SMTL ID : 5xj7.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

monomer

Ligands

7 x 78M: (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE(Non-covalent)

78M.1: 8 residues within 4Å: Chain A: M.1, A.4, L.5, V.8, I.9, V.81, F.84 Ligands: 78M.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.8, A:V.8, A:I.9 78M.2: 3 residues within 4Å: Chain A: F.124 Ligands: 78M.3, 87O.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.124 78M.3: 4 residues within 4Å: Chain A: V.156, A.157 Ligands: 78M.2, 87O.8 No protein-ligand interaction detected (PLIP) 78M.4: 7 residues within 4Å: Chain A: W.80, F.84, F.165, V.169, A.172, L.173 Ligands: 78M.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.84, A:F.165, A:V.169, A:A.172, A:L.173 78M.5: 9 residues within 4Å: Chain A: I.132, W.135, K.136, Y.138, L.141, T.145, S.149, F.153 Ligands: 78M.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.132, A:W.135, A:F.153 Hydrogen bonds: A:R.192 Salt bridges: A:K.136 78M.6: 6 residues within 4Å: Chain A: L.141, T.145, I.148, L.185, L.186 Ligands: 78M.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.141, A:T.145, A:I.148, A:L.186 78M.7: 8 residues within 4Å: Chain A: F.57, F.58, F.115, L.123, F.126, W.129, F.133, R.137 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.57, A:F.58, A:F.115, A:F.126, A:F.126, A:W.129 Hydrogen bonds: A:R.137

2 x 87O: phosphono hexadecanoate(Non-covalent)

87O.8: 11 residues within 4Å: Chain A: S.118, S.120, F.124, L.127, V.128, G.131, F.153, A.157, Y.159 Ligands: 78M.2, 78M.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.124, A:V.128, A:F.153, A:F.153, A:F.153, A:A.157 Hydrogen bonds: A:S.118, A:S.120 Water bridges: A:S.120, A:Y.159 87O.9: 17 residues within 4Å: Chain A: G.40, A.41, T.42, F.57, H.93, G.104, K.105, G.106, V.107, A.108, A.110, L.111, V.114, F.126, W.129, A.146, A.150 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.57, A:F.57, A:V.107, A:A.110, A:L.111, A:V.114, A:F.126, A:F.126, A:W.129, A:W.129, A:W.129, A:A.146 Hydrogen bonds: A:T.42, A:T.42, A:K.105, A:G.106, A:V.107, A:A.108 Water bridges: A:G.40, A:G.40 Salt bridges: A:H.93

2 x K: POTASSIUM ION(Non-covalent)

K.10: 4 residues within 4Å: Chain A: P.96, F.98, F.99, F.101 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:P.96, A:F.98, A:F.101, H2O.2 K.11: 5 residues within 4Å: Chain A: N.38, K.105, N.181, R.184 Ligands: PO4.12 No protein-ligand interaction detected (PLIP)

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

PO4.12: 7 residues within 4Å: Chain A: S.36, T.42, R.46, N.181, E.190, H.191 Ligands: K.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.36, A:N.181 Water bridges: A:K.105, A:V.139 Salt bridges: A:R.46, A: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: 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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