SMTL ID : 2og1.1

Crystal Structure of BphD, a C-C hydrolase from Burkholderia xenovorans LB400

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 8 residues within 4Å: Chain A: G.41, G.42, G.43, A.46, N.51, N.111, R.190, W.266 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.41, A:G.43, A:N.51, A:N.111, A:W.266 Water bridges: A:G.42, A:G.42, A:R.190, A:R.190 Salt bridges: A:R.190 SO4.2: 1 residues within 4Å: Chain A: R.196 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.196 SO4.3: 4 residues within 4Å: Chain A: D.102, I.103, D.104, R.105 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.104, A:R.105 Water bridges: A:T.35, A:T.35, A:D.102 SO4.7: 7 residues within 4Å: Chain B: G.41, G.42, G.43, A.46, N.51, F.175, R.190 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.41, B:G.43, B:N.51, B:N.51 Salt bridges: B:R.190 SO4.9: 8 residues within 4Å: Chain C: G.41, G.42, G.43, A.46, N.51, N.111, R.190, W.266 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.41, C:G.43, C:N.51, C:N.111, C:W.266 Water bridges: C:G.42, C:G.42, C:R.190, C:R.190 Salt bridges: C:R.190 SO4.10: 1 residues within 4Å: Chain C: R.196 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.196 SO4.11: 4 residues within 4Å: Chain C: D.102, I.103, D.104, R.105 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.104, C:R.105 Water bridges: C:T.35, C:T.35, C:D.102 SO4.15: 7 residues within 4Å: Chain D: G.41, G.42, G.43, A.46, N.51, F.175, R.190 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.41, D:G.43, D:N.51, D:N.51 Salt bridges: D:R.190

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: W.49, Y.53, E.185, L.186 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.49, A:E.185 Water bridges: A:Y.53, A:Y.53, A:G.189 GOL.12: 4 residues within 4Å: Chain C: W.49, Y.53, E.185, L.186 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:W.49, C:E.185 Water bridges: C:Y.53, C:Y.53, C:G.189

6 x EOH: ETHANOL(Non-functional Binders)

EOH.5: 3 residues within 4Å: Chain A: K.14, N.16, A.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.14, A:N.16, A:N.16 Water bridges: A:A.100 EOH.6: 2 residues within 4Å: Chain A: A.30, G.31 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.30 Hydrogen bonds: A:G.31 EOH.8: 6 residues within 4Å: Chain B: E.6, S.7, S.10, H.26, N.28, K.76 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.6 Hydrogen bonds: B:N.28, B:N.28 EOH.13: 3 residues within 4Å: Chain C: K.14, N.16, A.100 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.14, C:N.16, C:N.16 Water bridges: C:A.100 EOH.14: 2 residues within 4Å: Chain C: A.30, G.31 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.30 Hydrogen bonds: C:G.31 EOH.16: 6 residues within 4Å: Chain D: E.6, S.7, S.10, H.26, N.28, K.76 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:E.6 Hydrogen bonds: D:N.28, D:N.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horsman, G.P. et al., Kinetic and structural insight into the mechanism of BphD, a C-C bond hydrolase from the biphenyl degradation pathway. Biochemistry (2006)

Release Date

2007-01-16

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

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

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