SMTL ID : 7b1k.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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: 32 residues within 4Å: Chain A: S.33, D.34, T.37, D.63, S.64, D.66, G.67, Y.68, A.70, R.71, V.76, S.77, G.80, A.81, D.84, F.127, F.135, P.139, P.141, A.142, P.178, K.179, Y.180, F.185, I.188, F.189, L.207, Y.211, Y.214 Ligands: CA.2, FLC.6, NA.7 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:D.84, A:P.139, A:Y.180, A:F.185, A:F.185, A:F.185, A:I.188, A:F.189, A:F.189, A:L.207, A:L.207, A:Y.211, A:Y.211, A:Y.211, A:Y.214, A:Y.214 Hydrogen bonds: A:S.33, A:D.34, A:T.37, A:T.37, A:G.67, A:R.71, A:S.77, A:D.84, A:A.142 Salt bridges: A:R.71, A:K.179, A:K.179 58A.12: 32 residues within 4Å: Chain B: S.33, D.34, T.37, 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.127, F.135, P.139, P.141, A.142, K.179, Y.180, F.185, I.188, F.189, L.207, C.208, Y.211, Y.214 Ligands: CA.13, FLC.17, NA.21 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:D.84, B:Y.180, B:F.185, B:F.185, B:I.188, B:I.188, B:F.189, B:F.189, B:F.189, B:F.189, B:L.207, B:Y.211, B:Y.211, B:Y.211 Hydrogen bonds: B:S.33, B:D.34, B:T.37, B:T.37, B:G.67, B:S.77, B:A.142 Salt bridges: B:R.71, B:K.179, B:K.179

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.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.63, A:D.63, A:D.66, A:D.84 CA.13: 5 residues within 4Å: Chain B: D.63, D.66, G.67, D.84 Ligands: 58A.12 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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 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:S.87, A:D.88, H2O.1 MG.14: 5 residues within 4Å: Chain B: N.40, D.63, D.84, S.87, D.88 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.84, B:D.84, B:D.88, H2O.1

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

CL.4: 3 residues within 4Å: Chain A: R.123, L.124, I.140 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: R.123, F.127, F.135, I.136 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: R.123, L.124, I.140 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: R.123, F.135, I.136 Ligand excluded by PLIP

3 x FLC: CITRATE ANION(Non-covalent)

FLC.6: 5 residues within 4Å: Chain A: N.131, V.132, K.133, K.179 Ligands: 58A.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:K.179 Water bridges: A:R.71, A:R.71, A:F.127, A:V.132 Salt bridges: A:R.71, A:K.133, A:K.179, A:K.179, A:K.179 FLC.17: 7 residues within 4Å: Chain B: R.71, F.127, N.131, V.132, K.133, K.179 Ligands: 58A.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.131 Salt bridges: B:R.71, B:K.179, B:K.179 FLC.18: 4 residues within 4Å: Chain B: R.27, I.30, I.32, Y.35 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.35 Hydrogen bonds: B:I.30, B:Y.35

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.33, A:S.77 NA.21: 7 residues within 4Å: Chain B: T.31, S.33, D.34, T.75, S.77, G.80 Ligands: 58A.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.31, B:T.31

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

OLC.8: 9 residues within 4Å: Chain A: L.50, N.51, S.52, F.53, S.54, L.55, L.58, N.103, I.197 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.55, A:L.58 Hydrogen bonds: A:N.51, A:N.103 OLC.9: 2 residues within 4Å: Chain A: I.200, H.202 No protein-ligand interaction detected (PLIP) OLC.10: 9 residues within 4Å: Chain A: Y.101, E.105, S.106, N.107, L.110 Chain B: I.42, L.46, L.50 Ligands: OLC.11 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.110, B:I.42, B:L.46, B:L.50, B:L.50 Hydrogen bonds: A:Y.101, A:E.105 OLC.11: 1 residues within 4Å: Ligands: OLC.10 No protein-ligand interaction detected (PLIP) OLC.19: 6 residues within 4Å: Chain B: F.150, Q.152, L.153, I.154, L.209 Ligands: OLC.20 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.150, B:F.150, B:L.153, B:I.154, B:I.154, B:L.209 OLC.20: 8 residues within 4Å: Chain B: L.153, I.154, N.155, I.159, I.162, L.163, L.166 Ligands: OLC.19 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.154, B:I.154, B:I.159, B:I.159, B:I.162, B:L.163, B:L.166 Hydrogen bonds: B:N.155

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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