SMTL ID : 9kqj.1

Cryo-EM structure of PSS1 with calcium

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.95 Å

Oligo State

homo-dimer

Ligands

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

PSF.1: 13 residues within 4Å: Chain A: F.93, T.94, R.95, P.96, W.101, L.181, F.267, P.269, A.270, S.271, W.272, T.273, R.336 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.181, A:W.272 Hydrogen bonds: A:T.94, A:R.95, A:A.270, A:S.271, A:S.271, A:T.273 Salt bridges: A:R.336 PSF.2: 14 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, Q.266 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Q.266 Hydrogen bonds: A:E.30, A:D.31, A:D.31, A:T.33, A:I.34, A:I.34, A:Q.266 Salt bridges: A:R.95, A:R.262, A:R.262, A:R.262 PSF.14: 13 residues within 4Å: Chain B: F.93, T.94, R.95, P.96, W.101, L.181, F.267, P.269, A.270, S.271, W.272, T.273, R.336 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.181, B:W.272 Hydrogen bonds: B:T.94, B:R.95, B:A.270, B:S.271, B:S.271, B:T.273 Salt bridges: B:R.336 PSF.15: 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, W.247, F.250, R.262, A.263, Q.266 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.263, B:Q.266 Hydrogen bonds: B:E.30, B:D.31, B:D.31, 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)

LBN.3: 15 residues within 4Å: Chain A: I.73, L.110, L.113, F.114, F.117, S.128, L.129, W.132 Chain B: I.69, V.76, I.77, L.110, F.114 Ligands: LBN.16, LBN.21 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:I.69, B:I.77, B:I.77, B:L.110, B:F.114, A:I.73, A:L.110, A:L.113, A:F.114, A:F.117, A:F.117, A:W.132 LBN.4: 15 residues within 4Å: Chain A: I.167, F.168, G.171, H.172, W.174, G.175, M.178, A.315, S.320, W.321, I.324, L.325, G.328, G.329 Ligands: D12.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.174, A:I.324, A:L.325 Salt bridges: A:D.166, A:H.172 LBN.7: 29 residues within 4Å: Chain A: Q.285, A.288, G.289, Y.291, L.292, F.293, I.295, I.296, W.297, T.331, T.334, V.335, Y.338, Y.341, L.342, D.344, T.345, C.347, K.348, C.354, F.357, G.358, I.381, V.384, W.387, L.388 Chain B: I.43, L.46 Ligands: LBN.13 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.288, A:Y.291, A:L.292, A:L.292, A:F.293, A:I.295, A:I.296, A:W.297, A:W.297, A:T.331, A:V.335, A:Y.338, A:Y.338, A:Y.341, A:F.357, A:I.381, A:V.384, A:W.387, A:L.388, A:L.388, B:I.43, B:L.46 Hydrogen bonds: A:Q.285, A:Y.341 pi-Cation interactions: A:Y.341 LBN.8: 12 residues within 4Å: Chain A: W.70, I.77, Y.111, M.130, W.132, L.133, F.311, P.318, L.319, R.323 Ligands: C14.6, LBN.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.77, A:Y.111, A:F.311, A:L.319, A:R.323 pi-Cation interactions: A:W.70, A:W.70, A:W.132 LBN.11: 15 residues within 4Å: Chain A: P.40, H.41, T.42, I.43, T.44, S.47, I.50, M.54 Chain B: L.292, Y.341, K.348, R.349, V.350, F.362 Ligands: LBN.20 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.50, A:I.50, B:L.292, B:F.362 Hydrogen bonds: A:I.43, A:T.44, A:T.44 Salt bridges: A:H.41 LBN.13: 17 residues within 4Å: Chain A: L.292, Y.341, K.348, R.349, V.350, F.362 Chain B: P.40, H.41, T.42, I.43, T.44, L.46, S.47, I.50, V.51, M.54 Ligands: LBN.7 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.46, B:I.50, B:V.51, A:L.292, A:F.362 Hydrogen bonds: B:I.43, B:T.44, B:T.44 Salt bridges: B:H.41 LBN.16: 15 residues within 4Å: Chain A: I.69, I.73, V.76, I.77, F.114 Chain B: I.73, L.110, L.113, F.114, F.117, S.128, L.129, W.132 Ligands: LBN.3, LBN.8 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:I.69, A:I.73, A:I.77, A:F.114, B:I.73, B:L.110, B:L.113, B:F.114, B:F.117, B:F.117, B:W.132 LBN.17: 14 residues within 4Å: Chain B: I.167, F.168, G.171, H.172, W.174, M.178, K.308, A.315, W.321, I.324, L.325, G.328, G.329 Ligands: D12.18 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.174, B:I.324, B:L.325 Hydrogen bonds: B:S.320 Salt bridges: B:D.166, B:H.172, B:K.308 LBN.20: 25 residues within 4Å: Chain A: I.43, L.46 Chain B: Q.285, A.288, G.289, L.292, F.293, I.295, I.296, W.297, T.331, T.334, V.335, Y.338, Y.341, D.344, T.345, C.347, K.348, C.354, F.357, I.381, V.384, L.388 Ligands: LBN.11 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.292, B:L.292, B:F.293, B:I.295, B:I.296, B:I.296, B:W.297, B:T.331, B:V.335, B:Y.338, B:Y.341, B:F.357, B:I.381, B:V.384, B:L.388, B:L.388, A:I.43, A:L.46 Hydrogen bonds: B:Q.285, B:Y.341 pi-Cation interactions: B:Y.341 LBN.21: 12 residues within 4Å: Chain B: W.70, I.77, Y.111, M.130, W.132, L.133, F.311, P.318, L.319, R.323 Ligands: LBN.3, C14.19 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.77, B:Y.111, B:F.311, B:R.323 pi-Cation interactions: B:W.70, B:W.70, B:W.132

