.213, A:V.237 Hydrogen bonds: A:G.38, A:G.39, A:G.40, A:M.110 C0E.8: 19 residues within 4Å: Chain B: G.38, G.39, G.40, A.43, N.48, N.108, A.109, M.110, G.135, G.136, I.150, L.153, F.172, L.210, W.213, F.236, V.237, H.262 Ligands: MLI.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.109, B:I.150, B:L.210, B:W.213, B:V.237 Hydrogen bonds: B:G.38, B:G.39, B:G.40, B:M.110 C0E.12: 19 residues within 4Å: Chain C: G.38, G.39, G.40, A.43, N.48, N.108, A.109, M.110, G.135, G.136, I.150, L.153, F.172, L.210, W.213, F.236, V.237, H.262 Ligands: MLI.11 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:A.109, C:I.150, C:L.210, C:W.213, C:V.237 Hydrogen bonds: C:G.38, C:G.39, C:G.40, C:M.110 C0E.16: 19 residues within 4Å: Chain D: G.38, G.39, G.40, A.43, N.48, N.108, A.109, M.110, G.135, G.136, I.150, L.153, F.172, L.210, W.213, F.236, V.237, H.262 Ligands: MLI.15 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:A.109, D:I.150, D:L.210, D:W.213, D:V.237 Hydrogen bonds: D:G.38, D:G.39, D:G.40, D:M.110

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

Related Entries With Identical Sequence