SMTL ID : 9b4g.1

Structure of inhibitor-bound human PSS1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

P5S.1: 17 residues within 4Å: Chain A: F.93, T.94, R.95, L.100, M.178, L.181, L.182, F.267, T.268, P.269, A.270, S.271, W.272, T.273, G.322, G.329, R.336 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.100, A:L.181, A:F.267 Hydrogen bonds: A:T.94, A:A.270, A:S.271, A:S.271, A:T.273, A:T.273, A:T.273 Salt bridges: A:R.336 P5S.2: 16 residues within 4Å: Chain A: V.29, E.30, D.31, I.32, T.33, I.34, F.37, Y.38, R.95, P.96, H.97, L.100, F.250, R.262, A.263, Q.266 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:H.97, A:L.100, A:A.263 Hydrogen bonds: A:D.31, A:T.33, A:T.33, A:I.34, A:Q.266 Salt bridges: A:R.95, A:R.262, A:R.262, A:R.262 P5S.10: 17 residues within 4Å: Chain B: F.93, T.94, R.95, L.100, M.178, L.181, L.182, F.267, T.268, P.269, A.270, S.271, W.272, T.273, G.322, G.329, R.336 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.100, B:L.181, B:F.267 Hydrogen bonds: B:T.94, B:A.270, B:S.271, B:S.271, B:T.273, B:T.273, B:T.273 Salt bridges: B:R.336 P5S.11: 16 residues within 4Å: Chain B: V.29, E.30, D.31, I.32, T.33, I.34, F.37, Y.38, R.95, P.96, H.97, L.100, F.250, R.262, A.263, Q.266 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:H.97, B:L.100, B:A.263 Hydrogen bonds: B:D.31, B:T.33, B:T.33, B:I.34, B:Q.266 Salt bridges: B:R.95, B:R.262, B:R.262, B:R.262

4 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

LBN.3: 25 residues within 4Å: Chain A: Q.285, A.288, G.289, Y.291, L.292, F.293, W.297, T.331, T.334, Y.338, Y.341, L.342, D.344, C.347, K.348, C.354, F.357, G.358, V.385, L.388, L.389, A.392 Chain B: I.43, L.46 Ligands: LBN.9 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.288, A:Y.291, A:L.292, A:F.293, A:F.293, A:F.293, A:W.297, A:T.331, A:Y.338, A:F.357, A:F.357, A:V.385, A:L.388, A:A.392, B:I.43, B:L.46 pi-Cation interactions: A:Y.341 LBN.8: 13 residues within 4Å: Chain A: P.40, H.41, T.42, I.43, T.44, S.47, I.50 Chain B: Y.341, K.348, R.349, V.350, F.362 Ligands: LBN.12 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.50, A:I.50, B:F.362 Hydrogen bonds: A:I.43, A:T.44, A:T.44, A:S.47 Salt bridges: A:H.41 LBN.9: 13 residues within 4Å: Chain A: Y.341, K.348, R.349, V.350, F.362 Chain B: P.40, H.41, T.42, I.43, T.44, S.47, I.50 Ligands: LBN.3 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.50, B:I.50, A:F.362 Hydrogen bonds: B:I.43, B:T.44, B:T.44, B:S.47 Salt bridges: B:H.41 LBN.12: 25 residues within 4Å: Chain A: I.43, L.46 Chain B: Q.285, A.288, G.289, Y.291, L.292, F.293, W.297, T.331, T.334, Y.338, Y.341, L.342, D.344, C.347, K.348, C.354, F.357, G.358, V.385, L.388, L.389, A.392 Ligands: LBN.8 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.288, B:Y.291, B:L.292, B:F.293, B:F.293, B:F.293, B:W.297, B:T.331, B:Y.338, B:F.357, B:F.357, B:V.385, B:L.388, B:A.392, A:I.43, A:L.46 pi-Cation interactions: B:Y.341

2 x 01: (2R)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dihexadecanoate

01.4: 18 residues within 4Å: Chain A: E.26, F.36, F.37, R.39, P.40, H.41, T.42, L.45, F.48, V.85, L.86, A.87, F.88, H.97, R.102 Chain B: R.22, E.26, R.349 17 PLIP interactions: 8 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:R.22, B:R.349, B:R.349, A:H.41, A:F.88 Water bridges: B:N.25, B:T.352 Salt bridges: B:K.18, B:R.349, B:R.349, A:H.97, A:R.102 Hydrophobic interactions: A:H.41, A:L.45, A:L.45, A:F.48, A:V.85 01.13: 18 residues within 4Å: Chain A: R.22, E.26, R.349 Chain B: E.26, F.36, F.37, R.39, P.40, H.41, T.42, L.45, F.48, V.85, L.86, A.87, F.88, H.97, R.102 17 PLIP interactions: 9 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:H.41, B:L.45, B:L.45, B:F.48, B:V.85 Hydrogen bonds: B:H.41, B:F.88, A:R.22, A:R.349, A:R.349 Salt bridges: B:H.97, B:R.102, A:K.18, A:R.349, A:R.349 Water bridges: A:N.25, A:T.352

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

6OU.5: 11 residues within 4Å: Chain A: I.167, F.168, G.171, H.172, W.174, A.177, M.178, L.181, W.321, I.324, L.325 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.174, A:W.174, A:W.174, A:W.174, A:A.177, A:M.178, A:L.181, A:I.324 Salt bridges: A:H.172, A:H.172 6OU.14: 11 residues within 4Å: Chain B: I.167, F.168, G.171, H.172, W.174, A.177, M.178, L.181, W.321, I.324, L.325 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.174, B:W.174, B:W.174, B:W.174, B:A.177, B:M.178, B:L.181, B:I.324 Salt bridges: B:H.172, B:H.172

2 x CA: CALCIUM ION

CA.6: 4 residues within 4Å: Chain A: E.197, E.200, Q.217, D.221 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.197, A:E.200, A:D.221 CA.15: 4 residues within 4Å: Chain B: E.197, E.200, Q.217, D.221 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.197, B:E.200, B:D.221

2 x 02: (7P)-7-[(4S)-4-{4-[3,5-bis(trifluoromethyl)phenoxy]phenyl}-5-(2,2-difluoropropyl)-6-oxo-1,4,5,6-tetrahydropyrrolo[3,4-c]pyrazol-3-yl]-1,3-benzoxazol-2(3H)-one

02.7: 16 residues within 4Å: Chain A: W.70, L.110, Y.111, F.114, L.115, L.118, M.130, L.133, D.134, L.307, F.313, Q.314, H.317, L.319, S.320, R.323 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.114, A:L.115, A:L.133, A:L.133, A:D.134, A:L.307, A:F.313, A:L.319, A:L.319, A:L.319, A:R.323 Hydrogen bonds: A:D.134, A:D.134, A:Q.314 pi-Stacking: A:F.114, A:F.313, A:H.317 02.16: 16 residues within 4Å: Chain B: W.70, L.110, Y.111, F.114, L.115, L.118, M.130, L.133, D.134, L.307, F.313, Q.314, H.317, L.319, S.320, R.323 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.114, B:L.115, B:L.133, B:L.133, B:D.134, B:L.307, B:F.313, B:L.319, B:L.319, B:L.319, B:R.323 Hydrogen bonds: B:D.134, B:D.134, B:Q.314 pi-Stacking: B:F.114, B:F.313, B:H.317

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Long, T. et al., Molecular insights into human phosphatidylserine synthase 1 reveal its inhibition promotes LDL uptake. Cell (2024)

Release Date

2024-09-04

Peptides

Phosphatidylserine synthase 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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Phosphatidylserine synthase 1

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