SMTL ID : 4ict.1 (1 other biounit)

Substrate and reaction specificity of Mycobacterium tuberculosis cytochrome P450 CYP121

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.56, S.59, M.60, K.61, H.341 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.59, A:M.60, A:K.61 Water bridges: A:R.56 Salt bridges: A:R.56, A:H.341 SO4.2: 3 residues within 4Å: Chain A: S.10, R.12, R.15 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.10 Water bridges: A:A.11, A:R.12, A:R.15, A:R.15 Salt bridges: A:R.15 SO4.3: 4 residues within 4Å: Chain A: V.3, L.4, L.5, R.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.5 Salt bridges: A:R.30 SO4.4: 7 residues within 4Å: Chain A: R.132, N.133, F.159, S.163, R.379, E.388 Chain B: R.389 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Water bridges: B:R.389, B:R.389, A:R.132, A:S.163, A:R.379 Salt bridges: B:R.389, A:R.132, A:R.379 SO4.7: 5 residues within 4Å: Chain B: R.56, S.59, M.60, K.61, H.341 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.59, B:M.60, B:K.61 Water bridges: B:R.56 Salt bridges: B:R.56, B:H.341 SO4.8: 3 residues within 4Å: Chain B: S.10, R.12, R.15 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.10 Water bridges: B:A.11, B:R.12, B:R.15, B:R.15 Salt bridges: B:R.15 SO4.9: 4 residues within 4Å: Chain B: V.3, L.4, L.5, R.30 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.5 Salt bridges: B:R.30 SO4.10: 7 residues within 4Å: Chain A: R.389 Chain B: R.132, N.133, F.159, S.163, R.379, E.388 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Water bridges: B:S.163, B:R.379, B:E.388, A:R.389, A:R.389 Salt bridges: B:R.132, B:R.379, A:R.389

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

HEM.5: 22 residues within 4Å: Chain A: M.60, M.84, H.144, F.228, A.231, G.232, S.235, T.236, F.239, F.278, L.282, R.284, L.307, A.335, F.336, G.337, Q.340, H.341, C.343, P.344, G.345 Ligands: 1ED.6 17 PLIP interactions: 16 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.228, A:F.228, A:A.231, A:F.239, A:F.278, A:F.278, A:L.282, A:L.307, A:F.336, A:P.344 Water bridges: A:M.84, A:R.93 Salt bridges: A:R.284, A:H.341 pi-Stacking: A:F.336 Metal complexes: A:C.343, H2O.1 HEM.11: 22 residues within 4Å: Chain B: M.60, M.84, H.144, F.228, A.231, G.232, S.235, T.236, F.239, F.278, L.282, R.284, L.307, A.335, F.336, G.337, Q.340, H.341, C.343, P.344, G.345 Ligands: 1ED.12 18 PLIP interactions: 17 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:F.228, B:F.228, B:A.231, B:F.239, B:F.278, B:F.278, B:L.282, B:L.307, B:F.336, B:P.344 Water bridges: B:M.84, B:R.93, B:H.341 Salt bridges: B:R.284, B:H.341 pi-Stacking: B:F.336 Metal complexes: B:C.343, H2O.23

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

1ED.6: 9 residues within 4Å: Chain A: V.76, V.80, V.81, N.83, A.165, F.166, T.227, Q.383 Ligands: HEM.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.76, A:F.166, A:T.227 Hydrogen bonds: A:N.83 Water bridges: A:T.75, A:V.81, A:N.83, A:A.165 pi-Stacking: A:F.166 1ED.12: 9 residues within 4Å: Chain B: V.76, V.80, V.81, N.83, A.165, F.166, T.227, Q.383 Ligands: HEM.11 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.76, B:F.166, B:T.227 Hydrogen bonds: B:N.83 Water bridges: B:T.75, B:T.75, B:V.81, B:N.83 pi-Stacking: B:F.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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome P450 121

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