SMTL ID : 9kqi.1

Cryo-EM structure of PSS1 with calcium

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.02 Å

Oligo State

homo-dimer

Ligands

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

PSF.1: 16 residues within 4Å: Chain A: P.92, F.93, T.94, R.95, P.96, W.101, L.181, F.267, T.268, P.269, A.270, S.271, W.272, T.273, A.332, R.336 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.181, A:F.267 Hydrogen bonds: A:T.94, A:R.95, A:A.270, A:S.271, A:S.271, A:T.273, A:T.273 Salt bridges: A:R.336 PSF.2: 15 residues within 4Å: Chain A: V.29, E.30, D.31, T.33, I.34, F.37, Y.38, R.95, P.96, H.97, L.100, F.250, R.262, Q.266 Ligands: T7X.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.37, A:L.100, A:Q.266 Hydrogen bonds: A:D.31, A:T.33, A:I.34, A:I.34, A:R.262, A:Q.266 Salt bridges: A:R.95, A:R.262, A:R.262 PSF.14: 16 residues within 4Å: Chain B: P.92, F.93, T.94, R.95, P.96, W.101, L.181, F.267, T.268, P.269, A.270, S.271, W.272, T.273, A.332, R.336 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.181, B:F.267, B:A.332 Hydrogen bonds: B:T.94, B:R.95, B:A.270, B:S.271, B:S.271, B:T.273, B:T.273 Salt bridges: B:R.336 PSF.15: 16 residues within 4Å: Chain B: V.29, E.30, D.31, T.33, I.34, F.37, Y.38, R.95, P.96, H.97, L.100, F.250, R.262, A.263, Q.266 Ligands: T7X.16 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.37, B:L.100, B:Q.266 Hydrogen bonds: B:D.31, B:T.33, B:I.34, B:I.34, B:Q.266 Salt bridges: B:R.95, B:R.262, B:R.262

2 x T7X: Phosphatidylinositol(Non-covalent)

T7X.3: 21 residues within 4Å: Chain A: E.26, F.36, F.37, Y.38, R.39, P.40, H.41, T.42, T.44, F.48, V.85, L.86, F.88, H.97, A.99, L.100, R.102 Chain B: K.18, E.26, R.349 Ligands: PSF.2 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.37, A:T.44, A:F.48, A:V.85, A:V.85, A:A.99, A:L.100 Hydrogen bonds: A:E.26, A:H.41, A:V.85, A:F.88, A:R.102, B:K.18, B:E.26 Salt bridges: A:H.97, A:R.102, A:R.102, B:K.18, B:R.349 T7X.16: 20 residues within 4Å: Chain A: K.18, E.26, R.349 Chain B: E.26, F.36, F.37, Y.38, R.39, H.41, T.42, T.44, F.48, V.85, L.86, F.88, H.97, A.99, L.100, R.102 Ligands: PSF.15 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.37, B:T.44, B:F.48, B:V.85, B:A.99, B:L.100 Hydrogen bonds: B:E.26, B:H.41, B:V.85, B:F.88, A:K.18 Salt bridges: B:H.97, B:R.102, B:R.102, A:K.18, A:R.349

