SMTL ID : 6c6p.1

Human squalene epoxidase (SQLE, squalene monooxygenase) structure with FAD and NB-598

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

7 x CPS: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE(Non-covalent)

CPS.1: 7 residues within 4Å: Chain A: F.446, P.447, Y.450 Chain B: P.428, L.431, L.432 Ligands: CPS.2 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.446, A:Y.450, A:Y.450, B:L.431, B:L.432 CPS.2: 8 residues within 4Å: Chain A: Y.439, C.442, S.443, F.446 Chain B: G.435, Y.439 Ligands: CPS.1, CPS.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.446, A:F.446 CPS.3: 8 residues within 4Å: Chain A: K.317, L.318, G.321, I.322, A.330, E.333, A.334, S.337 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.322, A:A.330, A:E.333, A:A.334 Hydrogen bonds: A:L.318, A:G.321, A:S.337, A:S.337 CPS.6: 10 residues within 4Å: Chain A: N.399, G.405, H.406, A.409 Chain B: Y.378, L.381, I.412, Y.413, Y.416 Ligands: CPS.7 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.409, B:Y.378, B:L.381, B:I.412, B:I.412, B:Y.413, B:Y.416 Hydrogen bonds: A:N.399 Water bridges: A:Y.378, A:H.406 CPS.7: 11 residues within 4Å: Chain A: Y.378, L.381, C.385, I.412, Y.413, Y.416 Chain B: N.399, G.405, H.406, A.409 Ligands: CPS.6 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.378, A:L.381, A:I.412, A:Y.413, A:Y.416, B:A.409 Water bridges: A:Y.378, A:Y.378, B:H.406 Hydrogen bonds: B:N.399 CPS.8: 9 residues within 4Å: Chain A: G.435, Y.439 Chain B: Y.439, C.442, S.443, F.446, P.447 Ligands: CPS.2, CPS.9 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.446 CPS.9: 7 residues within 4Å: Chain A: P.428, L.431, L.432 Chain B: F.446, P.447, Y.450 Ligands: CPS.8 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.446, B:Y.450, B:Y.450, B:Y.450, A:P.428, A:L.431, A:L.431, A:L.432

2 x EMV: (2E)-N-({3-[([3,3'-bithiophen]-5-yl)methoxy]phenyl}methyl)-N-ethyl-6,6-dimethylhept-2-en-4-yn-1-amine(Non-covalent)

EMV.4: 25 residues within 4Å: Chain A: F.50, Q.52, Y.79, I.81, I.92, L.208, L.217, Y.219, L.229, P.299, L.300, T.301, G.302, L.353, L.357, F.361, F.379, P.389, V.390, L.393, L.403, H.406, F.407, V.410 Ligands: FAD.5 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.50, A:Y.79, A:I.92, A:L.208, A:L.217, A:L.217, A:Y.219, A:L.300, A:L.353, A:L.357, A:L.357, A:L.357, A:F.361, A:F.379, A:P.389, A:V.390, A:H.406, A:V.410 Hydrogen bonds: A:Y.79 pi-Stacking: A:F.50, A:Y.79 EMV.10: 23 residues within 4Å: Chain B: F.50, Q.52, Y.79, I.81, I.92, L.208, L.217, Y.219, P.299, L.300, T.301, G.302, L.353, L.357, F.361, F.379, P.389, V.390, L.393, H.406, F.407, V.410 Ligands: FAD.11 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.50, B:Y.79, B:I.92, B:L.208, B:L.217, B:Y.219, B:L.300, B:L.353, B:L.357, B:L.357, B:L.357, B:F.361, B:F.379, B:P.389, B:H.406, B:V.410 pi-Stacking: B:Y.79

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.5: 31 residues within 4Å: Chain A: G.14, A.15, G.16, V.17, L.18, I.36, E.37, R.38, R.45, V.47, G.48, E.49, F.50, R.118, G.132, V.133, V.134, A.168, D.169, G.170, F.190, M.272, P.273, G.291, D.292, P.299, G.302, G.303, G.304, M.305 Ligands: EMV.4 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:V.47, A:V.47, A:F.190, A:M.272, A:P.299 Hydrogen bonds: A:A.15, A:A.15, A:V.17, A:L.18, A:R.38, A:R.38, A:G.48, A:E.49, A:F.50, A:F.50, A:R.118, A:V.134, A:V.134, A:D.292, A:G.304, A:M.305, A:T.306 Water bridges: A:G.16, A:R.45, A:G.170, A:A.293, A:R.297, A:R.297, A:G.303, A:A.308 Salt bridges: A:R.45 pi-Cation interactions: A:R.38 FAD.11: 30 residues within 4Å: Chain B: G.14, G.16, V.17, L.18, I.36, E.37, R.38, R.45, V.47, G.48, E.49, F.50, R.118, G.132, V.133, V.134, A.168, D.169, G.170, F.190, M.272, P.273, G.291, D.292, P.299, G.302, G.303, G.304, M.305 Ligands: EMV.10 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:V.47, B:F.190, B:M.272, B:P.299 Hydrogen bonds: B:V.17, B:L.18, B:R.38, B:R.45, B:R.45, B:G.48, B:E.49, B:F.50, B:F.50, B:R.118, B:V.134, B:V.134, B:D.292, B:G.304, B:M.305, B:T.306 Water bridges: B:G.16, B:G.16, B:L.171, B:L.171, B:A.293, B:R.297, B:R.297, B:R.297, B:G.303 pi-Cation interactions: B:R.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Padyana, A.K. et al., Structure and inhibition mechanism of the catalytic domain of human squalene epoxidase. Nat Commun (2019)

Release Date

2019-01-16

Peptides

Squalene monooxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Squalene monooxygenase

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