SMTL ID : 5wp2.1

1.44 Angstrom crystal structure of CYP121 from Mycobacterium tuberculosis in complex with substrate and CN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

monomer

Ligands

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

HEM.1: 29 residues within 4Å: Chain A: M.61, M.85, I.101, H.145, F.229, A.232, G.233, S.236, T.237, F.240, L.273, F.279, L.283, R.285, L.308, L.335, A.336, F.337, G.338, Q.341, H.342, F.343, C.344, P.345, G.346, L.349, G.350 Ligands: YTT.2, CYN.3 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:F.229, A:F.229, A:A.232, A:F.240, A:F.279, A:L.308, A:F.337, A:P.345 Hydrogen bonds: A:H.342 Water bridges: A:M.85, A:R.94, A:Q.341, A:F.343 Salt bridges: A:R.285, A:H.342 pi-Stacking: A:F.337 Metal complexes: A:C.344

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

YTT.2: 16 residues within 4Å: Chain A: M.61, T.76, V.77, V.81, V.82, N.84, A.166, F.167, W.181, V.227, T.228, A.232, Q.384, R.385 Ligands: HEM.1, CYN.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.77, A:T.228 Hydrogen bonds: A:N.84, A:R.385 Water bridges: A:T.76, A:V.82, A:Q.384, A:R.385 pi-Stacking: A:F.167

1 x CYN: CYANIDE ION(Non-covalent)

CYN.3: 5 residues within 4Å: Chain A: A.232, S.236, R.385 Ligands: HEM.1, YTT.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.236, A:R.385

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

SO4.4: 2 residues within 4Å: Chain A: S.11, R.13 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.11, A:S.11 Water bridges: A:A.12, A:R.13, A:R.13, A:R.13, A:R.13, A:R.16, A:R.16 SO4.5: 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:R.57, A:M.61, A:K.62 Water bridges: A:R.57 Salt bridges: A:R.57, A:H.342 SO4.6: 5 residues within 4Å: Chain A: P.329, N.330, P.331, T.332, S.333 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.329, A:T.332, A:T.332, A:S.333 Water bridges: A:T.332, A:T.332 SO4.7: 3 residues within 4Å: Chain A: P.157, K.158, R.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.158 Salt bridges: A:R.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fielding, A.J. et al., Probing Ligand Exchange in the P450 Enzyme CYP121 from Mycobacterium tuberculosis: Dynamic Equilibrium of the Distal Heme Ligand as a Function of pH and Temperature. J. Am. Chem. Soc. (2017)

Release Date

2018-05-30

Peptides

Mycocyclosin synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mycocyclosin synthase

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