SMTL ID : 5aew.1 (4 other biounits)

Crystal structure of II9 variant of Biphenyl dioxygenase from Burkholderia xenovorans LB400 in complex with biphenyl

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-3-3-mer

Ligands

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

FES.1: 8 residues within 4Å: Chain A: C.100, H.102, R.103, M.105, C.120, Y.122, H.123, W.125 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions, Metal complexes: A:C.100, A:H.102, A:C.120, A:H.123, H2O.1 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 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.100, C:C.120, C:H.123 FES.6: 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 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.233, A:H.239, A:D.388, A:D.388, H2O.2 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.11 FE2.7: 4 residues within 4Å: Chain E: Q.226, H.233, H.239, D.388 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.233, E:H.239, E:D.388, H2O.15

2 x BNL: BIPHENYL(Non-covalent)

BNL.3: 9 residues within 4Å: Chain A: Q.226, F.227, D.230, M.231, H.233, H.323, L.333, F.378, F.384 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.323, A:L.333, A:F.378, A:F.384 pi-Stacking: A:F.227, A:H.233 BNL.8: 10 residues within 4Å: Chain E: Q.226, F.227, D.230, M.231, H.233, A.234, G.321, H.323, L.333, I.336 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:Q.226, E:F.227, E:A.234, E:H.323, E:L.333, E:I.336 pi-Stacking: E:H.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dhindwal, S. et al., Structural Basis of the Enhanced Pollutant-Degrading Capabilities of an Engineered Biphenyl Dioxygenase. J.Bacteriol. (2016)

Release Date

2016-04-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

C
U

E
W

B
T

D
V

F
X

BIPHENYL DIOXYGENASE SUBUNIT ALPHA

BIPHENYL DIOXYGENASE SUBUNIT BETA

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