SMTL ID : 2puh.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 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.180 NA.4: 1 residues within 4Å: Ligands: MLI.5 No protein-ligand interaction detected (PLIP) NA.7: 1 residues within 4Å: Ligands: MLI.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.180 NA.10: 1 residues within 4Å: Ligands: MLI.11 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.180

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

MLI.2: 3 residues within 4Å: Chain A: S.180, I.182 Ligands: NA.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.180 MLI.5: 3 residues within 4Å: Chain B: S.180, I.182 Ligands: NA.4 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.180 MLI.8: 3 residues within 4Å: Chain C: S.180, I.182 Ligands: NA.7 1 PLIP interactions: 1 interactions with chain C Water bridges: C:S.180 MLI.11: 3 residues within 4Å: Chain D: S.180, I.182 Ligands: NA.10 1 PLIP interactions: 1 interactions with chain D Water bridges: D:S.180

4 x HPK: (3E)-2,6-DIOXO-6-PHENYLHEX-3-ENOATE(Non-covalent)

HPK.3: 19 residues within 4Å: Chain A: G.41, G.42, G.43, A.46, N.51, N.111, A.112, M.113, G.138, G.139, I.153, L.156, F.175, R.190, L.213, W.216, V.240, H.265, W.266 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.112, A:I.153, A:L.156, A:F.175, A:F.175, A:L.213, A:W.216, A:V.240 Hydrogen bonds: A:G.42, A:G.43, A:N.51, A:N.111, A:M.113, A:W.266 Salt bridges: A:R.190 HPK.6: 19 residues within 4Å: Chain B: G.41, G.42, G.43, A.46, N.51, N.111, A.112, M.113, G.138, G.139, I.153, L.156, F.175, R.190, L.213, W.216, V.240, H.265, W.266 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.112, B:I.153, B:L.156, B:F.175, B:F.175, B:L.213, B:W.216, B:V.240 Hydrogen bonds: B:G.42, B:G.43, B:N.51, B:N.111, B:M.113, B:W.266 Salt bridges: B:R.190 HPK.9: 19 residues within 4Å: Chain C: G.41, G.42, G.43, A.46, N.51, N.111, A.112, M.113, G.138, G.139, I.153, L.156, F.175, R.190, L.213, W.216, V.240, H.265, W.266 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:A.112, C:I.153, C:L.156, C:F.175, C:F.175, C:L.213, C:W.216, C:V.240 Hydrogen bonds: C:G.42, C:G.43, C:N.51, C:N.111, C:M.113, C:W.266 Salt bridges: C:R.190 HPK.12: 19 residues within 4Å: Chain D: G.41, G.42, G.43, A.46, N.51, N.111, A.112, M.113, G.138, G.139, I.153, L.156, F.175, R.190, L.213, W.216, V.240, H.265, W.266 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:A.112, D:I.153, D:L.156, D:F.175, D:F.175, D:L.213, D:W.216, D:V.240 Hydrogen bonds: D:G.42, D:G.43, D:N.51, D:N.111, D:M.113, D:W.266 Salt bridges: D:R.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horsman, G.P. et al., The Tautomeric Half-reaction of BphD, a C-C Bond Hydrolase: KINETIC AND STRUCTURAL EVIDENCE SUPPORTING A KEY ROLE FOR HISTIDINE 265 OF THE CATALYTIC TRIAD. J.Biol.Chem. (2007)

Release Date

2007-05-22

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