SMTL ID : 8aq2.1

In meso structure of the membrane integral lipoprotein N-acyltransferase Lnt from P. aeruginosa covalently linked with TITC

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

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

OLC.1: 7 residues within 4Å: Chain A: A.37, A.40, L.41, L.44, L.61, A.88 Ligands: OLC.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.37, A:A.40, A:L.44, A:L.61 OLC.2: 17 residues within 4Å: Chain A: I.93, S.96, I.97, L.111, G.114, F.115, E.289, V.354, P.355, F.356, G.357, E.358, W.429, F.430 Ligands: OLC.3, OLC.4, QGT.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.93, A:I.97, A:L.111, A:F.115, A:F.115, A:F.356 Hydrogen bonds: A:E.289 OLC.3: 9 residues within 4Å: Chain A: S.96, L.111, L.258, F.356, I.370, L.375, P.376, W.429 Ligands: OLC.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.111, A:F.356, A:F.356, A:F.356, A:I.370 OLC.4: 13 residues within 4Å: Chain A: F.115, G.118, V.119, F.121, F.122, L.162, P.355, F.356, Y.359, P.361 Ligands: OLC.2, QGT.11, GOL.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.115, A:V.119, A:F.121, A:F.122, A:P.355, A:F.356 OLC.5: 6 residues within 4Å: Chain A: D.50, Y.51, P.53, L.54, L.57 Ligands: OLC.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.51, A:L.54, A:L.57 Hydrogen bonds: A:F.49 OLC.6: 7 residues within 4Å: Chain A: M.21, I.56, R.67, L.202, V.203, P.206, W.226 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.56 Hydrogen bonds: A:R.67, A:R.67 OLC.7: 4 residues within 4Å: Chain A: K.72, W.76, F.121 Ligands: OLC.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.76, A:F.121, A:F.121 Salt bridges: A:K.72 OLC.8: 12 residues within 4Å: Chain A: F.83, G.87, S.91, W.92, Y.94, V.95, M.112, L.113, T.116, T.432, S.433 Ligands: GOL.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.83, A:F.83, A:Y.94, A:L.113, A:T.116 Hydrogen bonds: A:T.432 OLC.9: 7 residues within 4Å: Chain A: W.29, W.76, W.79, W.80, G.114, G.118 Ligands: OLC.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.76, A:W.79 OLC.10: 5 residues within 4Å: Chain A: L.514, W.515, G.519, L.522, Q.525 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.514, A:W.515, A:W.515, A:W.515 Hydrogen bonds: A:L.522, A:Q.525

2 x QGT: ~{N}-tridecylmethanethioamide(Covalent)

QGT.11: 13 residues within 4Å: Chain A: I.93, F.115, L.162, T.163, G.164, F.165, K.350, C.402, Y.403, F.430, H.439 Ligands: OLC.2, OLC.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.93, A:F.115, A:L.162, A:F.165, A:F.165, A:F.430 Hydrogen bonds: A:H.439 QGT.12: 1 residues within 4Å: Chain A: C.133 No protein-ligand interaction detected (PLIP)

1 x FLC: CITRATE ANION(Non-covalent)

FLC.13: 2 residues within 4Å: Chain A: L.295, Y.334 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.334

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 2 residues within 4Å: Chain A: Y.231, H.235 No protein-ligand interaction detected (PLIP) GOL.15: 3 residues within 4Å: Chain A: W.160, L.162 Ligands: OLC.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.160, A:L.162 GOL.16: 1 residues within 4Å: Ligands: OLC.8 No protein-ligand interaction detected (PLIP) GOL.17: 2 residues within 4Å: Chain A: W.79, A.117 No protein-ligand interaction detected (PLIP) GOL.18: 3 residues within 4Å: Chain A: K.72, W.128, R.132 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.132 GOL.19: 2 residues within 4Å: Chain A: W.23 Ligands: GOL.20 No protein-ligand interaction detected (PLIP) GOL.20: 8 residues within 4Å: Chain A: R.17, G.18, S.19, H.20, M.21, R.22, W.23 Ligands: GOL.19 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.18, A:S.19, A:H.20, A:M.21, A:R.22, A:W.23, A:W.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smithers, L. et al., Structure snapshots reveal the mechanism of a bacterial membrane lipoprotein N -acyltransferase. Sci Adv (2023)

Release Date

2023-07-12

Peptides

Apolipoprotein N-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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Apolipoprotein N-acyltransferase

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