SMTL ID : 9kqf.1

Cryo-EM structure of PSS1 in the absence of calcium or L-serine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.25 Å

Oligo State

homo-dimer

Ligands

4 x PSF: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE(Non-covalent)

PSF.1: 15 residues within 4Å: Chain A: F.93, T.94, R.95, P.96, L.100, W.101, M.178, L.182, F.267, P.269, A.270, S.271, W.272, T.273, R.336 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.100, A:L.182 Hydrogen bonds: A:T.94, A:R.95, A:A.270, A:S.271, A:T.273 Salt bridges: A:R.336 PSF.2: 15 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, F.250, R.262, A.263, Q.266 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.37, A:A.263 Hydrogen bonds: A:T.33, A:I.34, A:Y.38 Salt bridges: A:R.95, A:R.262, A:R.262 PSF.13: 15 residues within 4Å: Chain B: P.92, F.93, T.94, R.95, P.96, L.100, W.101, M.178, F.267, P.269, A.270, S.271, T.273, A.332, R.336 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.100, B:A.332 Hydrogen bonds: B:T.94, B:R.95, B:A.270, B:S.271, B:T.273 Salt bridges: B:R.336 PSF.14: 15 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, F.250, R.262, A.263, Q.266 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.263 Hydrogen bonds: B:T.33, B:I.34, B:Y.38, B:Q.266 Salt bridges: B:R.95, B:R.262, B:R.262

10 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)(Covalent)

LBN.3: 15 residues within 4Å: Chain A: I.73, L.110, L.113, F.114, F.117, L.129, W.132 Chain B: I.69, I.73, V.76, I.77, L.110, F.114 Ligands: LBN.15, LBN.20 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.73, A:L.110, A:L.113, A:L.113, A:F.114, A:F.117, A:F.117, A:L.129, A:W.132, B:I.69, B:I.69, B:I.73, B:I.77, B:L.110, B:F.114 LBN.4: 9 residues within 4Å: Chain A: I.167, F.168, G.171, H.172, G.175, A.315, I.324, L.325 Ligands: D12.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.324 LBN.7: 26 residues within 4Å: Chain A: Q.285, A.288, G.289, Y.291, L.292, F.293, I.296, W.297, T.331, T.334, Y.338, Y.341, L.342, D.344, T.345, C.347, K.348, C.354, F.357, G.358, I.381, V.384, L.388 Chain B: I.43, L.46 Ligands: LBN.8 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.288, A:Y.291, A:L.292, A:F.293, A:I.296, A:W.297, A:W.297, A:T.331, A:T.334, A:Y.338, A:Y.338, A:Y.341, A:F.357, A:F.357, A:I.381, A:V.384, A:L.388, B:L.46 Hydrogen bonds: A:Y.341 pi-Cation interactions: A:Y.341 LBN.8: 15 residues within 4Å: Chain A: L.292, Y.341, K.348, R.349, V.350 Chain B: P.40, H.41, T.42, I.43, T.44, L.46, S.47, I.50, M.54 Ligands: LBN.7 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.43, B:L.46, B:I.50, A:L.292 Hydrogen bonds: B:T.44, B:T.44, B:T.44 LBN.9: 18 residues within 4Å: Chain A: W.70, L.74, I.77, L.107, Y.111, F.114, V.126, M.130, W.132, L.133, F.311, H.317, P.318, L.319, R.323, F.326 Ligands: C14.6, LBN.15 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.70, A:L.74, A:I.77, A:Y.111, A:F.114, A:V.126, A:M.130, A:F.311, A:P.318, A:L.319, A:L.319, A:F.326 Salt bridges: A:H.317 pi-Cation interactions: A:W.70, A:W.132 LBN.11: 15 residues within 4Å: Chain A: P.40, H.41, T.42, I.43, T.44, L.46, S.47, I.50, M.54 Chain B: L.292, Y.341, K.348, R.349, V.350 Ligands: LBN.19 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.43, A:L.46, A:I.50, B:L.292 Hydrogen bonds: A:T.44 LBN.15: 13 residues within 4Å: Chain A: I.69, I.73, V.76, L.110 Chain B: I.73, L.110, L.113, F.114, F.117, L.129, W.132 Ligands: LBN.3, LBN.9 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.73, B:L.110, B:L.113, B:L.113, B:F.114, B:F.114, B:F.117, B:F.117, B:F.117, B:L.129, B:W.132, B:W.132, A:I.69, A:I.73, A:V.76, A:L.110, A:L.110 LBN.16: 10 residues within 4Å: Chain B: I.167, F.168, G.171, H.172, G.175, K.308, A.315, I.324, L.325 Ligands: D12.17 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.324 Salt bridges: B:K.308 LBN.19: 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, T.345, C.347, K.348, C.354, F.357, G.358, I.381, V.384, L.388 Ligands: LBN.11 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.288, B:Y.291, B:L.292, B:F.293, B:W.297, B:T.331, B:T.334, B:Y.338, B:Y.341, B:F.357, B:F.357, B:I.381, B:V.384, B:L.388, A:I.43, A:L.46 Hydrogen bonds: B:Y.341 pi-Cation interactions: B:Y.341 LBN.20: 19 residues within 4Å: Chain B: E.66, W.70, L.74, I.77, L.107, Y.111, F.114, V.126, M.130, W.132, L.133, H.317, P.318, L.319, G.322, R.323, F.326 Ligands: LBN.3, C14.18 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.70, B:L.74, B:I.77, B:L.107, B:Y.111, B:F.114, B:V.126, B:M.130, B:P.318, B:L.319, B:L.319, B:F.326 Salt bridges: B:H.317 pi-Cation interactions: B:W.70, B:W.132

