SMTL ID : 2uvn.1

Crystal structure of econazole-bound CYP130 from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 25 residues within 4Å: Chain A: M.98, H.104, R.108, F.115, Y.162, F.243, M.247, G.251, T.254, V.255, P.296, V.297, L.300, R.302, Y.325, T.353, F.354, S.355, A.358, H.359, C.361, L.362, G.363, A.367 Ligands: ECN.2 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:F.115, A:Y.162, A:F.243, A:V.255, A:P.296, A:P.296, A:L.300, A:T.353, A:L.362, A:L.362, A:A.367 Hydrogen bonds: A:Y.325, A:S.355 Salt bridges: A:H.104, A:R.108, A:R.302, A:H.359 pi-Stacking: A:F.354 Metal complexes: A:C.361 HEM.10: 26 residues within 4Å: Chain B: M.98, H.104, R.108, F.115, F.243, M.247, G.251, T.254, V.255, M.258, P.296, V.297, L.300, R.302, Y.325, T.353, F.354, S.355, A.358, H.359, H.360, C.361, L.362, G.363, A.367 Ligands: ECN.11 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:F.115, B:F.243, B:P.296, B:P.296, B:V.297, B:V.297, B:L.300, B:T.353, B:L.362, B:L.362, B:A.367 Hydrogen bonds: B:Y.325, B:S.355 Salt bridges: B:H.104, B:R.108, B:R.302, B:H.359 pi-Stacking: B:F.354 Metal complexes: B:C.361 HEM.23: 25 residues within 4Å: Chain C: M.98, H.104, R.108, F.115, Y.162, F.243, M.247, G.251, T.254, V.255, P.296, V.297, L.300, R.302, Y.325, T.353, F.354, S.355, A.358, H.359, C.361, L.362, G.363, A.367 Ligands: ECN.24 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:F.115, C:Y.162, C:F.243, C:V.255, C:P.296, C:P.296, C:L.300, C:T.353, C:L.362, C:L.362, C:A.367 Hydrogen bonds: C:S.355 Salt bridges: C:H.104, C:R.108, C:R.302, C:H.359 pi-Stacking: C:F.354 Metal complexes: C:C.361 HEM.32: 26 residues within 4Å: Chain D: M.98, H.104, R.108, F.115, F.243, M.247, G.251, T.254, V.255, M.258, P.296, V.297, L.300, R.302, Y.325, T.353, F.354, S.355, A.358, H.359, H.360, C.361, L.362, G.363, A.367 Ligands: ECN.33 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:F.115, D:F.243, D:P.296, D:P.296, D:V.297, D:V.297, D:L.300, D:T.353, D:L.362, D:L.362, D:A.367 Hydrogen bonds: D:Y.325, D:Y.325, D:S.355 Salt bridges: D:H.104, D:R.108, D:R.302, D:H.359 pi-Stacking: D:F.354 Metal complexes: D:C.361

4 x ECN: 1-[(2S)-2-[(4-CHLOROBENZYL)OXY]-2-(2,4-DICHLOROPHENYL)ETHYL]-1H-IMIDAZOLE(Non-covalent)

ECN.2: 16 residues within 4Å: Chain A: L.78, D.92, T.93, P.94, P.95, M.96, M.98, F.243, T.246, T.249, G.250, G.251, T.254, L.300, Y.399 Ligands: HEM.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.78, A:P.94, A:T.246, A:L.300, A:Y.399 Halogen bonds: A:D.92, A:T.246, A:T.249 ECN.11: 15 residues within 4Å: Chain B: D.92, T.93, P.94, P.95, M.96, M.98, F.243, T.246, G.250, G.251, T.254, L.300, Y.399, V.400 Ligands: HEM.10 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.94, B:T.246, B:L.300, B:Y.399, B:V.400 Halogen bonds: B:D.92 ECN.24: 16 residues within 4Å: Chain C: L.78, D.92, T.93, P.94, P.95, M.96, M.98, F.243, T.246, T.249, G.250, G.251, T.254, L.300, Y.399 Ligands: HEM.23 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.78, C:P.94, C:T.246, C:L.300, C:Y.399 Halogen bonds: C:D.92, C:T.246, C:T.249 ECN.33: 15 residues within 4Å: Chain D: D.92, T.93, P.94, P.95, M.96, M.98, F.243, T.246, G.250, G.251, T.254, L.300, Y.399, V.400 Ligands: HEM.32 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:P.94, D:T.246, D:L.300, D:Y.399, D:V.400 Halogen bonds: D:D.92

