SMTL ID : 1kw9.1

Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 2.0A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-octamer

Ligands

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

FE2.1: 5 residues within 4Å: Chain A: H.145, H.209, Y.249, E.260 Ligands: BPY.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.145, A:H.209, A:E.260, H2O.8 FE2.3: 5 residues within 4Å: Chain B: H.145, H.209, Y.249, E.260 Ligands: BPY.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.145, B:H.209, B:E.260, H2O.15 FE2.5: 5 residues within 4Å: Chain C: H.145, H.209, Y.249, E.260 Ligands: BPY.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.145, C:H.209, C:E.260, H2O.22 FE2.7: 5 residues within 4Å: Chain D: H.145, H.209, Y.249, E.260 Ligands: BPY.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.145, D:H.209, D:E.260, H2O.30 FE2.9: 5 residues within 4Å: Chain E: H.145, H.209, Y.249, E.260 Ligands: BPY.10 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.145, E:H.209, E:E.260, H2O.37 FE2.11: 5 residues within 4Å: Chain F: H.145, H.209, Y.249, E.260 Ligands: BPY.12 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.145, F:H.209, F:E.260, H2O.44 FE2.13: 5 residues within 4Å: Chain G: H.145, H.209, Y.249, E.260 Ligands: BPY.14 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.145, G:H.209, G:E.260, H2O.52 FE2.15: 5 residues within 4Å: Chain H: H.145, H.209, Y.249, E.260 Ligands: BPY.16 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.145, H:H.209, H:E.260, H2O.59

8 x BPY: BIPHENYL-2,3-DIOL(Non-covalent)

BPY.2: 13 residues within 4Å: Chain A: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.172, A:F.186, A:F.186, A:F.201 pi-Stacking: A:H.240 BPY.4: 13 residues within 4Å: Chain B: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.172, B:F.186, B:F.186, B:F.201 pi-Stacking: B:H.240 BPY.6: 13 residues within 4Å: Chain C: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.5 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.172, C:F.186, C:F.186, C:F.201 pi-Stacking: C:H.240 BPY.8: 13 residues within 4Å: Chain D: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.7 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.172, D:F.186, D:F.186, D:F.201 pi-Stacking: D:H.240 BPY.10: 13 residues within 4Å: Chain E: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.9 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:I.172, E:F.186, E:F.186, E:F.201 Hydrogen bonds: E:Y.249 pi-Stacking: E:H.240 BPY.12: 13 residues within 4Å: Chain F: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.11 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:I.172, F:F.186, F:F.186, F:F.201 Hydrogen bonds: F:Y.249 pi-Stacking: F:H.240 BPY.14: 13 residues within 4Å: Chain G: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.13 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:I.172, G:F.186, G:F.186, G:F.201 Hydrogen bonds: G:Y.249 pi-Stacking: G:H.240 BPY.16: 13 residues within 4Å: Chain H: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.15 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:I.172, H:F.186, H:F.186, H:F.201 Hydrogen bonds: H:H.209, H:Y.249, H:E.260 pi-Stacking: H:H.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sato, N. et al., Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase. J.Mol.Biol. (2002)

Release Date

2003-01-29

Peptides

2,3-Dihydroxybiphenyl dioxygenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

E
B

F
B

G
B

H
B

2,3-Dihydroxybiphenyl dioxygenase

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