SMTL ID : 2zi8.1

Crystal structure of the HsaC extradiol dioxygenase from M. tuberculosis in complex with 3,4-dihydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione (DHSA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-octamer

Ligands

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

FE2.1: 6 residues within 4Å: Chain A: H.145, H.215, M.217, Y.256, E.266 Ligands: SDT.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.145, A:H.215, A:E.266, H2O.6 FE2.3: 5 residues within 4Å: Chain B: H.145, H.215, Y.256, E.266 Ligands: SDT.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.145, B:H.215, B:E.266, H2O.17, H2O.19 FE2.5: 6 residues within 4Å: Chain C: H.145, H.215, M.217, Y.256, E.266 Ligands: SDT.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.145, C:H.215, C:E.266, H2O.24 FE2.7: 5 residues within 4Å: Chain D: H.145, H.215, Y.256, E.266 Ligands: SDT.8 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.145, D:H.215, D:E.266, H2O.35, H2O.38 FE2.9: 6 residues within 4Å: Chain E: H.145, H.215, M.217, Y.256, E.266 Ligands: SDT.10 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.145, E:H.215, E:E.266, H2O.43 FE2.11: 5 residues within 4Å: Chain F: H.145, H.215, Y.256, E.266 Ligands: SDT.12 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.145, F:H.215, F:E.266, H2O.54, H2O.56 FE2.13: 6 residues within 4Å: Chain G: H.145, H.215, M.217, Y.256, E.266 Ligands: SDT.14 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.145, G:H.215, G:E.266, H2O.62 FE2.15: 5 residues within 4Å: Chain H: H.145, H.215, Y.256, E.266 Ligands: SDT.16 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:H.145, H:H.215, H:E.266, H2O.73, H2O.75

8 x SDT: 3,4-dihydroxy-9,10-secoandrosta-1(10),2,4-triene-9,17-dione(Non-covalent)

SDT.2: 14 residues within 4Å: Chain A: H.145, M.172, L.190, F.192, H.200, V.214, H.215, H.247, N.249, D.250, Y.256, E.266, V.287 Ligands: FE2.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.190, A:F.192, A:F.192, A:V.214, A:V.287 Hydrogen bonds: A:Y.256 Water bridges: A:H.247 pi-Stacking: A:H.247 SDT.4: 14 residues within 4Å: Chain B: M.172, F.192, H.200, L.205, V.214, H.215, H.247, N.249, D.250, Y.256, E.266, V.287, F.294 Ligands: FE2.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.192, B:L.205, B:V.214, B:N.249, B:V.287, B:F.294 Hydrogen bonds: B:D.250 pi-Stacking: B:H.247 SDT.6: 14 residues within 4Å: Chain C: H.145, M.172, L.190, F.192, H.200, V.214, H.215, H.247, N.249, D.250, Y.256, E.266, V.287 Ligands: FE2.5 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.190, C:F.192, C:F.192, C:V.214, C:V.287 Hydrogen bonds: C:Y.256 Water bridges: C:H.247 pi-Stacking: C:H.247 SDT.8: 14 residues within 4Å: Chain D: M.172, F.192, H.200, L.205, V.214, H.215, H.247, N.249, D.250, Y.256, E.266, V.287, F.294 Ligands: FE2.7 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.192, D:L.205, D:V.214, D:N.249, D:V.287, D:F.294 Hydrogen bonds: D:D.250 pi-Stacking: D:H.247 SDT.10: 14 residues within 4Å: Chain E: H.145, M.172, L.190, F.192, H.200, V.214, H.215, H.247, N.249, D.250, Y.256, E.266, V.287 Ligands: FE2.9 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:L.190, E:F.192, E:F.192, E:V.214, E:V.287 Hydrogen bonds: E:Y.256 Water bridges: E:H.247 pi-Stacking: E:H.247 SDT.12: 14 residues within 4Å: Chain F: M.172, F.192, H.200, L.205, V.214, H.215, H.247, N.249, D.250, Y.256, E.266, V.287, F.294 Ligands: FE2.11 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:F.192, F:L.205, F:V.214, F:N.249, F:V.287, F:F.294 Hydrogen bonds: F:D.250 pi-Stacking: F:H.247 SDT.14: 14 residues within 4Å: Chain G: H.145, M.172, L.190, F.192, H.200, V.214, H.215, H.247, N.249, D.250, Y.256, E.266, V.287 Ligands: FE2.13 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:L.190, G:F.192, G:F.192, G:V.214, G:V.287 Hydrogen bonds: G:Y.256 Water bridges: G:H.247 pi-Stacking: G:H.247 SDT.16: 14 residues within 4Å: Chain H: M.172, F.192, H.200, L.205, V.214, H.215, H.247, N.249, D.250, Y.256, E.266, V.287, F.294 Ligands: FE2.15 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:F.192, H:L.205, H:V.214, H:N.249, H:V.287, H:F.294 Hydrogen bonds: H:H.215, H:H.215, H:D.250 pi-Stacking: H:H.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yam, K.C. et al., Studies of a ring-cleaving dioxygenase illuminate the role of cholesterol metabolism in the pathogenesis of Mycobacterium tuberculosis. Plos Pathog. (2009)

Release Date

2009-02-24

Peptides

PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC

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