SMTL ID : 8aq3.1

In surfo structure of the membrane integral lipoprotein N-acyltransferase Lnt from E. coli in complex with PE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

monomer

Ligands

3 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.1: 27 residues within 4Å: Chain A: W.94, V.95, S.98, I.99, L.163, F.166, Q.253, K.256, W.257, E.287, S.288, K.355, V.359, P.360, F.361, G.362, E.363, P.381, M.382, S.383, A.407, Y.408, S.431, N.432, D.433, W.435, F.436 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:W.94, A:V.95, A:I.99, A:F.166, A:F.166, A:V.359, A:F.361, A:A.407, A:Y.408, A:W.435, A:W.435, A:F.436, A:F.436 Hydrogen bonds: A:Q.253, A:S.288, A:S.288, A:M.382, A:Y.408, A:N.432 Salt bridges: A:K.256, A:K.355 6OU.2: 19 residues within 4Å: Chain A: A.42, C.43, T.45, L.46, S.49, P.50, Y.51, D.52, S.90, N.93, V.97, D.177, K.438, S.439, I.440, W.443, R.450, I.478 Ligands: LMT.18 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.42, A:T.45, A:L.46, A:L.46, A:P.50, A:P.50, A:W.443, A:I.478 Hydrogen bonds: A:N.93, A:K.438 6OU.20: 12 residues within 4Å: Chain A: L.151, V.154, F.157, G.160, W.161, E.414, N.508, W.509, W.512, T.515, A.516, G.519 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.151, A:V.154, A:V.154, A:F.157, A:F.157, A:W.512, A:W.512, A:T.515, A:A.516 Hydrogen bonds: A:G.160, A:E.414, A:N.508, A:N.508

4 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)

PG5.3: 3 residues within 4Å: Chain A: F.226, R.229, Y.230 No protein-ligand interaction detected (PLIP) PG5.4: 3 residues within 4Å: Chain A: R.505 Ligands: GOL.15, GOL.16 No protein-ligand interaction detected (PLIP) PG5.5: 4 residues within 4Å: Chain A: G.278, S.281, K.311, G.312 No protein-ligand interaction detected (PLIP) PG5.6: 3 residues within 4Å: Chain A: P.366, L.367 Ligands: GOL.11 No protein-ligand interaction detected (PLIP)

1 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.7: 7 residues within 4Å: Chain A: I.27, E.28, R.33, A.66, L.67, N.70, V.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.28, A:R.33

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.8: 2 residues within 4Å: Chain A: Y.270, F.300 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 3 residues within 4Å: Chain A: R.72, L.74, Q.75 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.74, A:Q.75 Salt bridges: A:R.72

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 2 residues within 4Å: Chain A: Y.96, G.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.96 GOL.11: 5 residues within 4Å: Chain A: T.164, F.364, P.366 Ligands: PG5.6, LMT.13 No protein-ligand interaction detected (PLIP) GOL.14: 1 residues within 4Å: Ligands: LMT.18 No protein-ligand interaction detected (PLIP) GOL.15: 2 residues within 4Å: Chain A: R.505 Ligands: PG5.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.505 GOL.16: 2 residues within 4Å: Chain A: Q.232 Ligands: PG5.4 No protein-ligand interaction detected (PLIP)

5 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.12: 2 residues within 4Å: Chain A: R.417, W.509 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.417, A:R.417, A:D.418 LMT.13: 3 residues within 4Å: Chain A: W.161, L.163 Ligands: GOL.11 No protein-ligand interaction detected (PLIP) LMT.17: 2 residues within 4Å: Chain A: D.52, P.55 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.55 LMT.18: 5 residues within 4Å: Chain A: A.42, F.85, G.89 Ligands: 6OU.2, GOL.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.42, A:F.85 LMT.19: 2 residues within 4Å: Chain A: C.43, V.53 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.53

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.21: 2 residues within 4Å: Chain A: R.309, G.342 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain A: T.140, W.141, K.209, R.213 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain A: R.29, R.31 Ligand excluded by PLIP

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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