SMTL ID : 1knd.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-octamer

Ligands

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

FE2.1: 5 residues within 4Å: Chain A: H.145, H.209, Y.249, E.259 Ligands: CAQ.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.145, A:H.209, A:E.259, H2O.2, H2O.5 FE2.2: 2 residues within 4Å: Chain A: Q.167, H.188 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.188 FE2.6: 5 residues within 4Å: Chain B: H.145, H.209, Y.249, E.259 Ligands: CAQ.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.145, B:H.209, B:E.259, H2O.7, H2O.10 FE2.7: 2 residues within 4Å: Chain B: Q.167, H.188 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.188 FE2.11: 5 residues within 4Å: Chain C: H.145, H.209, Y.249, E.259 Ligands: CAQ.13 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.145, C:H.209, C:E.259, H2O.11, H2O.14 FE2.12: 2 residues within 4Å: Chain C: Q.167, H.188 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.188 FE2.16: 5 residues within 4Å: Chain D: H.145, H.209, Y.249, E.259 Ligands: CAQ.18 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.145, D:H.209, D:E.259, H2O.16, H2O.19 FE2.17: 2 residues within 4Å: Chain D: Q.167, H.188 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.188 FE2.21: 5 residues within 4Å: Chain E: H.145, H.209, Y.249, E.259 Ligands: CAQ.23 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.145, E:H.209, E:E.259, H2O.21, H2O.24 FE2.22: 2 residues within 4Å: Chain E: Q.167, H.188 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.188 FE2.26: 5 residues within 4Å: Chain F: H.145, H.209, Y.249, E.259 Ligands: CAQ.28 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.145, F:H.209, F:E.259, H2O.25, H2O.28 FE2.27: 2 residues within 4Å: Chain F: Q.167, H.188 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:H.188 FE2.31: 5 residues within 4Å: Chain G: H.145, H.209, Y.249, E.259 Ligands: CAQ.33 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:H.145, G:H.209, G:E.259, H2O.30, H2O.33 FE2.32: 2 residues within 4Å: Chain G: Q.167, H.188 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:H.188 FE2.36: 5 residues within 4Å: Chain H: H.145, H.209, Y.249, E.259 Ligands: CAQ.38 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:H.145, H:H.209, H:E.259, H2O.35, H2O.38 FE2.37: 2 residues within 4Å: Chain H: Q.167, H.188 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:H.188

8 x CAQ: CATECHOL(Non-covalent)

CAQ.3: 13 residues within 4Å: Chain A: H.145, I.172, F.186, H.194, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.1, TBU.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.172, A:F.186, A:F.186, A:H.240, A:P.279 Water bridges: A:H.240, A:E.259 pi-Stacking: A:H.240 CAQ.8: 13 residues within 4Å: Chain B: H.145, I.172, F.186, H.194, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.6, TBU.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.172, B:F.186, B:F.186, B:H.240, B:P.279 Water bridges: B:H.240, B:E.259 pi-Stacking: B:H.240 CAQ.13: 13 residues within 4Å: Chain C: H.145, I.172, F.186, H.194, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.11, TBU.15 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.172, C:F.186, C:F.186, C:H.240, C:P.279 Water bridges: C:H.240, C:E.259 pi-Stacking: C:H.240 CAQ.18: 13 residues within 4Å: Chain D: H.145, I.172, F.186, H.194, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.16, TBU.20 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.172, D:F.186, D:F.186, D:H.240, D:P.279 Water bridges: D:H.240, D:E.259 pi-Stacking: D:H.240 CAQ.23: 13 residues within 4Å: Chain E: H.145, I.172, F.186, H.194, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.21, TBU.25 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:I.172, E:F.186, E:F.186, E:H.240, E:P.279 Hydrogen bonds: E:Y.249 Water bridges: E:H.240, E:E.259 pi-Stacking: E:H.240 CAQ.28: 13 residues within 4Å: Chain F: H.145, I.172, F.186, H.194, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.26, TBU.30 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:I.172, F:F.186, F:F.186, F:H.240, F:P.279 Hydrogen bonds: F:Y.249 Water bridges: F:H.240, F:E.259 pi-Stacking: F:H.240 CAQ.33: 13 residues within 4Å: Chain G: H.145, I.172, F.186, H.194, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.31, TBU.35 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:I.172, G:F.186, G:F.186, G:H.240, G:P.279 Hydrogen bonds: G:Y.249 Water bridges: G:H.240, G:E.259 pi-Stacking: G:H.240 CAQ.38: 13 residues within 4Å: Chain H: H.145, I.172, F.186, H.194, H.209, H.240, N.242, D.243, Y.249, E.259, P.279 Ligands: FE2.36, TBU.40 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:I.172, H:F.186, H:F.186, H:H.240, H:P.279 Hydrogen bonds: H:Y.249 Water bridges: H:H.240, H:E.259 pi-Stacking: H:H.240