2 x D12: DODECANE(Non-covalent)

D12.5: 2 residues within 4Å: Chain A: F.168 Ligands: LBN.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.168 D12.17: 3 residues within 4Å: Chain B: I.167, F.168 Ligands: LBN.16 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.167, B:F.168

2 x C14: TETRADECANE(Non-covalent)

C14.6: 5 residues within 4Å: Chain A: V.104, L.107, P.318, W.321 Ligands: LBN.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.104, A:L.107, A:P.318, A:P.318, A:W.321 C14.18: 5 residues within 4Å: Chain B: V.104, L.107, P.318, W.321 Ligands: LBN.20 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.104, B:L.107, B:P.318, B:P.318, B:W.321

2 x T7X: Phosphatidylinositol(Non-covalent)

T7X.10: 22 residues within 4Å: Chain A: E.26, F.37, Y.38, R.39, P.40, H.41, T.42, T.44, L.45, V.85, L.86, A.87, F.88, H.97, A.99, R.102, M.103 Chain B: Y.17, K.18, N.25, E.26, R.349 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.37, A:F.37, A:T.44, A:L.45, A:A.99 Hydrogen bonds: A:E.26, A:E.26, A:H.41, A:V.85, A:R.102, A:R.102, B:Y.17, B:N.25, B:R.349 Salt bridges: A:H.97, A:R.102, A:R.102, B:K.18, B:R.349 T7X.12: 21 residues within 4Å: Chain A: Y.17, N.25, E.26, R.349 Chain B: E.26, F.37, Y.38, R.39, P.40, H.41, T.42, T.44, L.45, V.85, L.86, A.87, F.88, H.97, A.99, R.102, M.103 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.37, B:F.37, B:T.44, B:L.45, B:A.99 Hydrogen bonds: B:E.26, B:E.26, B:H.41, B:L.86, B:R.102, B:R.102, A:Y.17, A:N.25, A:R.349 Salt bridges: B:H.97, B:R.102, B:R.102, A:K.18, A:R.349

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ning, Y. et al., Structural basis for catalytic mechanism of human phosphatidylserine synthase 1. Cell Discov (2025)

Release Date

2025-04-02

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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