SMTL ID : 7drj.1

Crystal structure of phosphatidylglycerol phosphate synthase in complex with phosphatidylglycerol phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x PO9: [(2R)-2-hexadecanoyloxy-3-[oxidanyl-[(2S)-2-oxidanyl-3-phosphonooxy-propoxy]phosphoryl]oxy-propyl] (Z)-octadec-9-enoate(Non-covalent)

PO9.1: 27 residues within 4Å: Chain A: F.53, S.74, L.75, D.77, F.78, D.98, P.99, D.102, K.103, R.130, R.138, A.150, G.154, K.155, I.156, K.157, T.158, A.159, M.162, V.163, T.166, W.167, L.170, L.186, Y.201 Ligands: ZN.12, ZN.13 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.53, A:L.75, A:K.155, A:I.156, A:V.163, A:L.170, A:L.186 Hydrogen bonds: A:D.102, A:K.103, A:Y.201 Water bridges: A:D.98, A:K.157 Salt bridges: A:K.103, A:R.130, A:R.138, A:K.157 PO9.17: 26 residues within 4Å: Chain B: S.74, L.75, D.77, F.78, D.98, P.99, D.102, K.103, R.130, R.138, A.150, G.154, K.155, K.157, T.158, A.159, V.160, M.162, V.163, T.166, L.182, L.186, Y.201 Ligands: BU1.20, ZN.26, ZN.27 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.75, B:V.160, B:V.163, B:V.163, B:T.166, B:L.182, B:L.186 Hydrogen bonds: B:D.102, B:G.154, B:T.158, B:Y.201 Salt bridges: B:K.103, B:R.130, B:R.138, B:K.157

14 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.2: 2 residues within 4Å: Chain A: F.193, L.196 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.193, A:L.196 BU1.3: 5 residues within 4Å: Chain A: R.130, I.199, F.202 Ligands: BU1.9, OLC.24 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.130 BU1.6: 3 residues within 4Å: Chain A: V.44, D.45, F.46 No protein-ligand interaction detected (PLIP) BU1.7: 3 residues within 4Å: Chain A: L.54, G.55, L.174 No protein-ligand interaction detected (PLIP) BU1.8: 3 residues within 4Å: Chain A: V.29, V.32, P.36 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.32 BU1.9: 3 residues within 4Å: Chain A: F.202 Ligands: BU1.3, OLC.24 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.202 BU1.10: 2 residues within 4Å: Chain A: F.193 Ligands: BU1.11 No protein-ligand interaction detected (PLIP) BU1.11: 2 residues within 4Å: Chain A: I.189 Ligands: BU1.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.189 BU1.19: 1 residues within 4Å: Chain B: F.193 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.193 BU1.20: 1 residues within 4Å: Ligands: PO9.17 No protein-ligand interaction detected (PLIP) BU1.21: 1 residues within 4Å: Chain B: A.133 No protein-ligand interaction detected (PLIP) BU1.22: 2 residues within 4Å: Chain B: I.178, L.180 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.180 BU1.23: 2 residues within 4Å: Chain B: L.54, G.55 No protein-ligand interaction detected (PLIP) BU1.25: 3 residues within 4Å: Chain B: L.40, V.44, F.46 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.45

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

OLC.4: 6 residues within 4Å: Chain A: F.48, I.61, I.65, F.68, I.69, L.72 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.61, A:F.68 Hydrogen bonds: A:F.68 OLC.5: 8 residues within 4Å: Chain A: N.120, I.126, Y.188, V.191, I.192 Chain B: L.43, Q.115 Ligands: OLC.24 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.126, A:Y.188, A:Y.188, A:Y.188, A:V.191, A:I.192 Hydrogen bonds: B:Q.115 Water bridges: B:D.45 OLC.16: 11 residues within 4Å: Chain A: P.36, I.39, L.40, L.43, V.44 Chain B: N.120, V.122, I.125, I.126, Y.188, V.191 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.122, B:V.122, B:I.125, B:I.126, A:I.39, A:L.43, A:V.44 OLC.18: 4 residues within 4Å: Chain B: F.41, F.48, I.61, I.65 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.48, B:I.65 OLC.24: 13 residues within 4Å: Chain A: V.122, I.125, I.126, A.129 Chain B: I.35, P.36, I.39, L.40, V.44, L.104 Ligands: BU1.3, OLC.5, BU1.9 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.35, B:I.39, B:L.104, A:V.122, A:I.125, A:I.126, A:A.129

4 x ZN: ZINC ION(Non-covalent)

ZN.12: 7 residues within 4Å: Chain A: D.77, F.78, D.80, G.81, D.98 Ligands: PO9.1, ZN.13 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.77, A:D.80, A:D.98, H2O.1 ZN.13: 6 residues within 4Å: Chain A: R.31, D.77, D.98, D.102 Ligands: PO9.1, ZN.12 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.77, A:D.77, A:D.98, A:D.102, A:D.102 ZN.26: 5 residues within 4Å: Chain B: D.77, D.98, D.102 Ligands: PO9.17, ZN.27 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.77, B:D.77, B:D.98, B:D.102, B:D.102 ZN.27: 6 residues within 4Å: Chain B: D.77, D.80, G.81, D.98 Ligands: PO9.17, ZN.26 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.77, B:D.77, B:D.80, B:D.98, H2O.3

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.14: 1 residues within 4Å: Chain A: I.185 No protein-ligand interaction detected (PLIP) ACY.15: 2 residues within 4Å: Chain A: D.45, G.47 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.45, A:F.48 ACY.28: 2 residues within 4Å: Chain B: D.45, G.47 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, B. et al., The phosphatidylglycerol phosphate synthase PgsA utilizes a trifurcated amphipathic cavity for catalysis at the membrane-cytosol interface. Curr Res Struct Biol (2021)

Release Date

2021-12-08

Peptides

CDP-diacylglycerol--glycerol-3-phosphate 3-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--glycerol-3-phosphate 3-phosphatidyltransferase

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