SMTL ID : 8q2p.1

Structure of the membrane integral lipoprotein N-acyltransferase Lnt from E. coli by using Se-MAG for the the lipid cubic phase crystallization

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

15 x IRY: [(2~{S})-2,3-bis(oxidanyl)propyl] 8-hexylselanyloctanoate

IRY.1: 12 residues within 4Å: Chain A: R.13, F.20, I.39, M.42, G.43, A.46, L.47, F.49, N.50, L.187, V.188 Ligands: IRY.17 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.20, A:F.20, A:F.20, A:I.39, A:A.46 Hydrogen bonds: A:R.13, A:R.13, A:F.49, A:F.49, A:N.50 IRY.13: 18 residues within 4Å: Chain A: V.75, L.97, Y.100, L.143, G.145, F.146, W.148, V.339, P.340, F.341, P.346, C.387, Y.388, N.412, D.413, F.416, H.425 Ligands: IRY.14 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.75, A:L.97, A:Y.100, A:L.143, A:L.143, A:F.146, A:P.340, A:F.341, A:P.346, A:F.416 Hydrogen bonds: A:D.413 Water bridges: A:E.267 IRY.14: 14 residues within 4Å: Chain A: S.78, I.79, L.93, L.96, L.97, Y.100, V.339, F.341, G.342, E.343, W.415, F.416 Ligands: OLC.4, IRY.13 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.79, A:I.79, A:L.96, A:Y.100, A:F.341 Hydrogen bonds: A:S.78 Water bridges: A:K.335 IRY.15: 7 residues within 4Å: Chain A: L.163, I.166, W.213, P.482 Ligands: OLC.3, PG5.10, IRY.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.166, A:W.213, A:P.482 IRY.16: 12 residues within 4Å: Chain A: W.121, A.125, A.171, F.174, M.178, L.182, R.193, P.194, V.197, L.494, F.498 Ligands: IRY.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.121, A:A.125, A:F.174, A:V.197, A:L.494 IRY.17: 9 residues within 4Å: Chain A: M.42, A.186, L.187, R.190, N.191, W.192, L.195 Ligands: IRY.1, IRY.23 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.186 IRY.18: 13 residues within 4Å: Chain A: F.65, G.69, N.73, W.74, Y.76, V.77, V.94, V.95, G.417, K.418, S.419 Ligands: OLC.2, OLC.12 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.65, A:Y.76, A:Y.76, A:V.77, A:V.94, A:V.95 Hydrogen bonds: A:K.418 IRY.19: 12 residues within 4Å: Chain A: P.53, L.54, A.57, A.58, F.61, L.103, G.106, L.107, G.110, V.111, R.114 Ligands: OLC.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.54, A:A.57, A:A.58, A:F.61 Hydrogen bonds: A:R.114 Water bridges: A:L.54 IRY.20: 11 residues within 4Å: Chain A: L.131, V.134, E.394, T.486, G.487, N.488, W.489, W.492, A.496, G.499 Ligands: IRY.21 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.131, A:W.492 Hydrogen bonds: A:E.394, A:T.486, A:N.488, A:W.489 IRY.21: 7 residues within 4Å: Chain A: Q.133, F.137, L.138, E.170, N.488, W.492 Ligands: IRY.20 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.137, A:F.137, A:L.138, A:W.492 Hydrogen bonds: A:Q.133, A:N.488 Water bridges: A:E.136, A:Q.150, A:E.170 IRY.22: 7 residues within 4Å: Chain A: W.34, P.159, A.203, L.204, F.206, P.207 Ligands: IRY.23 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.159, A:P.159, A:A.203, A:F.206, A:F.206 IRY.23: 10 residues within 4Å: Chain A: Y.31, D.32, V.33, W.34, P.35, I.38, M.42 Ligands: GOL.11, IRY.17, IRY.22 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.34, A:P.35, A:I.38, A:I.38 Hydrogen bonds: A:Y.31, A:W.34 IRY.24: 12 residues within 4Å: Chain A: L.14, L.15, L.18, F.61, C.62, F.65, V.95, L.96, A.99 Ligands: OLC.2, OLC.4, IRY.25 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.14, A:F.65, A:F.65, A:V.95, A:A.99 IRY.25: 6 residues within 4Å: Chain A: G.87, P.88, I.91, F.92 Ligands: OLC.2, IRY.24 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.88, A:P.88, A:F.92 Hydrogen bonds: A:G.87 IRY.26: 5 residues within 4Å: Chain A: R.485, T.486, W.489, L.497 Ligands: OLC.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.489 Hydrogen bonds: A:W.489

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

OLC.2: 8 residues within 4Å: Chain A: F.65, Y.76, I.91, V.95 Ligands: OLC.4, IRY.18, IRY.24, IRY.25 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.65, A:I.91, A:I.91, A:V.95 OLC.3: 8 residues within 4Å: Chain A: I.166, M.167, P.482, R.485, T.486, L.494 Ligands: IRY.15, IRY.26 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.166, A:L.494 OLC.4: 8 residues within 4Å: Chain A: F.61, L.96, A.99, Y.100 Ligands: OLC.2, IRY.14, IRY.19, IRY.24 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.61, A:F.61, A:F.61 Hydrogen bonds: A:L.96 OLC.12: 12 residues within 4Å: Chain A: L.19, A.22, C.23, T.25, L.26, Y.31, S.70, N.73, W.74, S.419, I.420 Ligands: IRY.18 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.22, A:L.26, A:L.26 Hydrogen bonds: A:N.73, A:N.73, A:W.74, A:I.420

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: Y.250, F.280, A.283, E.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.250 GOL.6: 7 residues within 4Å: Chain A: G.258, K.259, S.260, S.261, K.291, G.292, S.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.260, A:K.291 GOL.7: 4 residues within 4Å: Chain A: W.141, V.142, L.143 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.143, A:T.144 GOL.8: 8 residues within 4Å: Chain A: L.143, T.144, F.344, V.345, P.346, L.347 Ligands: GOL.7, GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.347 GOL.9: 6 residues within 4Å: Chain A: F.344, L.347, E.348, S.349, R.367 Ligands: GOL.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.347, A:S.349, A:S.349, A:R.367, A:R.367 GOL.11: 2 residues within 4Å: Chain A: V.33 Ligands: IRY.23 No protein-ligand interaction detected (PLIP)

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

PG5.10: 4 residues within 4Å: Chain A: L.204, P.205, L.208 Ligands: IRY.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boland, C. et al., Se-MAG Is a Convenient Additive for Experimental Phasing and Structure Determination of Membrane Proteins Crystallised by the Lipid Cubic Phase (In Meso) Method. Crystals (2023)

Release Date

2024-05-15

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