SMTL ID : 6t0g.1

Crystal structure of CYP124 in complex with vitamin D3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

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

HEM.1: 28 residues within 4Å: Chain A: 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, F.385, C.386, L.387, G.388, A.392, E.395 Ligands: VD3.2 25 PLIP interactions: 25 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:L.387, A:A.392 Water bridges: A:S.97, A:R.327, A:R.327, A:Y.350, A:Y.350, A:F.378, A:G.381, A:H.384 Salt bridges: A:H.125, A:R.129, A:R.327, A:H.384 Metal complexes: A:C.386

1 x VD3: (1S,3Z)-3-[(2E)-2-[(1R,3AR,7AS)-7A-METHYL-1-[(2R)-6-METHYLHEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLI DENE]-4-METHYLIDENE-CYCLOHEXAN-1-OL(Non-covalent)

VD3.2: 12 residues within 4Å: Chain A: N.100, T.102, Q.106, F.114, I.118, I.204, L.205, L.270, V.273, A.274, F.423 Ligands: HEM.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.102, A:Q.106, A:F.114, A:I.118, A:I.204, A:L.270, A:A.274, A:F.423

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

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PGE.5: 5 residues within 4Å: Chain A: H.91, P.92, D.93, I.94 Ligands: PGE.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:H.91, A:D.93, A:I.94 Hydrogen bonds: A:D.93, A:D.93 PGE.6: 3 residues within 4Å: Chain A: H.91, I.94 Ligands: PGE.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.94

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

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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