SMTL ID : 8aq4.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

monomer

Ligands

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

PG5.1: 2 residues within 4Å: Chain A: L.224, P.227 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.224 PG5.4: 3 residues within 4Å: Chain A: S.346, E.348, S.349 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.346, A:E.348 PG5.10: 2 residues within 4Å: Chain A: F.226, R.229 No protein-ligand interaction detected (PLIP) PG5.11: 3 residues within 4Å: Chain A: V.365, P.366 Ligands: GOL.17 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.417, R.505, T.506, W.509 Ligands: GOL.3, GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.417, A:R.417, A:W.509 GOL.3: 2 residues within 4Å: Ligands: GOL.2, GOL.5 No protein-ligand interaction detected (PLIP) GOL.5: 7 residues within 4Å: Chain A: E.414, R.417, T.506, G.507, W.509 Ligands: GOL.2, GOL.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.414 GOL.15: 1 residues within 4Å: Ligands: LMT.19 No protein-ligand interaction detected (PLIP) GOL.16: 1 residues within 4Å: Chain A: G.107 No protein-ligand interaction detected (PLIP) GOL.17: 5 residues within 4Å: Chain A: L.163, T.164, F.364 Ligands: PG5.11, LMT.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.164, A:T.164

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

6OU.6: 17 residues within 4Å: Chain A: L.39, A.42, C.43, L.46, S.49, P.50, Y.51, D.52, S.90, N.93, V.97, K.438, S.439, W.443, F.446, Q.447, R.450 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.42, A:L.46, A:P.50, A:Y.51, A:W.443, A:W.443, A:W.443, A:F.446, A:Q.447 Hydrogen bonds: A:N.93, A:K.438, A:K.438 6OU.8: 19 residues within 4Å: Chain A: V.95, S.98, Y.120, K.256, W.257, E.287, S.288, K.355, F.361, G.362, E.363, F.377, P.381, M.382, C.407, N.432, W.435, F.436 Ligands: QGT.7 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.95, A:Y.120, A:F.361, A:F.361, A:F.377, A:W.435, A:F.436 Hydrogen bonds: A:Q.253, A:E.287, A:S.288, A:S.288, A:K.355, A:G.362, A:N.432 Salt bridges: A:K.256 6OU.9: 9 residues within 4Å: Chain A: L.151, V.154, F.157, W.161, E.414, N.508, W.509, W.512, G.519 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.151, A:V.154, A:F.157, A:F.157, A:W.512, A:W.512, A:W.512 Hydrogen bonds: A:N.508, A:W.512

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

QGT.7: 12 residues within 4Å: Chain A: V.95, L.117, Y.120, L.163, F.166, V.359, P.360, C.407, Y.408, F.436, H.445 Ligands: 6OU.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.95, A:L.117, A:Y.120, A:L.163, A:F.166, A:F.166, A:F.166, A:V.359, A:P.360, A:F.436

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

PG6.12: 6 residues within 4Å: Chain A: R.33, F.40, A.66, L.67, N.70, V.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.33, A:N.70

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

TRS.13: 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.14: 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

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

LMT.18: 2 residues within 4Å: Chain A: W.54, P.55 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.54 LMT.19: 4 residues within 4Å: Chain A: F.85, G.89, V.115 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.85, A:V.115 LMT.20: 6 residues within 4Å: Chain A: L.123, L.127, W.161, L.163, T.164 Ligands: GOL.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.123, A:L.127 Hydrogen bonds: A:L.163

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

CL.21: 3 residues within 4Å: Chain A: R.309, K.341, 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

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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