SMTL ID : 6vum.1

Structure of nevanimibe-bound human tetrameric ACAT1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.67 Å

Oligo State

homo-tetramer

Ligands

4 x OLA: OLEIC ACID(Non-covalent)

OLA.1: 16 residues within 4Å: Chain A: F.258, I.261, R.262, M.265, F.302, A.303, P.304, L.306, F.384, L.389, F.392, L.428, S.456, V.459, H.460 Ligands: ROV.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.258, A:F.258, A:I.261, A:L.306, A:F.384, A:L.389, A:L.428, A:V.459 Salt bridges: A:R.262 OLA.7: 16 residues within 4Å: Chain B: F.258, I.261, R.262, M.265, F.302, A.303, P.304, F.384, W.388, L.389, V.424, L.428, S.456, V.459, H.460 Ligands: ROV.11 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.258, B:I.261, B:R.262, B:F.384, B:V.424, B:V.424, B:L.428 Salt bridges: B:R.262 OLA.12: 16 residues within 4Å: Chain C: F.258, I.261, R.262, M.265, F.302, A.303, P.304, L.306, F.384, L.389, F.392, L.428, S.456, V.459, H.460 Ligands: ROV.16 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.258, C:F.258, C:I.261, C:L.306, C:F.384, C:L.389, C:L.428, C:V.459 Salt bridges: C:R.262 OLA.18: 16 residues within 4Å: Chain D: F.258, I.261, R.262, M.265, F.302, A.303, P.304, F.384, W.388, L.389, V.424, L.428, S.456, V.459, H.460 Ligands: ROV.22 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.258, D:I.261, D:R.262, D:F.384, D:V.424, D:V.424, D:L.428 Salt bridges: D:R.262

10 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 3 residues within 4Å: Chain A: W.186, W.189, I.190 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.186 CLR.3: 10 residues within 4Å: Chain A: F.227, M.228, H.268, V.271, R.272, V.275, P.276, L.279, D.435, W.438 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.227, A:V.271, A:R.272, A:V.275, A:P.276, A:L.279, A:W.438, A:W.438 CLR.4: 15 residues within 4Å: Chain A: L.129, I.138, I.141, Y.142, F.145, I.146, C.333, Y.336, F.378, L.379, F.382, W.408 Chain B: H.137, T.140, I.141 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.129, A:I.138, A:Y.142, A:I.146, A:Y.336, A:F.378, A:F.378, A:L.379, A:F.382, A:F.382, A:F.382, B:I.141 Hydrogen bonds: B:T.140 CLR.9: 15 residues within 4Å: Chain A: H.137, T.140, I.141 Chain B: I.138, I.141, Y.142, F.145, I.146, L.149, G.332, C.333, F.378, L.379, F.382, W.408 16 PLIP interactions: 3 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:I.141, B:I.141, B:I.141, B:Y.142, B:F.145, B:I.146, B:L.149, B:F.378, B:F.378, B:L.379, B:F.382, B:F.382, B:F.382, B:W.408 Hydrogen bonds: A:H.137, A:T.140 CLR.10: 8 residues within 4Å: Chain B: M.228, H.268, V.271, R.272, V.275, P.276, D.435, W.438 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.271, B:R.272, B:V.275, B:P.276, B:W.438, B:W.438, B:W.438 CLR.13: 3 residues within 4Å: Chain C: W.186, W.189, I.190 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.186 CLR.14: 10 residues within 4Å: Chain C: F.227, M.228, H.268, V.271, R.272, V.275, P.276, L.279, D.435, W.438 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.227, C:V.271, C:R.272, C:V.275, C:P.276, C:L.279, C:W.438, C:W.438 CLR.15: 15 residues within 4Å: Chain C: L.129, I.138, I.141, Y.142, F.145, I.146, C.333, Y.336, F.378, L.379, F.382, W.408 Chain D: H.137, T.140, I.141 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.129, C:I.138, C:Y.142, C:I.146, C:Y.336, C:F.378, C:F.378, C:L.379, C:F.382, C:F.382, C:F.382, D:I.141 Hydrogen bonds: D:T.140 CLR.20: 15 residues within 4Å: Chain C: H.137, T.140, I.141 Chain D: I.138, I.141, Y.142, F.145, I.146, L.149, G.332, C.333, F.378, L.379, F.382, W.408 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.141, D:I.141, D:Y.142, D:F.145, D:I.146, D:L.149, D:F.378, D:F.378, D:L.379, D:F.382, D:F.382, D:F.382, D:W.408, C:I.141 Hydrogen bonds: C:H.137, C:T.140 CLR.21: 8 residues within 4Å: Chain D: M.228, H.268, V.271, R.272, V.275, P.276, D.435, W.438 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.271, D:R.272, D:V.275, D:P.276, D:W.438, D:W.438, D:W.438

