SMTL ID : 6c6n.1

Human squalene epoxidase (SQLE, squalene monooxygenase) structure with FAD and Cmpd-4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: H.57, S.97, Q.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.103 GOL.2: 4 residues within 4Å: Chain A: E.69, G.70, L.71, D.72 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.70, A:D.72 Water bridges: A:L.71, A:A.73 GOL.3: 5 residues within 4Å: Chain A: H.57, V.58, D.61, K.310, K.313 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.313 GOL.12: 5 residues within 4Å: Chain B: H.57, S.97, N.99, Q.101, Q.103 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.97, B:N.99, B:Q.103

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

SO4.4: 5 residues within 4Å: Chain A: I.46, F.193, L.194, R.227, R.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.194 Salt bridges: A:R.227, A:R.270 SO4.13: 6 residues within 4Å: Chain B: D.44, I.46, G.192, L.194, R.227, R.270 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.227, B:R.270

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

CPS.5: 10 residues within 4Å: Chain A: N.399, G.405, H.406, A.409 Chain B: Y.378, L.381, C.385, I.412, Y.413, Y.416 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:Y.413, B:Y.416 Hydrogen bonds: A:N.399 Water bridges: A:Y.378, A:Y.378, B:Y.378 CPS.6: 11 residues within 4Å: Chain A: Y.378, L.381, C.385, I.412, Y.413, Y.416 Chain B: N.399, V.402, G.405, H.406, A.409 12 PLIP interactions: 9 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, A:Y.413, A:Y.413, B:Y.378, B:H.406 CPS.7: 7 residues within 4Å: Chain A: F.446, P.447, Y.450 Chain B: P.428, L.431, L.432 Ligands: CPS.8 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.446, A:Y.450, A:Y.450, A:Y.450, B:L.431, B:L.432 CPS.8: 8 residues within 4Å: Chain A: Y.439, C.442, S.443, F.446, P.447 Chain B: G.435 Ligands: CPS.7, CPS.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.446, A:F.446 Hydrogen bonds: A:S.443 CPS.9: 7 residues within 4Å: Chain A: K.317, L.318, G.321, I.322, A.330, E.333, S.337 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.333 Hydrogen bonds: A:L.318, A:G.321, A:S.337, A:S.337 CPS.14: 9 residues within 4Å: Chain A: G.435, Y.439 Chain B: Y.439, C.442, S.443, F.446, P.447 Ligands: CPS.8, CPS.15 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.446 CPS.15: 6 residues within 4Å: Chain A: P.428, L.431, L.432 Chain B: F.446, Y.450 Ligands: CPS.14 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:P.428, A:L.432, B:F.446, B:Y.450, B:Y.450, B:Y.450

2 x EKV: N-[(3-{[dimethyl(2-methylphenyl)silyl]methoxy}phenyl)methyl]-N-ethyl-6-methoxy-6-methylhepta-2,4-diyn-1-amine(Non-covalent)

EKV.10: 27 residues within 4Å: Chain A: F.50, Q.52, Y.79, I.81, I.92, Y.94, A.206, L.208, L.217, Y.219, P.299, L.300, G.302, L.353, L.357, F.361, C.375, F.379, P.389, V.390, L.392, L.393, L.403, H.406, F.407, V.410 Ligands: FAD.11 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.50, A:F.50, A:Y.79, A:I.92, A:A.206, A:L.208, A:L.217, A:Y.219, A:Y.219, A:Y.219, A:L.353, A:L.357, A:L.357, A:F.361, A:F.379, A:P.389, A:H.406, A:V.410 Hydrogen bonds: A:Y.79 EKV.16: 27 residues within 4Å: Chain B: F.50, Y.79, I.81, Y.94, A.206, E.207, L.208, L.217, Y.219, P.299, L.300, T.301, G.302, L.353, L.357, F.361, C.375, F.379, P.389, V.390, L.392, L.393, L.403, H.406, F.407, V.410 Ligands: FAD.17 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.50, B:F.50, B:Y.79, B:A.206, B:L.208, B:L.217, B:Y.219, B:Y.219, B:L.353, B:L.357, B:L.357, B:F.361, B:F.379, B:F.379, B:P.389, B:V.390, B:H.406, B:V.410

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

FAD.11: 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: EKV.10 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 Water bridges: A:G.16, A:G.19, A:R.45, A:H.110, A:D.292, A:A.293, A:R.297, A:R.297, A:G.303, A:T.306 Salt bridges: A:R.45 FAD.17: 31 residues within 4Å: Chain B: 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.175, M.272, P.273, G.291, D.292, P.299, G.302, G.303, G.304, M.305 Ligands: EKV.16 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:V.47, B:M.272, B:P.299 Hydrogen bonds: B:A.15, B:A.15, B:V.17, B:L.18, B:R.38, B:R.38, 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 Water bridges: B:G.16, B:G.19, B:E.49, B:A.293, B:R.297, B:R.297, B:G.303, B:T.306, B:A.308 Salt bridges: B:R.45

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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