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

TBU.4: 6 residues within 4Å: Chain A: H.208, S.235, Y.249, H.284, R.288 Ligands: TBU.5 Ligand excluded by PLIP TBU.5: 9 residues within 4Å: Chain A: V.147, F.186, F.201, H.208, H.209, Y.249, P.279 Ligands: CAQ.3, TBU.4 Ligand excluded by PLIP TBU.9: 6 residues within 4Å: Chain B: H.208, S.235, Y.249, H.284, R.288 Ligands: TBU.10 Ligand excluded by PLIP TBU.10: 9 residues within 4Å: Chain B: V.147, F.186, F.201, H.208, H.209, Y.249, P.279 Ligands: CAQ.8, TBU.9 Ligand excluded by PLIP TBU.14: 6 residues within 4Å: Chain C: H.208, S.235, Y.249, H.284, R.288 Ligands: TBU.15 Ligand excluded by PLIP TBU.15: 9 residues within 4Å: Chain C: V.147, F.186, F.201, H.208, H.209, Y.249, P.279 Ligands: CAQ.13, TBU.14 Ligand excluded by PLIP TBU.19: 6 residues within 4Å: Chain D: H.208, S.235, Y.249, H.284, R.288 Ligands: TBU.20 Ligand excluded by PLIP TBU.20: 9 residues within 4Å: Chain D: V.147, F.186, F.201, H.208, H.209, Y.249, P.279 Ligands: CAQ.18, TBU.19 Ligand excluded by PLIP TBU.24: 6 residues within 4Å: Chain E: H.208, S.235, Y.249, H.284, R.288 Ligands: TBU.25 Ligand excluded by PLIP TBU.25: 9 residues within 4Å: Chain E: V.147, F.186, F.201, H.208, H.209, Y.249, P.279 Ligands: CAQ.23, TBU.24 Ligand excluded by PLIP TBU.29: 6 residues within 4Å: Chain F: H.208, S.235, Y.249, H.284, R.288 Ligands: TBU.30 Ligand excluded by PLIP TBU.30: 9 residues within 4Å: Chain F: V.147, F.186, F.201, H.208, H.209, Y.249, P.279 Ligands: CAQ.28, TBU.29 Ligand excluded by PLIP TBU.34: 6 residues within 4Å: Chain G: H.208, S.235, Y.249, H.284, R.288 Ligands: TBU.35 Ligand excluded by PLIP TBU.35: 9 residues within 4Å: Chain G: V.147, F.186, F.201, H.208, H.209, Y.249, P.279 Ligands: CAQ.33, TBU.34 Ligand excluded by PLIP TBU.39: 6 residues within 4Å: Chain H: H.208, S.235, Y.249, H.284, R.288 Ligands: TBU.40 Ligand excluded by PLIP TBU.40: 9 residues within 4Å: Chain H: V.147, F.186, F.201, H.208, H.209, Y.249, P.279 Ligands: CAQ.38, TBU.39 Ligand excluded by PLIP

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

2002-03-27

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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