SMTL ID : 5xj6.1

Crystal structure of PlsY (YgiH), an integral membrane glycerol 3-phosphate acyltransferase - the glycerol 3-phosphate form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

monomer

Ligands

1 x G3P: SN-GLYCEROL-3-PHOSPHATE(Non-covalent)

G3P.1: 11 residues within 4Å: Chain A: S.36, N.38, T.42, R.46, K.105, V.107, V.139, S.143, H.178, N.181 Ligands: PO4.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.36, A:T.42, A:S.143, A:S.143, A:N.181, A:N.181, A:R.184 Water bridges: A:N.38, A:T.42, A:R.46, A:R.46 Salt bridges: A:R.46, A:K.105

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

OLC.2: 17 residues within 4Å: Chain A: A.41, T.42, T.45, K.50, F.57, V.107, A.110, L.111, F.126, W.129, F.133, A.146, T.147, A.150, A.167, I.170, Q.201 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.57, A:V.107, A:A.110, A:L.111, A:F.126, A:W.129, A:W.129, A:W.129, A:A.146, A:T.147, A:A.150, A:A.167, A:I.170 Hydrogen bonds: A:T.45, A:Q.201 OLC.3: 5 residues within 4Å: Chain A: V.8, V.81, F.84, V.169 Ligands: OLC.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.8, A:V.169 OLC.4: 5 residues within 4Å: Chain A: A.172, I.175, Y.176, R.179 Ligands: OLC.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.172, A:I.175, A:Y.176 Hydrogen bonds: A:R.179 OLC.5: 6 residues within 4Å: Chain A: Y.12, Y.95, F.101, Y.176 Ligands: OLC.3, OLC.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.12, A:Y.95, A:Y.95, A:F.101, A:Y.176

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 9 residues within 4Å: Chain A: N.38, G.40, H.93, G.104, K.105, G.106, V.107, A.108 Ligands: G3P.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.38, A:D.60, A:K.105, A:G.106, A:V.107, A:A.108 Water bridges: A:G.40 Salt bridges: A:H.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Z. et al., Structural insights into the committed step of bacterial phospholipid biosynthesis. Nat Commun (2017)

Release Date

2017-12-06

Peptides

Glycerol-3-phosphate acyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Glycerol-3-phosphate acyltransferase

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