SMTL ID : 4iq9.1 (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

monomer

Ligands

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

HEM.1: 22 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 Ligands: 1GB.10 15 PLIP interactions: 14 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.229, A:F.229, A:A.232, A:T.237, A:F.240, A:F.279, A:F.279, A:L.308, A:F.337, A:P.345 Water bridges: A:M.85 Salt bridges: A:R.285, A:H.342 Metal complexes: A:C.344, H2O.1

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

SO4.2: 5 residues within 4Å: Chain A: R.57, S.60, M.61, K.62, H.342 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.60, A:M.61, A:K.62 Water bridges: A:R.57 Salt bridges: A:R.57, A:H.342 SO4.3: 5 residues within 4Å: Chain A: R.133, N.134, F.160, S.164, R.380 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.133, A:R.380 Salt bridges: A:R.133, A:R.380 SO4.4: 5 residues within 4Å: Chain A: P.329, N.330, P.331, T.332, S.333 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.330, A:T.332, A:S.333 SO4.5: 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 SO4.6: 4 residues within 4Å: Chain A: T.3, L.5, L.6, R.31 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.3, A:L.6 Water bridges: A:R.31, A:R.31, A:R.31 Salt bridges: A:R.31 SO4.7: 4 residues within 4Å: Chain A: Y.47, A.48, E.316, H.317 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.316 Water bridges: A:Y.47, A:A.48, A:E.316 Salt bridges: A:H.317 SO4.8: 3 residues within 4Å: Chain A: P.18, D.19, A.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.19, A:A.20

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 8 residues within 4Å: Chain A: M.61, T.64, R.71, N.73, L.75, V.82, P.284 Ligands: 1GB.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.71, A:N.73, A:N.73, A:N.73 Water bridges: A:R.71, A:L.72 GOL.11: 3 residues within 4Å: Chain A: A.2, T.3, V.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.4 GOL.12: 2 residues within 4Å: Chain A: V.4, E.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.7 Water bridges: A:E.7 GOL.13: 4 residues within 4Å: Chain A: R.251, G.322, S.323, I.324 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.251, A:R.251, A:I.324 GOL.14: 5 residues within 4Å: Chain A: D.15, S.247, R.251, I.275, L.277 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.247, A:R.251, A:R.251 Water bridges: A:G.14, A:D.15, A:S.247, A:L.277 GOL.15: 1 residues within 4Å: Chain A: R.339 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.339, A:R.339 GOL.16: 4 residues within 4Å: Chain A: D.90, A.91, H.216, V.217 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.216 Water bridges: A:D.90, A:A.91, A:A.91, A:A.213, A:H.216, A:V.217 GOL.17: 5 residues within 4Å: Chain A: E.63, A.287, T.288, K.300, G.301 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.288, A:T.288, A:K.300, A:K.300

1 x 1GB: (3S,6S)-3-(4-hydroxybenzyl)-6-(1H-indol-3-ylmethyl)piperazine-2,5-dione(Non-covalent)

1GB.10: 12 residues within 4Å: Chain A: V.77, V.81, V.82, N.84, A.166, F.167, W.181, T.228, Q.384, R.385 Ligands: HEM.1, GOL.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.77, A:F.167, A:F.167, A:T.228 Hydrogen bonds: A:N.84 Water bridges: A:T.76, A:V.82, A:A.166

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytochrome P450 121

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