SMTL ID : 6vp0.1

Human Diacylglycerol Acyltransferase 1 in complex with oleoyl-CoA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.1: 19 residues within 4Å: Chain A: L.89, N.90, V.93, I.97, F.277, R.280, R.281, E.284, L.335, Y.339 Chain B: F.76, S.77, S.78, D.79, I.88, W.91, N.451, A.455 Ligands: POV.4 17 PLIP interactions: 9 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:L.89, A:V.93, A:V.93, A:I.97, A:L.335, A:Y.339, A:Y.339, B:F.76, B:I.88, B:I.88, B:W.91, B:W.91, B:N.451, B:A.455 Salt bridges: A:R.280, A:R.281 Hydrogen bonds: B:S.78 POV.4: 12 residues within 4Å: Chain A: L.96, S.99, N.100, L.103, L.291, Q.298, L.332, I.336 Ligands: POV.1, AV0.6, P5S.9, AV0.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.96, A:L.103, A:L.291, A:L.332, A:I.336 Hydrogen bonds: A:N.100 POV.7: 19 residues within 4Å: Chain A: F.76, S.77, S.78, D.79, I.88, W.91, N.451, A.455 Chain B: L.89, N.90, V.93, I.97, F.277, R.280, R.281, E.284, L.335, Y.339 Ligands: POV.10 17 PLIP interactions: 8 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:F.76, A:I.88, A:I.88, A:W.91, A:W.91, A:N.451, A:A.455, B:L.89, B:V.93, B:V.93, B:I.97, B:L.335, B:Y.339, B:Y.339 Hydrogen bonds: A:S.78 Salt bridges: B:R.280, B:R.281 POV.10: 11 residues within 4Å: Chain B: L.96, S.99, N.100, L.291, Q.298, L.332, I.336 Ligands: P5S.3, AV0.6, POV.7, AV0.12 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.96, B:L.291, B:L.332, B:I.336 Hydrogen bonds: B:N.100

4 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.2: 10 residues within 4Å: Chain A: D.313, M.314, Y.316, L.324, W.429, T.432, G.433, I.463, G.464, M.471 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.324, A:I.463 Hydrogen bonds: A:D.313, A:M.314, A:T.432 P5S.3: 9 residues within 4Å: Chain A: W.299, L.324, K.325, A.327, V.328, I.463 Chain B: L.98 Ligands: AV0.6, POV.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.327 P5S.8: 12 residues within 4Å: Chain B: F.311, K.312, D.313, M.314, Y.316, I.319, L.324, W.429, T.432, I.463, G.464, M.471 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.319, B:L.324, B:I.463 Hydrogen bonds: B:D.313, B:M.314, B:T.432 P5S.9: 10 residues within 4Å: Chain A: I.97, L.98, A.101 Chain B: W.299, L.324, K.325, V.328, I.463 Ligands: POV.4, AV0.12 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.324, B:I.463, A:I.97, A:L.98, A:A.101

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.5: 17 residues within 4Å: Chain A: W.334, F.338, W.364, T.371, F.373, W.374, Q.375, W.377, H.382, I.386, Y.390, K.391, K.400, R.404, S.411, H.415, L.461 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:W.334, A:F.338, A:W.364, A:F.373, A:W.377, A:W.377, A:L.461 Hydrogen bonds: A:Q.375, A:W.377, A:N.378, A:Y.390, A:K.400, A:R.404, A:S.411, A:S.411, A:H.415 Salt bridges: A:H.382, A:H.382 3VV.11: 18 residues within 4Å: Chain B: W.334, F.338, T.371, F.373, W.374, Q.375, W.377, N.378, V.381, H.382, I.386, Y.390, K.400, R.404, V.407, S.411, H.415, L.461 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:W.334, B:W.334, B:F.338, B:F.373, B:W.374, B:W.377, B:W.377, B:V.381, B:L.461 Hydrogen bonds: B:Q.375, B:W.377, B:N.378, B:Y.390, B:K.400, B:R.404, B:S.411, B:S.411 Salt bridges: B:H.382, B:H.382

2 x AV0: Lauryl Maltose Neopentyl Glycol(Non-covalent)

AV0.6: 10 residues within 4Å: Chain A: Q.290, L.291, G.294, L.295, Q.298, W.299 Ligands: P5S.3, POV.4, POV.10, AV0.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.290, A:L.295, A:W.299 AV0.12: 9 residues within 4Å: Chain B: N.100, L.103, L.291, Q.298, W.299 Ligands: POV.4, AV0.6, P5S.9, POV.10 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.100, B:L.103, B:L.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Structure and mechanism of human diacylglycerol O-acyltransferase 1. Nature (2020)

Release Date

2020-05-13

Peptides

Diacylglycerol O-acyltransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

Membrane

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

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