SMTL ID : 7pow.1

Crystal structure of phosphatidyl serine synthase (PSS) in transition state.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-dimer

Ligands

1 x SMW: (2S)-2-amino-3-[[[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl]methoxy-hydroxy-phosphoryl]oxy-[(2R)-2,3-bis[[(Z)-octadec-9-enoyl]oxy]propoxy]-dihydroxy-lambda^5-phosphanyl]oxy-propanoic acid(Non-covalent)

SMW.1: 34 residues within 4Å: Chain A: S.14, D.15, T.18, L.39, I.41, I.42, D.44, S.45, D.47, G.48, A.51, R.52, T.56, V.57, S.58, G.61, A.62, D.65, S.66, D.69, F.108, F.116, P.122, K.160, I.167, F.170, A.171, C.175, I.178, L.188, I.191, Y.192 Ligands: CA.2, OLC.8 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:I.42, A:I.42, A:D.47, A:D.65, A:P.122, A:I.167, A:F.170, A:F.170, A:F.170, A:F.170, A:I.178, A:I.191, A:Y.192, A:Y.192 Hydrogen bonds: A:S.14, A:T.18, A:D.44, A:G.48, A:R.52, A:S.58, A:D.65, A:S.66 Water bridges: A:R.52, A:G.61, A:G.61 Salt bridges: A:R.52

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.44, D.47, D.65 Ligands: SMW.1, MG.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.44, A:D.44, A:D.47, A:D.65, A:D.65 CA.15: 5 residues within 4Å: Chain B: D.44, D.47, D.65 Ligands: 58A.14, MG.16 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.44, B:D.44, B:D.47, B:D.65, B:D.65

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: N.21, D.44, D.65, D.69 Ligands: CA.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.44, A:D.65, A:D.65, A:D.69, H2O.1 MG.16: 5 residues within 4Å: Chain B: D.44, D.65, S.68, D.69 Ligands: CA.15 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.44, B:D.65, B:D.65, H2O.2, H2O.2

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: R.104, P.120, I.121, P.122 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: R.104, F.108, F.116, I.117 Ligand excluded by PLIP CL.6: 8 residues within 4Å: Chain A: R.107, I.153, S.154, D.155 Chain B: M.4, F.5, S.6, I.7 Ligand excluded by PLIP CL.7: 8 residues within 4Å: Chain A: M.4, F.5, S.6, I.7 Chain B: R.107, I.153, S.154, D.155 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: R.104, P.120, I.121, P.122 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: R.104, F.116, I.117 Ligand excluded by PLIP

10 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.8: 11 residues within 4Å: Chain A: L.31, S.33, S.35, L.36, L.39, C.175, L.176, I.178, V.179 Ligands: SMW.1, OLC.20 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.39, A:I.178, A:V.179 Hydrogen bonds: A:S.33 Water bridges: A:S.35 OLC.9: 8 residues within 4Å: Chain A: N.88 Chain B: T.24, L.27, L.31, L.39, F.43 Ligands: OLC.11, OLC.21 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.24, B:L.27, B:L.39 Water bridges: A:N.88, A:N.88 OLC.10: 6 residues within 4Å: Chain A: L.46, V.50, K.53, T.54, G.55 Ligands: OLC.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.46, A:T.54 OLC.11: 5 residues within 4Å: Chain A: N.88, L.91 Chain B: L.20, I.23 Ligands: OLC.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.20, B:I.23, B:I.23, A:L.91 OLC.12: 8 residues within 4Å: Chain A: I.13, L.20, F.43, T.54, T.56 Ligands: OLC.10, OLC.13, OLC.20 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.13, A:L.20, A:F.43, A:T.54 OLC.13: 9 residues within 4Å: Chain A: R.8, I.11, I.13, Y.16, V.17, M.19, L.20, I.23 Ligands: OLC.12 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.16, A:Y.16, A:V.17, A:L.20, A:L.20, A:L.20, A:I.23 Hydrogen bonds: A:R.8, A:R.8, A:Y.16 OLC.20: 8 residues within 4Å: Chain A: L.31, L.36, L.39, F.43 Chain B: N.88, L.91 Ligands: OLC.8, OLC.12 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.91, A:L.31, A:L.36, A:L.39, A:F.43 Water bridges: B:N.88, B:N.88, B:N.88 OLC.21: 10 residues within 4Å: Chain B: L.31, N.32, S.33, L.36, L.39, C.175, I.178, V.179 Ligands: OLC.9, 58A.14 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.36, B:L.39, B:L.39, B:I.178, B:V.179, B:V.179 OLC.22: 5 residues within 4Å: Chain B: Y.49, V.50, K.53, T.54, G.55 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.49, B:V.50, B:K.53, B:T.54 OLC.23: 10 residues within 4Å: Chain A: F.5, I.7, R.8, I.11 Chain B: I.92, I.95, I.96, L.99, L.103, I.153 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.92, B:I.95, B:I.95, B:I.96, B:L.99, B:L.103

1 x 58A: 5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9E)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine(Non-covalent)

58A.14: 35 residues within 4Å: Chain B: S.14, D.15, T.18, L.39, I.42, D.44, S.45, D.47, G.48, A.51, R.52, T.56, V.57, S.58, G.61, A.62, D.65, F.116, P.120, P.122, A.123, K.160, F.166, I.167, F.170, A.171, L.174, C.175, L.188, C.189, I.191, Y.192 Ligands: CA.15, SER.19, OLC.21 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:L.39, B:D.65, B:F.116, B:P.120, B:A.123, B:F.166, B:I.167, B:F.170, B:F.170, B:F.170, B:F.170, B:L.174, B:I.191, B:Y.192, B:Y.192 Hydrogen bonds: B:D.15, B:T.18, B:T.18, B:G.48, B:R.52, B:S.58, B:D.65 Water bridges: B:T.12, B:R.52, B:G.61 Salt bridges: B:R.52

1 x SER: SERINE(Non-covalent)

SER.19: 6 residues within 4Å: Chain B: A.62, D.65, S.66, D.69, F.108 Ligands: 58A.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Centola, M. et al., Crystal structures of phosphatidyl serine synthase PSS reveal the catalytic mechanism of CDP-DAG alcohol O-phosphatidyl transferases. Nat Commun (2021)

Release Date

2021-12-08

Peptides

CDP-diacylglycerol--serine O-phosphatidyltransferase: 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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CDP-diacylglycerol--serine O-phosphatidyltransferase