28 x F: FLUORIDE ION(Non-covalent)

F.3: 3 residues within 4Å: Chain A: E.50, Y.51, R.319 Ligand excluded by PLIP F.4: 1 residues within 4Å: Chain A: R.381 Ligand excluded by PLIP F.5: 4 residues within 4Å: Chain A: T.20, A.21, G.396, G.397 Ligand excluded by PLIP F.9: 1 residues within 4Å: Chain A: R.414 Ligand excluded by PLIP F.12: 3 residues within 4Å: Chain B: R.48, Y.51, E.86 Ligand excluded by PLIP F.13: 3 residues within 4Å: Chain B: A.388, E.389, S.390 Ligand excluded by PLIP F.14: 3 residues within 4Å: Chain B: Y.335, P.348, R.349 Ligand excluded by PLIP F.15: 2 residues within 4Å: Chain B: P.29, R.32 Ligand excluded by PLIP F.16: 1 residues within 4Å: Chain B: R.58 Ligand excluded by PLIP F.17: 4 residues within 4Å: Chain B: E.124, R.128, V.373, E.377 Ligand excluded by PLIP F.18: 3 residues within 4Å: Chain B: T.20, A.21, G.396 Ligand excluded by PLIP F.19: 1 residues within 4Å: Chain B: R.113 Ligand excluded by PLIP F.20: 3 residues within 4Å: Chain B: P.166, R.210, R.211 Ligand excluded by PLIP F.22: 3 residues within 4Å: Chain C: W.63, S.64, R.67 Ligand excluded by PLIP F.25: 3 residues within 4Å: Chain C: E.50, Y.51, R.319 Ligand excluded by PLIP F.26: 1 residues within 4Å: Chain C: R.381 Ligand excluded by PLIP F.27: 4 residues within 4Å: Chain C: T.20, A.21, G.396, G.397 Ligand excluded by PLIP F.31: 1 residues within 4Å: Chain C: R.414 Ligand excluded by PLIP F.34: 3 residues within 4Å: Chain D: R.48, Y.51, E.86 Ligand excluded by PLIP F.35: 3 residues within 4Å: Chain D: A.388, E.389, S.390 Ligand excluded by PLIP F.36: 3 residues within 4Å: Chain D: Y.335, P.348, R.349 Ligand excluded by PLIP F.37: 2 residues within 4Å: Chain D: P.29, R.32 Ligand excluded by PLIP F.38: 1 residues within 4Å: Chain D: R.58 Ligand excluded by PLIP F.39: 4 residues within 4Å: Chain D: E.124, R.128, V.373, E.377 Ligand excluded by PLIP F.40: 3 residues within 4Å: Chain D: T.20, A.21, G.396 Ligand excluded by PLIP F.41: 1 residues within 4Å: Chain D: R.113 Ligand excluded by PLIP F.42: 3 residues within 4Å: Chain D: P.166, R.210, R.211 Ligand excluded by PLIP F.44: 3 residues within 4Å: Chain A: W.63, S.64, R.67 Ligand excluded by PLIP

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 4 residues within 4Å: Chain A: V.387, A.388, E.389, S.390 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.389, A:S.390 SO4.7: 5 residues within 4Å: Chain A: R.349, N.350, H.356 Chain D: H.42, Y.54 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Salt bridges: D:H.42, A:R.349, A:H.356 Hydrogen bonds: A:N.350 SO4.8: 1 residues within 4Å: Chain A: R.58 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.58 SO4.21: 4 residues within 4Å: Chain B: R.349, F.354, H.360, R.368 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.349 Salt bridges: B:H.360, B:R.368 SO4.28: 4 residues within 4Å: Chain C: V.387, A.388, E.389, S.390 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.389, C:S.390 SO4.29: 5 residues within 4Å: Chain B: H.42, Y.54 Chain C: R.349, N.350, H.356 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:Y.54, C:N.350 Salt bridges: B:H.42, C:R.349, C:H.356 SO4.30: 1 residues within 4Å: Chain C: R.58 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.58 SO4.43: 4 residues within 4Å: Chain D: R.349, F.354, H.360, R.368 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.349 Salt bridges: D:H.360, D:R.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ouellet, H. et al., Mycobacterium Tuberculosis Cyp130: Crystal Structure, Biophysical Characterization, and Interactions with Antifungal Azole Drugs. J.Biol.Chem. (2008)

Release Date

2007-12-18

Peptides

CYTOCHROME P450 130: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

CYTOCHROME P450 130

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