2 x D12: DODECANE(Non-covalent)

D12.5: 2 residues within 4Å: Chain A: L.325 Ligands: LBN.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.325 D12.18: 2 residues within 4Å: Chain B: L.325 Ligands: LBN.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.325

2 x C14: TETRADECANE(Non-covalent)

C14.6: 4 residues within 4Å: Chain A: P.318, W.321, G.329 Ligands: LBN.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.318, A:W.321 C14.19: 6 residues within 4Å: Chain B: V.104, P.318, W.321, G.322, G.329 Ligands: LBN.21 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.104, B:P.318, B:W.321

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain A: E.197, E.200, Q.217, D.221 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.197, A:E.200 CA.22: 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.197, B:E.200

2 x T7X: Phosphatidylinositol(Non-covalent)

T7X.10: 20 residues within 4Å: Chain A: E.26, Q.28, F.36, F.37, Y.38, R.39, P.40, H.41, T.42, F.48, V.85, L.86, F.88, H.97, A.99, R.102 Chain B: Y.17, K.18, N.25, R.349 19 PLIP interactions: 8 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:Y.17, B:K.18, B:K.18, B:N.25, B:R.349, B:R.349, A:E.26, A:Q.28, A:H.41, A:R.102 Salt bridges: B:K.18, B:R.349, A:H.97, A:R.102, A:R.102 Hydrophobic interactions: A:F.36, A:F.37, A:F.48, A:A.99 T7X.12: 19 residues within 4Å: Chain A: Y.17, K.18, N.25, R.349 Chain B: E.26, Q.28, F.36, F.37, Y.38, R.39, P.40, H.41, T.42, V.85, L.86, F.88, H.97, A.99, R.102 19 PLIP interactions: 8 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:Y.17, A:K.18, A:K.18, A:N.25, A:R.349, A:R.349, B:E.26, B:Q.28, B:H.41, B:L.86, B:R.102 Salt bridges: A:K.18, A:R.349, B:H.97, B:R.102, B:R.102 Hydrophobic interactions: B:F.36, B:F.37, B:A.99

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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