SMTL ID : 5xj8.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 2 residues within 4Å: Chain A: K.136, R.192 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.136, A:R.192 PO4.2: 7 residues within 4Å: Chain A: V.39, G.40, H.93, K.105, G.106, V.107, A.108 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.105, A:G.106, A:V.107, A:A.108 Salt bridges: A:H.93 PO4.3: 9 residues within 4Å: Chain B: N.38, G.40, H.93, G.104, K.105, G.106, V.107, A.108 Ligands: NKO.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.38, B:A.41, B:K.105, B:K.105, B:G.106, B:V.107, B:A.108 Salt bridges: B:H.93

1 x NKO: (2R)-2-hydroxy-3-(phosphonooxy)propyl hexadecanoate(Non-covalent)

NKO.4: 24 residues within 4Å: Chain B: S.36, N.38, G.40, A.41, T.42, N.43, R.46, F.57, K.105, V.107, L.111, V.114, F.126, W.129, V.139, S.140, S.143, A.146, T.147, A.150, I.170, H.178, N.181 Ligands: PO4.3 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:F.57, B:F.57, B:V.107, B:V.107, B:L.111, B:L.111, B:V.114, B:F.126, B:W.129, B:W.129, B:A.146, B:T.147, B:A.150, B:I.170 Hydrogen bonds: B:S.36, B:S.36, B:S.36, B:N.38, B:A.41, B:T.42, B:T.42, B:V.139, B:S.143, B:N.181 Water bridges: B:S.140 Salt bridges: B:R.46, B:K.105

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: 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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Glycerol-3-phosphate acyltransferase

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