SMTL ID : 6t0j.1

Crystal structure of CYP124 in complex with SQ109

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

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

HEM.1: 28 residues within 4Å: Chain A: M.117, I.118, H.125, R.129, I.183, L.270, L.271, A.274, G.275, T.278, T.279, A.282, P.321, V.322, M.325, R.327, Y.350, G.377, F.378, G.379, A.383, H.384, C.386, L.387, G.388, A.392, E.395 Ligands: RWZ.2 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:I.118, A:I.183, A:L.270, A:A.274, A:A.282, A:P.321, A:V.322, A:V.322, A:Y.350, A:F.378, A:F.378, A:L.387, A:A.392 Water bridges: A:R.327, A:R.327, A:Y.350, A:Y.350, A:F.378, A:G.381 Salt bridges: A:H.125, A:R.129, A:R.327, A:H.384 Metal complexes: A:C.386

1 x RWZ: N-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-N'-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]ethane-1,2-diamine(Non-covalent)

RWZ.2: 14 residues within 4Å: Chain A: L.67, F.70, T.102, N.104, F.114, I.204, L.205, F.207, V.273, A.274, M.325, F.423, I.424 Ligands: HEM.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.67, A:F.70, A:F.70, A:L.205, A:L.205, A:V.273, A:A.274, A:F.423, A:F.423, A:I.424 Hydrogen bonds: A:I.204 Water bridges: A:N.100

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: D.362, T.365, D.367, R.370 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.362, A:T.365, A:T.365, A:R.370 GOL.4: 3 residues within 4Å: Chain A: P.99, D.105, Q.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.106 Water bridges: A:Y.98, A:D.105, A:R.326 GOL.10: 3 residues within 4Å: Chain A: R.55, E.56, P.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.56 GOL.12: 8 residues within 4Å: Chain A: E.112, Y.113, G.227, A.228, T.231, S.261, R.262, A.265 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.112, A:E.112, A:G.227, A:T.231, A:S.261 Water bridges: A:S.261, A:S.261

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 7 residues within 4Å: Chain A: E.313, N.373, P.374, H.375, F.378, F.385, R.393 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.313, A:H.375, A:R.393 Water bridges: A:H.375, A:H.375

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.7: 5 residues within 4Å: Chain A: G.20, D.362, P.363, W.364, T.365 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.364, A:T.365, A:T.365 Water bridges: A:T.365 FMT.8: 2 residues within 4Å: Chain A: L.41, V.45 No protein-ligand interaction detected (PLIP) FMT.9: 4 residues within 4Å: Chain A: E.334, L.335, R.336, G.337 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.336, A:G.337 FMT.11: 4 residues within 4Å: Chain A: E.357, S.358, F.360, A.361 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.362

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bukhdruker, S. et al., Hydroxylation of Antitubercular Drug Candidate, SQ109, by Mycobacterial Cytochrome P450. Int J Mol Sci (2020)

Release Date

2020-10-14

Peptides

Methyl-branched lipid omega-hydroxylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methyl-branched lipid omega-hydroxylase

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