SMTL ID : 6t0h.1

Crystal structure of CYP124 in complex with 1-alpha-hydroxy-vitamin D3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.18 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: M9B.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 M9B: 1-alpha-hydroxy-vitamin D3(Non-covalent)

M9B.2: 17 residues within 4Å: Chain A: L.67, F.70, N.100, I.101, T.102, N.104, F.114, I.118, I.204, L.205, F.219, A.274, Y.324, Q.422, F.423 Ligands: HEM.1, GOL.7 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.101, A:T.102, A:F.114, A:I.118, A:I.204, A:L.205, A:F.219, A:A.274, A:F.423, A:F.423 Hydrogen bonds: A:Y.324 Water bridges: A:N.104, A:F.423

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: E.313, N.373, P.374, H.375, F.378, F.385, R.393 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.313, A:P.374, A:R.393 Water bridges: A:H.375 GOL.4: 6 residues within 4Å: Chain A: D.43, H.285, R.292, W.318, A.319, H.425 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.43, A:R.292, A:W.318, A:R.355 Water bridges: A:R.292 GOL.7: 7 residues within 4Å: Chain A: L.67, I.204, L.205, G.206, F.207, S.421 Ligands: M9B.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.204, A:F.207, A:S.421 Water bridges: A:Q.422 GOL.12: 4 residues within 4Å: Chain A: D.83, D.84, Y.87, L.335 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.83 Hydrogen bonds: A:D.84

6 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 6 residues within 4Å: Chain A: E.414, E.415, P.416, A.417, T.429, P.431 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.414, A:A.417, A:P.431 Hydrogen bonds: A:T.429, A:T.429 Water bridges: A:R.418 PGE.6: 7 residues within 4Å: Chain A: R.17, V.18, T.21, P.22, P.23, D.44, D.47 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.17, A:V.18, A:T.21, A:T.21, A:D.44, A:D.44 Water bridges: A:T.21, A:T.21 PGE.8: 6 residues within 4Å: Chain A: V.26, P.27, D.30, L.41, D.42, V.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.42 Water bridges: A:R.418 PGE.9: 8 residues within 4Å: Chain A: P.99, N.104, D.105, Q.106, R.326, T.328, G.343, K.345 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.99, A:T.328 Hydrogen bonds: A:N.104, A:R.326, A:R.326 PGE.10: 6 residues within 4Å: Chain A: R.238, E.257, R.258, L.259, S.260, S.261 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.257, A:E.257 Water bridges: A:R.238, A:R.238, A:S.260, A:S.261 PGE.11: 4 residues within 4Å: Chain A: R.238, V.239, N.240, H.241 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.238, A:N.240, A:H.241

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

MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.15: 2 residues within 4Å: Chain A: R.404, R.405 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: N.163, P.164, D.165 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: N.19, E.295, Q.296 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Varaksa, T. et al., Metabolic Fate of Human Immunoactive Sterols in Mycobacterium tuberculosis. J.Mol.Biol. (2021)

Release Date

2020-10-14

Peptides

CYP124 in complex with inhibitor carbethoxyhexyl imidazole: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CYP124 in complex with inhibitor carbethoxyhexyl imidazole

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