SMTL ID : 5n6h.1 (1 other biounit)

Structure of the membrane integral lipoprotein N-acyltransferase Lnt from E. coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

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

OLC.1: 9 residues within 4Å: Chain A: L.39, A.42, C.43, T.45, L.46, Y.51, S.90, N.93, I.440 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.42 Hydrogen bonds: A:N.93, A:N.93 OLC.2: 7 residues within 4Å: Chain A: R.33, F.40, A.66, L.67, F.69, N.70, V.208 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.40 Hydrogen bonds: A:R.33, A:F.69, A:N.70 Salt bridges: A:R.33 OLC.3: 13 residues within 4Å: Chain A: W.141, A.191, F.194, L.195, M.198, L.202, N.211, R.213, P.214, V.217, L.221, L.514, F.518 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.141, A:W.141, A:A.191, A:F.194, A:L.195, A:L.202, A:V.217, A:V.217, A:L.221, A:L.514, A:F.518 Hydrogen bonds: A:N.211 OLC.4: 6 residues within 4Å: Chain A: Q.30, R.72, Q.75, A.78, F.81 Ligands: OLC.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.78, A:F.81, A:F.81 Hydrogen bonds: A:R.72, A:Q.75 OLC.5: 9 residues within 4Å: Chain A: L.151, V.154, N.508, W.509, W.512, T.515, A.516, G.519 Ligands: OLC.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.151, A:V.154, A:W.512, A:W.512, A:A.516 Hydrogen bonds: A:N.508, A:W.509 OLC.6: 10 residues within 4Å: Chain A: R.72, P.73, L.74, A.77, A.78, L.123, G.126, L.127, R.134 Ligands: OLC.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.73, A:L.74, A:A.77, A:A.78 Hydrogen bonds: A:R.72 OLC.7: 6 residues within 4Å: Chain A: R.31, L.38, C.82, F.85, I.111, F.112 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.85, A:I.111 OLC.8: 7 residues within 4Å: Chain A: V.154, F.157, E.190, N.508, W.512 Ligands: OLC.5, GOL.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.154, A:F.157, A:F.157, A:W.512, A:W.512 Hydrogen bonds: A:E.190 OLC.9: 3 residues within 4Å: Chain A: L.183, I.186, R.505 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.183 Hydrogen bonds: A:R.505, A:R.505 OLC.10: 4 residues within 4Å: Chain A: F.102, F.361, P.366, P.381 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.361 OLC.11: 8 residues within 4Å: Chain A: L.38, A.42, F.85, G.89, N.93, Y.96, V.114, V.115 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.38, A:A.42, A:F.85, A:V.115 Hydrogen bonds: A:N.93 OLC.12: 7 residues within 4Å: Chain A: M.62, A.206, L.207, R.210, N.211, W.212, L.215 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.206, A:L.207, A:L.215

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 2 residues within 4Å: Chain A: W.161, L.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.163, A:L.163 GOL.14: 3 residues within 4Å: Chain A: F.157, W.161 Ligands: OLC.8 No protein-ligand interaction detected (PLIP) GOL.15: 2 residues within 4Å: Chain A: A.223, F.226 No protein-ligand interaction detected (PLIP) GOL.16: 7 residues within 4Å: Chain A: E.259, L.262, L.263, L.266, Q.297, P.299, F.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.259, A:Q.297, A:F.300 GOL.17: 3 residues within 4Å: Chain A: R.29, Q.30, R.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.30, A:R.31 GOL.18: 6 residues within 4Å: Chain A: G.278, K.279, S.281, K.311, G.312, S.313 No protein-ligand interaction detected (PLIP) GOL.19: 1 residues within 4Å: Chain A: F.364 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wiktor, M. et al., Structural insights into the mechanism of the membrane integral N-acyltransferase step in bacterial lipoprotein synthesis. Nat Commun (2017)

Release Date

2017-07-12

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.
Show / Hide

Apolipoprotein N-acyltransferase

Related Entries With Identical Sequence