SMTL ID : 1kmy.1

Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 2,3-dihydroxybiphenyl under Anaerobic Condition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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.259 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.259, H2O.5 FE2.4: 5 residues within 4Å: Chain B: H.145, H.209, Y.249, E.259 Ligands: BPY.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.145, B:H.209, B:E.259, H2O.9 FE2.7: 5 residues within 4Å: Chain C: H.145, H.209, Y.249, E.259 Ligands: BPY.8 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.145, C:H.209, C:E.259, H2O.14 FE2.10: 5 residues within 4Å: Chain D: H.145, H.209, Y.249, E.259 Ligands: BPY.11 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.145, D:H.209, D:E.259, H2O.18 FE2.13: 5 residues within 4Å: Chain E: H.145, H.209, Y.249, E.259 Ligands: BPY.14 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.145, E:H.209, E:E.259, H2O.23 FE2.16: 5 residues within 4Å: Chain F: H.145, H.209, Y.249, E.259 Ligands: BPY.17 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.145, F:H.209, F:E.259, H2O.27 FE2.19: 5 residues within 4Å: Chain G: H.145, H.209, Y.249, E.259 Ligands: BPY.20 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.145, G:H.209, G:E.259, H2O.31 FE2.22: 5 residues within 4Å: Chain H: H.145, H.209, Y.249, E.259 Ligands: BPY.23 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.145, H:H.209, H:E.259, H2O.36

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

BPY.2: 16 residues within 4Å: Chain A: H.145, I.172, M.174, F.186, H.194, F.201, H.208, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.1, TBU.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.172, A:F.186, A:F.186, A:F.201, A:H.240, A:P.279 pi-Stacking: A:H.209, A:H.240 BPY.5: 16 residues within 4Å: Chain B: H.145, I.172, M.174, F.186, H.194, F.201, H.208, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.4, TBU.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.172, B:F.186, B:F.186, B:F.201, B:H.240, B:P.279 pi-Stacking: B:H.209, B:H.240 BPY.8: 16 residues within 4Å: Chain C: H.145, I.172, M.174, F.186, H.194, F.201, H.208, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.7, TBU.9 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.172, C:F.186, C:F.186, C:F.201, C:H.240, C:P.279 pi-Stacking: C:H.209, C:H.240 BPY.11: 16 residues within 4Å: Chain D: H.145, I.172, M.174, F.186, H.194, F.201, H.208, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.10, TBU.12 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.172, D:F.186, D:F.186, D:F.201, D:H.240, D:P.279 pi-Stacking: D:H.209, D:H.240 BPY.14: 16 residues within 4Å: Chain E: H.145, I.172, M.174, F.186, H.194, F.201, H.208, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.13, TBU.15 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:I.172, E:F.186, E:F.186, E:F.201, E:H.240, E:P.279 Hydrogen bonds: E:Y.249 pi-Stacking: E:H.209, E:H.240 BPY.17: 16 residues within 4Å: Chain F: H.145, I.172, M.174, F.186, H.194, F.201, H.208, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.16, TBU.18 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:I.172, F:F.186, F:F.186, F:F.201, F:H.240, F:P.279 Hydrogen bonds: F:Y.249 pi-Stacking: F:H.209, F:H.240 BPY.20: 16 residues within 4Å: Chain G: H.145, I.172, M.174, F.186, H.194, F.201, H.208, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.19, TBU.21 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:I.172, G:F.186, G:F.186, G:F.201, G:H.240, G:P.279 Hydrogen bonds: G:Y.249 pi-Stacking: G:H.209, G:H.240 BPY.23: 16 residues within 4Å: Chain H: H.145, I.172, M.174, F.186, H.194, F.201, H.208, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.22, TBU.24 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:I.172, H:F.186, H:F.186, H:F.201, H:H.240, H:P.279 Hydrogen bonds: H:Y.249 pi-Stacking: H:H.209, H:H.240

8 x TBU: TERTIARY-BUTYL ALCOHOL(Non-functional Binders)

TBU.3: 5 residues within 4Å: Chain A: S.235, S.280, H.284, R.288 Ligands: BPY.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.235, A:R.288 TBU.6: 5 residues within 4Å: Chain B: S.235, S.280, H.284, R.288 Ligands: BPY.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.235, B:R.288 TBU.9: 5 residues within 4Å: Chain C: S.235, S.280, H.284, R.288 Ligands: BPY.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.235, C:R.288 TBU.12: 5 residues within 4Å: Chain D: S.235, S.280, H.284, R.288 Ligands: BPY.11 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.235, D:R.288 TBU.15: 5 residues within 4Å: Chain E: S.235, S.280, H.284, R.288 Ligands: BPY.14 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.235, E:R.288 TBU.18: 5 residues within 4Å: Chain F: S.235, S.280, H.284, R.288 Ligands: BPY.17 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.235, F:R.288 TBU.21: 5 residues within 4Å: Chain G: S.235, S.280, H.284, R.288 Ligands: BPY.20 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.235, G:R.288 TBU.24: 5 residues within 4Å: Chain H: S.235, S.280, H.284, R.288 Ligands: BPY.23 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:S.235, H:R.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vaillancourt, F.H. et al., Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol. J.Biol.Chem. (1998)

Release Date

2002-02-20

Peptides

2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE

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