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

LBN.4: 15 residues within 4Å: Chain A: I.73, L.110, L.113, F.114, F.117, Q.125, S.128, L.129, W.132 Chain B: I.69, I.73, V.76, I.77 Ligands: LBN.17, LBN.23 14 PLIP interactions: 10 interactions with chain A, 4 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, A:W.132, B:I.69, B:I.73, B:I.73, B:I.77 LBN.5: 13 residues within 4Å: Chain A: D.166, I.167, F.168, G.171, H.172, M.178, A.315, W.321, I.324, L.325, G.329 Ligands: D12.6, SER.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.324, A:L.325 Salt bridges: A:D.166, A:H.172 LBN.8: 25 residues within 4Å: Chain A: Q.285, A.288, G.289, L.292, F.293, I.295, 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, V.384, L.388 Chain B: I.43, L.46 Ligands: LBN.13 18 PLIP interactions: 2 interactions with chain B, 16 interactions with chain A Hydrophobic interactions: B:I.43, B:L.46, A:A.288, A:L.292, A:L.292, A:F.293, A:W.297, A:W.297, A:T.331, A:Y.338, A:Y.341, A:F.357, A:F.357, A:V.384, A:L.388, A:L.388 Hydrogen bonds: A:Y.341 pi-Cation interactions: A:Y.341 LBN.10: 15 residues within 4Å: Chain A: W.70, L.74, L.81, M.103, L.107, W.132, L.133, D.134, H.317, P.318, L.319, R.323, F.326 Ligands: C14.7, LBN.17 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.74, A:L.81, A:L.107, A:L.107, A:L.133, A:D.134, A:P.318, A:L.319, A:R.323, A:F.326, A:F.326 pi-Cation interactions: A:W.70, A:W.70, A:W.132 LBN.12: 14 residues within 4Å: Chain A: P.40, H.41, T.42, I.43, T.44, S.47, I.50, M.54 Chain B: Y.341, K.348, R.349, V.350, F.362 Ligands: LBN.21 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.50, B:F.362 Hydrogen bonds: A:T.44 Salt bridges: A:H.41 LBN.13: 14 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, M.54 Ligands: LBN.8 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.50, B:I.50, A:F.362 Hydrogen bonds: B:T.44 Salt bridges: B:H.41 LBN.17: 15 residues within 4Å: Chain A: I.69, I.73, V.76, L.110, F.114 Chain B: I.73, L.110, L.113, F.114, F.117, Q.125, S.128, L.129 Ligands: LBN.4, LBN.10 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.73, B:L.110, B:L.113, B:F.114, B:F.117, B:F.117, B:L.129, A:I.69, A:I.73, A:V.76, A:L.110, A:F.114 LBN.18: 13 residues within 4Å: Chain B: D.166, I.167, F.168, G.171, H.172, M.178, A.315, W.321, I.324, L.325, G.329 Ligands: D12.19, SER.24 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.324, B:L.325 Salt bridges: B:D.166, B:H.172 LBN.21: 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, Y.338, Y.341, L.342, D.344, T.345, C.347, K.348, C.354, F.357, I.381, V.384, L.388 Ligands: LBN.12 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.292, B:F.293, B:I.295, B:I.296, B:W.297, B:W.297, B:T.331, B:Y.338, B:Y.341, B:F.357, B:F.357, B:I.381, B:V.384, B:L.388, B:L.388, A:I.43, A:L.46 Hydrogen bonds: B:Y.341 pi-Cation interactions: B:Y.341 LBN.23: 15 residues within 4Å: Chain B: W.70, L.74, L.81, M.103, L.107, W.132, L.133, D.134, H.317, P.318, L.319, R.323, F.326 Ligands: LBN.4, C14.20 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.74, B:L.81, B:L.107, B:L.107, B:L.133, B:D.134, B:P.318, B:L.319, B:R.323, B:F.326, B:F.326 pi-Cation interactions: B:W.70, B:W.70, B:W.132

2 x D12: DODECANE(Non-covalent)(Non-functional Binders)

D12.6: 2 residues within 4Å: Chain A: I.167 Ligands: LBN.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.167 D12.19: 1 residues within 4Å: Ligands: LBN.18 No protein-ligand interaction detected (PLIP)

2 x C14: TETRADECANE(Non-covalent)

C14.7: 6 residues within 4Å: Chain A: V.104, P.318, W.321, G.322, G.329 Ligands: LBN.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.104, A:P.318, A:P.318, A:W.321 C14.20: 6 residues within 4Å: Chain B: V.104, P.318, W.321, G.322, G.329 Ligands: LBN.23 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.104, B:P.318, 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 Ligands: SER.11 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.200, SER.11 CA.22: 4 residues within 4Å: Chain B: E.197, E.200, Q.217 Ligands: SER.24 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain B Metal complexes: SER.24, B:E.197, B:E.200

2 x SER: SERINE(Non-covalent)

SER.11: 8 residues within 4Å: Chain A: H.172, W.196, E.200, E.301, T.304, F.305 Ligands: LBN.5, CA.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.200, A:E.301 Salt bridges: A:H.172 SER.24: 7 residues within 4Å: Chain B: H.172, W.196, E.200, E.301, T.304 Ligands: LBN.18, CA.22 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.172

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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