SMTL ID : 5xj5.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: S.36, N.38, T.42, N.43, R.46, K.105 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.36, A:N.38 Water bridges: A:T.42, A:T.42, A:N.43, A:R.46, A:K.105, A:K.105, A:N.181, A:N.181, A:N.181 Salt bridges: A:R.46, A:K.105 SO4.2: 2 residues within 4Å: Chain A: H.191, R.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.191, A:R.192 Salt bridges: A:R.192 SO4.3: 9 residues within 4Å: Chain A: G.40, A.41, H.93, G.104, K.105, G.106, V.107, A.108 Ligands: 78M.11 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:A.41, A:K.105, A:G.106, A:V.107, A:A.108 Water bridges: A:G.40, A:G.40, A:T.42, A:T.42, A:D.60 Salt bridges: A:H.93 SO4.4: 6 residues within 4Å: Chain A: Y.95, Y.176, R.177, R.179 Ligands: 78M.10, 78M.16 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.95 Water bridges: A:R.177, A:R.179, A:R.179 Salt bridges: A:R.177, A:R.179 SO4.5: 3 residues within 4Å: Chain A: R.46, H.191, R.192 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.46, A:R.46, A:R.46, A:R.46 Salt bridges: A:R.46 SO4.6: 3 residues within 4Å: Chain A: A.157, G.158, Y.159 No protein-ligand interaction detected (PLIP) SO4.7: 3 residues within 4Å: Chain A: G.49, K.50, K.51 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.50, A:K.51 Water bridges: A:K.51, A:K.51 Salt bridges: A:K.51

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

78M.8: 5 residues within 4Å: Chain A: V.128, G.131, I.132, L.134, W.135 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.132, A:L.134, A:W.135, A:W.135 78M.9: 8 residues within 4Å: Chain A: Y.138, L.141, I.144, T.145, I.148, S.149, L.185, L.186 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.141, A:I.144, A:I.148, A:L.185, A:L.186 Hydrogen bonds: A:L.185 78M.10: 8 residues within 4Å: Chain A: Y.12, L.91, Y.95, G.100, F.101, K.102 Ligands: SO4.4, 78M.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.12, A:L.91, A:Y.95 78M.11: 21 residues within 4Å: Chain A: A.41, T.42, F.57, V.107, A.110, L.111, V.114, S.125, F.126, W.129, S.143, A.146, T.147, A.150, F.151, A.167, I.170, G.171 Ligands: SO4.3, 78M.21, PGE.23 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.57, A:A.110, A:L.111, A:V.114, A:F.126, A:W.129, A:W.129, A:W.129, A:A.146, A:A.150, A:F.151, A:I.170 Hydrogen bonds: A:A.41, A:T.42, A:T.42 Water bridges: A:T.42, A:S.143, A:S.143 78M.12: 6 residues within 4Å: Chain A: M.1, S.3, L.7, S.74, F.75 Ligands: GLY.24 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.7, A:L.7 Water bridges: A:F.75 78M.13: 6 residues within 4Å: Chain A: M.1, G.2, L.5, I.9 Ligands: 78M.17, 78M.19 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.5, A:I.9 Hydrogen bonds: A:G.2 Water bridges: A:S.3 78M.14: 5 residues within 4Å: Chain A: I.17, V.22, K.25, L.26 Ligands: 78M.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.17, A:V.22 Hydrogen bonds: A:K.25 78M.15: 8 residues within 4Å: Chain A: E.21, K.25, D.30, R.32, F.98, F.99 Ligands: 78M.14, 78M.17 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.98, A:F.98, A:F.98, A:F.99, A:F.99 Hydrogen bonds: A:E.21, A:D.30, A:N.33 Salt bridges: A:K.25, A:R.32 78M.16: 4 residues within 4Å: Chain A: Y.95, Y.176 Ligands: SO4.4, 78M.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.176, A:Y.176 Hydrogen bonds: A:Y.95, A:Y.95 78M.17: 7 residues within 4Å: Chain A: V.97, F.98, F.99, G.100, K.102 Ligands: 78M.13, 78M.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.97, A:F.98 Hydrogen bonds: A:G.100, A:K.102 78M.18: 3 residues within 4Å: Chain A: F.155, V.156, G.158 No protein-ligand interaction detected (PLIP) 78M.19: 1 residues within 4Å: Ligands: 78M.13 No protein-ligand interaction detected (PLIP) 78M.20: 5 residues within 4Å: Chain A: I.66, L.69, I.70, K.73, S.74 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.66, A:L.69 Hydrogen bonds: A:S.74 78M.21: 12 residues within 4Å: Chain A: K.50, F.57, F.61, F.65, F.115, F.126, W.129, L.130, F.133 Ligands: 78M.11, 78M.22, PGE.23 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.57, A:F.57, A:F.61, A:F.65, A:F.115, A:F.126 Hydrogen bonds: A:K.50 Salt bridges: A:K.50 78M.22: 4 residues within 4Å: Chain A: F.126, L.134, R.137 Ligands: 78M.21 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.126 Hydrogen bonds: A:R.137

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.23: 12 residues within 4Å: Chain A: A.41, T.42, T.45, K.50, G.53, V.54, F.57, W.129, F.133, F.193 Ligands: 78M.11, 78M.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.50

1 x GLY: GLYCINE(Non-covalent)

GLY.24: 5 residues within 4Å: Chain A: K.73, S.74, F.75, G.76 Ligands: 78M.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.74 Water bridges: A:I.77

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.
Show / Hide

Glycerol-3-phosphate acyltransferase

Related Entries With Identical Sequence