SMTL ID : 4ipw.2 (2 other biounits)

Substrate and reaction specificity of Mycobacterium tuberculosis cytochrome P450 CYP121

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 23 residues within 4Å: Chain A: M.61, M.85, H.145, F.229, A.232, G.233, S.236, T.237, F.240, F.279, L.283, R.285, L.308, A.336, F.337, G.338, Q.341, H.342, C.344, P.345, G.346, G.350 Ligands: 1G7.6 14 PLIP interactions: 13 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.229, A:F.229, A:A.232, A:F.240, A:F.279, A:L.283, A:L.308, A:F.337, A:P.345 Salt bridges: A:R.285, A:H.342 pi-Stacking: A:F.337 Metal complexes: A:C.344, H2O.1 HEM.13: 23 residues within 4Å: Chain B: M.61, M.85, H.145, F.229, A.232, G.233, S.236, T.237, F.240, F.279, L.283, R.285, L.308, A.336, F.337, G.338, Q.341, H.342, C.344, P.345, G.346, G.350 Ligands: 1G7.18 14 PLIP interactions: 13 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:F.229, B:F.229, B:A.232, B:F.240, B:F.279, B:L.283, B:L.308, B:F.337, B:P.345 Salt bridges: B:R.285, B:H.342 pi-Stacking: B:F.337 Metal complexes: B:C.344, H2O.26

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

SO4.2: 6 residues within 4Å: Chain A: R.57, S.60, M.61, K.62, N.83, H.342 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.60, A:M.61, A:K.62 Water bridges: A:R.57, A:R.57, A:G.86, A:Q.341 Salt bridges: A:R.57, A:H.342 SO4.3: 3 residues within 4Å: Chain A: S.11, R.13, R.16 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.11 Water bridges: A:A.12, A:R.13, A:R.13 Salt bridges: A:R.16 SO4.4: 4 residues within 4Å: Chain A: T.3, L.5, L.6, R.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.3, A:L.6 Salt bridges: A:R.31 SO4.5: 6 residues within 4Å: Chain A: R.133, N.134, F.160, S.164, R.380 Chain B: R.390 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Water bridges: A:R.380, A:R.380, B:R.390 Salt bridges: A:R.133, A:R.380, B:R.390 SO4.14: 6 residues within 4Å: Chain B: R.57, S.60, M.61, K.62, N.83, H.342 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.60, B:M.61, B:K.62 Water bridges: B:R.57, B:R.57, B:G.86, B:Q.341 Salt bridges: B:R.57, B:H.342 SO4.15: 3 residues within 4Å: Chain B: S.11, R.13, R.16 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.11 Water bridges: B:A.12, B:R.13, B:R.13 Salt bridges: B:R.16 SO4.16: 4 residues within 4Å: Chain B: T.3, L.5, L.6, R.31 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.3, B:L.6 Salt bridges: B:R.31 SO4.17: 6 residues within 4Å: Chain A: R.390 Chain B: R.133, N.134, F.160, S.164, R.380 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Water bridges: A:R.390, B:R.380, B:R.380 Salt bridges: A:R.390, B:R.133, B:R.380

2 x 1G7: (3S,6S)-3-(3,4-dihydroxybenzyl)-6-(4-hydroxybenzyl)piperazine-2,5-dione(Non-covalent)

1G7.6: 11 residues within 4Å: Chain A: T.76, V.77, V.81, V.82, N.84, A.166, F.167, T.228, R.385 Ligands: HEM.1, GOL.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.228 Hydrogen bonds: A:T.76, A:N.84, A:A.166, A:R.385 Water bridges: A:T.76, A:V.77, A:M.85, A:Q.384, A:R.385 pi-Stacking: A:F.167 1G7.18: 11 residues within 4Å: Chain B: T.76, V.77, V.81, V.82, N.84, A.166, F.167, T.228, R.385 Ligands: HEM.13, GOL.19 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.228 Hydrogen bonds: B:N.84, B:A.166, B:R.385 Water bridges: B:T.76, B:T.76, B:V.77, B:M.85, B:Q.384, B:R.385 pi-Stacking: B:F.167

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: M.61, T.64, R.71, N.73, L.75, V.82, P.284 Ligands: 1G7.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.64, A:R.71, A:N.73, A:N.73 Water bridges: A:L.72 GOL.8: 7 residues within 4Å: Chain A: E.63, A.66, L.286, A.287, T.288, K.300, G.301 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.300 GOL.9: 6 residues within 4Å: Chain A: A.67, G.68, A.69, P.70, L.286, G.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.67, A:G.301 GOL.11: 7 residues within 4Å: Chain A: P.78, E.80, V.81, W.181, I.185, E.220, T.224 3 PLIP interactions: 3 interactions with chain A Water bridges: A:W.181, A:D.182, A:T.224 GOL.12: 5 residues within 4Å: Chain A: D.15, S.247, R.251, I.275, L.277 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.251, A:R.251 Water bridges: A:G.14, A:D.15, A:S.247, A:L.277 GOL.19: 8 residues within 4Å: Chain B: M.61, T.64, R.71, N.73, L.75, V.82, P.284 Ligands: 1G7.18 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.64, B:T.64, B:R.71, B:N.73, B:N.73 Water bridges: B:L.72 GOL.20: 7 residues within 4Å: Chain B: E.63, A.66, L.286, A.287, T.288, K.300, G.301 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.63 Water bridges: B:K.300 GOL.21: 6 residues within 4Å: Chain B: A.67, G.68, A.69, P.70, L.286, G.301 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.67, B:G.301 GOL.23: 7 residues within 4Å: Chain B: P.78, E.80, V.81, W.181, I.185, E.220, T.224 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.80, B:T.224 Water bridges: B:W.181, B:T.224 GOL.24: 5 residues within 4Å: Chain B: D.15, S.247, R.251, I.275, L.277 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.251, B:R.251 Water bridges: B:G.14, B:D.15, B:S.247, B:L.277

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.10: 5 residues within 4Å: Chain A: P.329, N.330, P.331, T.332, S.333 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.329, A:N.330, A:T.332, A:S.333 PO4.22: 5 residues within 4Å: Chain B: P.329, N.330, P.331, T.332, S.333 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.329, B:N.330, B:T.332, B:S.333 Water bridges: B:T.332, B:T.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fonvielle, M. et al., Substrate and Reaction Specificity of Mycobacterium tuberculosis Cytochrome P450 CYP121: INSIGHTS FROM BIOCHEMICAL STUDIES AND CRYSTAL STRUCTURES. J.Biol.Chem. (2013)

Release Date

2013-05-01

Peptides

Cytochrome P450 121: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome P450 121

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