SMTL ID : 2xrx.1 (3 other biounits)

CRYSTAL STRUCTURE OF BIPHENYL DIOXYGENASE IN COMPLEX WITH BIPHENYL FROM BURKHOLDERIA XENOVORANS LB400

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

hetero-3-3-mer

Ligands

3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 9 residues within 4Å: Chain A: C.100, H.102, R.103, G.104, M.105, C.120, Y.122, H.123, W.125 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.100, A:H.102, A:C.120, A:H.123 FES.4: 9 residues within 4Å: Chain C: C.100, H.102, R.103, M.105, C.120, Y.122, H.123, G.124, W.125 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.100, C:H.102, C:C.120, C:H.123 FES.7: 9 residues within 4Å: Chain E: C.100, H.102, R.103, M.105, C.120, Y.122, H.123, G.124, W.125 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.100, E:H.102, E:C.120, E:H.123

3 x FE2: FE (II) ION(Non-covalent)

FE2.2: 4 residues within 4Å: Chain A: Q.226, H.233, H.239, D.388 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.233, A:H.239, A:D.388, A:D.388 FE2.5: 4 residues within 4Å: Chain C: Q.226, H.233, H.239, D.388 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.233, C:H.239, C:D.388, C:D.388, H2O.4 FE2.8: 5 residues within 4Å: Chain E: Q.226, H.233, H.239, D.388 Ligands: BNL.9 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.233, E:H.239, E:D.388, E:D.388

3 x BNL: BIPHENYL(Non-covalent)

BNL.3: 10 residues within 4Å: Chain A: Q.226, F.227, D.230, H.233, A.234, G.321, H.323, L.333, F.336, F.384 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.234, A:H.323, A:L.333, A:F.336, A:F.336, A:F.384 pi-Stacking: A:F.227, A:H.233 BNL.6: 11 residues within 4Å: Chain C: Q.226, F.227, D.230, M.231, H.233, A.234, G.321, H.323, L.333, F.336, F.384 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Q.226, C:A.234, C:H.323, C:L.333, C:F.336, C:F.384 pi-Stacking: C:F.227, C:H.233 BNL.9: 11 residues within 4Å: Chain E: Q.226, F.227, D.230, H.233, V.287, G.321, H.323, L.333, F.336, F.384 Ligands: FE2.8 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:Q.226, E:V.287, E:H.323, E:L.333, E:F.336, E:F.384 pi-Stacking: E:F.227, E:H.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, P. et al., Structural Insight Into the Expanded Pcb-Degrading Abilities of a Biphenyl Dioxygenase Obtained by Directed Evolution. J.Mol.Biol. (2011)

Release Date

2010-11-24

Peptides

BIPHENYL DIOXYGENASE SUBUNIT ALPHA: ACE
BIPHENYL DIOXYGENASE SUBUNIT BETA: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

BIPHENYL DIOXYGENASE SUBUNIT ALPHA

BIPHENYL DIOXYGENASE SUBUNIT BETA

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