SMTL ID : 7b1l.1

Crystal structure of phosphatidyl serine synthase (PSS) in the closed conformation with bound citrate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

58A.1: 33 residues within 4Å: Chain A: S.33, D.34, T.37, L.58, I.60, I.61, D.63, S.64, D.66, G.67, A.70, R.71, T.75, V.76, S.77, G.80, A.81, D.84, F.135, P.139, P.141, F.189, A.190, L.207, C.208, Y.211 Ligands: CA.2, SER.5, SER.6, NA.7, OLC.11, OLC.14, OLC.15 21 PLIP interactions: 18 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:L.58, A:D.84, A:P.139, A:F.189, A:F.189, A:F.189, A:F.189, A:A.190, A:Y.211 Hydrogen bonds: A:S.33, A:D.34, A:T.37, A:T.37, A:G.67, A:R.71, A:S.77, S.5, S.5, S.6 Water bridges: A:R.71 Salt bridges: A:R.71 58A.18: 34 residues within 4Å: Chain B: S.33, D.34, T.37, I.60, I.61, D.63, S.64, D.66, G.67, A.70, R.71, T.75, V.76, S.77, G.80, A.81, D.84, F.135, P.139, P.141, A.142, K.179, F.185, F.189, A.190, L.207, I.210, Y.211 Ligands: CA.19, SER.22, SER.23, NA.24, OLC.25, OLC.26 28 PLIP interactions: 25 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:I.61, B:D.84, B:F.135, B:P.139, B:A.142, B:K.179, B:F.185, B:F.185, B:F.189, B:F.189, B:F.189, B:L.207, B:L.207, B:I.210, B:Y.211 Hydrogen bonds: B:S.33, B:D.34, B:T.37, B:T.37, B:G.67, B:R.71, B:S.77, S.22, S.22, S.22 Water bridges: B:R.71, B:R.71 Salt bridges: B:R.71

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.63, D.66, D.84 Ligands: 58A.1, MG.8 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.63, A:D.63, A:D.66, A:D.84, A:D.84 CA.19: 5 residues within 4Å: Chain B: D.63, D.66, D.84 Ligands: MG.16, 58A.18 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.63, B:D.63, B:D.66, B:D.84, B:D.84

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

CL.3: 3 residues within 4Å: Chain A: R.123, P.139, I.140 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: R.123, F.127, F.135, I.136 Ligand excluded by PLIP CL.9: 8 residues within 4Å: Chain A: M.23, F.24, S.25, I.26 Chain B: R.126, I.172, S.173, D.174 Ligand excluded by PLIP CL.17: 8 residues within 4Å: Chain A: R.126, I.172, S.173, D.174 Chain B: M.23, F.24, S.25, I.26 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: R.123, P.139, I.140 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: R.123, F.127, F.135, I.136 Ligand excluded by PLIP

4 x SER: SERINE(Non-covalent)

SER.5: 5 residues within 4Å: Chain A: A.81, D.84, S.85, F.127 Ligands: 58A.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.84, A:S.85 Water bridges: A:S.85 SER.6: 4 residues within 4Å: Chain A: S.64, Y.68, R.71 Ligands: 58A.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.68, A:R.71 Salt bridges: A:R.71 SER.22: 5 residues within 4Å: Chain B: A.81, D.84, S.85, F.127 Ligands: 58A.18 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:A.81, B:S.85, S.22 Water bridges: B:S.85, B:S.85 SER.23: 5 residues within 4Å: Chain B: S.64, Y.68, R.71, K.179 Ligands: 58A.18 5 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain B Hydrogen bonds: S.23, S.23, B:Y.68, B:R.71 Salt bridges: B:R.71

2 x NA: SODIUM ION(Non-functional Binders)

NA.7: 7 residues within 4Å: Chain A: T.31, S.33, D.34, T.75, S.77, G.80 Ligands: 58A.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.31, A:S.33, A:S.77 Water bridges: A:S.77 NA.24: 7 residues within 4Å: Chain B: T.31, S.33, D.34, T.75, S.77, G.80 Ligands: 58A.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.31, B:S.77, B:S.77 Water bridges: B:T.31

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 6 residues within 4Å: Chain A: N.40, D.63, D.84, S.87, D.88 Ligands: CA.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.63, A:D.84, A:D.84, A:D.88, H2O.1 MG.16: 5 residues within 4Å: Chain B: D.63, D.84, S.87, D.88 Ligands: CA.19 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.63, B:D.84, B:D.84, B:D.88, H2O.3

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

OLC.10: 10 residues within 4Å: Chain A: Y.101, E.105, S.106, N.107, L.110 Chain B: T.43, L.46, L.50, L.58 Ligands: OLC.12 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:T.43, B:L.46, B:L.58, A:L.110 Hydrogen bonds: A:Y.101, A:Y.101, A:E.105, A:S.106 OLC.11: 7 residues within 4Å: Chain A: Y.68, V.69, K.72, T.73, G.74 Ligands: 58A.1, OLC.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.68, A:V.69, A:K.72 Water bridges: A:K.72 OLC.12: 5 residues within 4Å: Chain A: N.107, L.110 Chain B: L.39, I.42 Ligands: OLC.10 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.110, B:I.42 Hydrogen bonds: A:N.107 OLC.13: 7 residues within 4Å: Chain A: I.32, L.39, F.62, V.69, T.73 Ligands: OLC.11, OLC.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.39, A:F.62, A:V.69, A:T.73 OLC.14: 10 residues within 4Å: Chain A: L.50, N.51, S.52, L.55, L.58, C.194, I.197, V.198 Ligands: 58A.1, OLC.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.55, A:L.58, A:L.58, A:V.198, A:V.198 Water bridges: A:S.54 OLC.15: 10 residues within 4Å: Chain A: T.43, L.50, L.55, L.58, F.62 Chain B: N.107, L.110 Ligands: 58A.1, OLC.13, OLC.14 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.110, A:T.43, A:L.50, A:L.55, A:L.58, A:F.62 Water bridges: B:N.107 OLC.25: 7 residues within 4Å: Chain B: L.50, N.51, S.52, L.58, C.194, V.198 Ligands: 58A.18 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.58, B:V.198 Water bridges: B:F.53, B:S.54 OLC.26: 5 residues within 4Å: Chain B: Y.68, K.72, T.73, G.74 Ligands: 58A.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.68, B:K.72, B:T.73

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

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