4 x ROV: nevanimibe(Non-covalent)

ROV.5: 12 residues within 4Å: Chain A: T.380, F.384, Y.416, Y.417, W.420, N.421, V.424, H.425, H.460, F.479 Ligands: OLA.1, COA.6 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.384, A:F.384, A:Y.416, A:W.420, A:W.420, A:N.421, A:V.424, A:F.479 Hydrogen bonds: A:N.421, A:H.460, A:H.460 ROV.11: 10 residues within 4Å: Chain B: T.380, F.384, W.420, N.421, V.424, S.456, H.460, F.479 Ligands: OLA.7, 3VV.8 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.384, B:W.420, B:N.421, B:V.424, B:F.479 Hydrogen bonds: B:N.421, B:H.460, B:H.460 pi-Stacking: B:W.420 ROV.16: 12 residues within 4Å: Chain C: T.380, F.384, Y.416, Y.417, W.420, N.421, V.424, H.425, H.460, F.479 Ligands: OLA.12, COA.17 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.384, C:F.384, C:Y.416, C:W.420, C:W.420, C:N.421, C:V.424, C:F.479 Hydrogen bonds: C:N.421, C:H.460, C:H.460 ROV.22: 11 residues within 4Å: Chain D: T.380, F.384, Y.417, W.420, N.421, V.424, S.456, H.460, F.479 Ligands: OLA.18, 3VV.19 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.384, D:W.420, D:N.421, D:V.424, D:F.479 Hydrogen bonds: D:N.421, D:H.460, D:H.460 pi-Stacking: D:W.420

2 x COA: COENZYME A(Non-covalent)

COA.6: 14 residues within 4Å: Chain A: Y.417, R.418, H.425, L.428, Y.429, Y.433, K.445, M.449, V.452, F.453, S.456, F.479, D.492 Ligands: ROV.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.417, A:F.453 Hydrogen bonds: A:R.418, A:R.418, A:S.456 Salt bridges: A:R.418, A:K.445, A:K.445 pi-Cation interactions: A:R.418, A:R.418 COA.17: 14 residues within 4Å: Chain C: Y.417, R.418, H.425, L.428, Y.429, Y.433, K.445, M.449, V.452, F.453, S.456, F.479, D.492 Ligands: ROV.16 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.417, C:F.453 Hydrogen bonds: C:R.418, C:R.418, C:S.456 Salt bridges: C:R.418, C:K.445, C:K.445 pi-Cation interactions: C:R.418, C:R.418

2 x 3VV: S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name)(Non-covalent)

3VV.8: 19 residues within 4Å: Chain B: Y.413, Y.417, R.418, H.425, Y.429, Y.433, M.449, V.452, F.453, S.456, L.478, F.479, F.482, F.486, D.492, S.506, L.509, G.510 Ligands: ROV.11 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.413, B:Y.417, B:V.452, B:L.478, B:F.482, B:F.486, B:L.509 Hydrogen bonds: B:S.456 Salt bridges: B:R.418 pi-Cation interactions: B:R.418, B:R.418 3VV.19: 19 residues within 4Å: Chain D: Y.413, Y.417, R.418, H.425, Y.429, Y.433, M.449, V.452, F.453, S.456, L.478, F.479, F.482, F.486, D.492, S.506, L.509, G.510 Ligands: ROV.22 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.413, D:Y.417, D:V.452, D:L.478, D:F.482, D:F.486, D:L.509 Hydrogen bonds: D:R.418, D:S.456 Salt bridges: D:R.418 pi-Cation interactions: D:R.418, D:R.418

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Long, T. et al., Structure of nevanimibe-bound tetrameric human ACAT1. Nature (2020)

Release Date

2020-05-13

Peptides

Sterol O-acyltransferase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Sterol O-acyltransferase 1