SMTL ID : 1kw3.1

Crystal structure of 2,3-dihydroxybiphenyal dioxygenase (BphC) at 1.45 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-octamer

Ligands

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

FE2.1: 4 residues within 4Å: Chain A: H.145, H.209, Y.249, E.260 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.145, A:H.209, A:E.260, H2O.3, H2O.12 FE2.4: 4 residues within 4Å: Chain B: H.145, H.209, Y.249, E.260 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.145, B:H.209, B:E.260, H2O.14, H2O.24 FE2.7: 4 residues within 4Å: Chain C: H.145, H.209, Y.249, E.260 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.145, C:H.209, C:E.260, H2O.26, H2O.35 FE2.10: 4 residues within 4Å: Chain D: H.145, H.209, Y.249, E.260 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.145, D:H.209, D:E.260, H2O.38, H2O.47 FE2.13: 4 residues within 4Å: Chain E: H.145, H.209, Y.249, E.260 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.145, E:H.209, E:E.260, H2O.49, H2O.58 FE2.16: 4 residues within 4Å: Chain F: H.145, H.209, Y.249, E.260 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.145, F:H.209, F:E.260, H2O.61, H2O.70 FE2.19: 4 residues within 4Å: Chain G: H.145, H.209, Y.249, E.260 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:H.145, G:H.209, G:E.260, H2O.72, H2O.81 FE2.22: 4 residues within 4Å: Chain H: H.145, H.209, Y.249, E.260 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:H.145, H:H.209, H:E.260, H2O.84, H2O.93

16 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 6 residues within 4Å: Chain A: P.126, F.127 Chain F: P.132, V.133, S.134, D.219 Ligand excluded by PLIP MPD.3: 4 residues within 4Å: Chain A: F.224, D.228 Chain H: L.236, K.286 Ligand excluded by PLIP MPD.5: 6 residues within 4Å: Chain B: P.126, F.127 Chain E: P.132, V.133, S.134, D.219 Ligand excluded by PLIP MPD.6: 4 residues within 4Å: Chain B: F.224, D.228 Chain G: L.236, K.286 Ligand excluded by PLIP MPD.8: 6 residues within 4Å: Chain C: P.126, F.127 Chain G: P.132, V.133, S.134, D.219 Ligand excluded by PLIP MPD.9: 4 residues within 4Å: Chain C: F.224, D.228 Chain F: L.236, K.286 Ligand excluded by PLIP MPD.11: 6 residues within 4Å: Chain D: P.126, F.127 Chain H: P.132, V.133, S.134, D.219 Ligand excluded by PLIP MPD.12: 4 residues within 4Å: Chain D: F.224, D.228 Chain E: L.236, K.286 Ligand excluded by PLIP MPD.14: 6 residues within 4Å: Chain B: P.132, V.133, S.134, D.219 Chain E: P.126, F.127 Ligand excluded by PLIP MPD.15: 4 residues within 4Å: Chain D: L.236, K.286 Chain E: F.224, D.228 Ligand excluded by PLIP MPD.17: 6 residues within 4Å: Chain A: P.132, V.133, S.134, D.219 Chain F: P.126, F.127 Ligand excluded by PLIP MPD.18: 4 residues within 4Å: Chain C: L.236, K.286 Chain F: F.224, D.228 Ligand excluded by PLIP MPD.20: 6 residues within 4Å: Chain C: P.132, V.133, S.134, D.219 Chain G: P.126, F.127 Ligand excluded by PLIP MPD.21: 4 residues within 4Å: Chain B: L.236, K.286 Chain G: F.224, D.228 Ligand excluded by PLIP MPD.23: 6 residues within 4Å: Chain D: P.132, V.133, S.134, D.219 Chain H: P.126, F.127 Ligand excluded by PLIP MPD.24: 4 residues within 4Å: Chain A: L.236, K.286 Chain H: F.224, D.228 Ligand excluded by PLIP

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

2003-01-28

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

Related Entries With Identical Sequence