SMTL ID : 6vz1.1

Cryo-EM structure of human diacylglycerol O-acyltransferase 1 complexed with acyl-CoA substrate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Covalent)(Non-covalent)

6OU.1: 18 residues within 4Å: Chain A: F.76, S.78, N.451, Y.452, A.455 Chain B: R.86, V.93, L.98, A.101, F.104, L.105, R.280, R.281, L.283, E.284, F.287, Y.339 Ligands: 6OU.5 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.104, B:L.105, B:L.105, B:E.284, B:F.287, A:A.455 Hydrogen bonds: B:R.280, B:R.280, B:R.281, B:R.281, B:Y.339, A:S.78, A:N.451 Salt bridges: B:R.86 6OU.2: 20 residues within 4Å: Chain A: R.86, L.89, C.92, V.93, M.95, L.96, S.99, N.100, F.288, L.291, L.332, L.335, I.336, F.338, Y.339, W.364 Chain B: I.88, W.91 Ligands: 6OU.4, 6OU.5 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:M.95, A:L.96, A:L.291, A:L.332, A:L.335, A:W.364, B:I.88, B:I.88, B:W.91, B:W.91 Hydrogen bonds: A:V.93 6OU.4: 20 residues within 4Å: Chain A: R.86, V.93, I.97, L.98, A.101, F.104, L.105, R.280, R.281, E.284, F.287, Y.339 Chain B: F.76, S.78, L.324, N.451, Y.452, A.455, L.459 Ligands: 6OU.2 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.93, A:I.97, A:L.98, A:F.104, A:L.105, A:F.287, A:F.287, B:L.324, B:L.459 Hydrogen bonds: A:R.280, A:Y.339, B:S.78, B:N.451 Salt bridges: A:R.86 6OU.5: 20 residues within 4Å: Chain A: F.76, I.88, W.91 Chain B: L.89, W.91, C.92, V.93, M.95, L.96, S.99, F.288, L.291, L.295, L.332, L.335, I.336, Y.339, W.458 Ligands: 6OU.1, 6OU.2 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:I.88, A:I.88, A:W.91, B:W.91, B:M.95, B:L.96, B:L.291, B:L.295, B:L.332, B:L.335, B:W.458 Hydrogen bonds: B:R.86, B:Y.339

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)(Covalent)

3VV.3: 15 residues within 4Å: Chain A: L.195, W.374, Q.375, V.381, H.382, I.386, Y.390, R.404, V.407, S.411, H.415, L.423, V.469, V.473, Y.476 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.195, A:Y.390, A:V.407, A:L.423, A:V.469, A:V.473, A:Y.476, A:Y.476 Hydrogen bonds: A:Q.375, A:S.411, A:S.411 Salt bridges: A:H.382, A:K.391, A:R.404, A:R.404 3VV.6: 18 residues within 4Å: Chain B: P.191, L.195, W.374, Q.375, W.377, H.382, I.386, Y.390, K.391, R.404, V.407, S.411, H.415, V.419, L.423, V.469, V.473, Y.476 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:P.191, B:Y.390, B:V.407, B:V.419, B:L.423, B:V.469, B:V.473, B:Y.476 Hydrogen bonds: B:Q.375, B:Y.390, B:Y.390, B:S.411 Salt bridges: B:H.382, B:K.391, B:R.404, B:R.404

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sui, X. et al., Structure and catalytic mechanism of a human triacylglycerol-synthesis enzyme. Nature (2020)

Release Date

2020-05-13

Peptides

Diacylglycerol O-acyltransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

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

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