SMTL ID : 9n0x.1

Cryo-EM structure of human PSS2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

homo-dimer

Ligands

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

P5S.1: 17 residues within 4Å: Chain A: F.117, S.118, R.119, Y.124, W.125, L.209, R.212, L.268, F.295, P.297, Y.298, S.299, W.300, V.301, R.363 Ligands: P5S.2, RXY.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.124, A:L.209, A:L.268, A:P.297, A:W.300 Hydrogen bonds: A:S.118, A:R.119, A:Y.298, A:S.299, A:V.301, A:R.363 Salt bridges: A:R.212, A:R.363 P5S.2: 9 residues within 4Å: Chain A: T.58, W.61, R.119, Y.124, L.278, I.291, Q.294, F.295 Ligands: P5S.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.61, A:Y.124, A:I.291, A:Q.294, A:F.295 Hydrogen bonds: A:T.58, A:R.290 Salt bridges: A:R.119, A:R.290 P5S.5: 16 residues within 4Å: Chain B: F.117, S.118, R.119, Y.124, W.125, R.212, L.268, F.295, P.297, Y.298, S.299, W.300, V.301, R.363 Ligands: P5S.6, RXY.8 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.124, B:L.268, B:W.300 Hydrogen bonds: B:S.118, B:R.119, B:Y.298, B:S.299, B:V.301 Salt bridges: B:R.212, B:R.363 P5S.6: 8 residues within 4Å: Chain B: W.61, R.119, Y.124, L.278, I.291, Q.294, F.295 Ligands: P5S.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.61, B:Y.124, B:L.278, B:I.291, B:Q.294, B:F.295 Hydrogen bonds: B:T.58, B:R.290 Salt bridges: B:R.119, B:R.290

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: E.225, E.228, E.240, D.249 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.228, A:E.240, A:E.240, A:D.249 CA.7: 4 residues within 4Å: Chain B: E.225, E.228, E.240, D.249 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.228, B:E.240, B:E.240, B:D.249

2 x RXY: (7Z,19R,22R)-25-amino-22-hydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphapentacos-7-en-19-yl (9Z)-octadec-9-enoate(Non-covalent)

RXY.4: 26 residues within 4Å: Chain A: W.125, F.196, A.199, H.200, L.202, G.203, L.206, K.207, M.210, V.323, F.324, A.327, F.332, L.351, V.352, F.354, V.355, N.356, G.358, G.359, M.362, I.365, A.382, V.385, A.386 Ligands: P5S.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.125, A:L.206, A:K.207, A:V.323, A:F.324, A:A.327, A:V.352, A:F.354, A:V.355, A:I.365, A:V.385, A:A.386 Hydrogen bonds: A:H.200 Salt bridges: A:K.207, A:K.207 RXY.8: 26 residues within 4Å: Chain B: W.125, F.196, A.199, H.200, L.202, G.203, L.206, K.207, M.210, V.323, F.324, A.327, F.332, L.351, V.352, F.354, V.355, N.356, G.358, G.359, M.362, I.365, A.382, V.385, A.386 Ligands: P5S.5 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.125, B:L.206, B:K.207, B:V.323, B:F.324, B:A.327, B:V.352, B:F.354, B:V.355, B:I.365, B:V.385, B:A.386 Hydrogen bonds: B:H.200 Salt bridges: B:H.200, B:K.207, B:K.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, D.Y. et al., Structure and Mechanism of Human Phosphatidylserine Synthase 2 and Its Regulation in SREBP pathways. To Be Published

Release Date

2025-05-07

Peptides

Phosphatidylserine synthase 2: 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 2