SMTL ID : 9g97.1

Lipid III flippase WzxE with NB10 nanobody in outward-facing conformation at 0.9688 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

hetero-1-1-mer

Ligands

7 x MPG: [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate(Non-covalent)

MPG.1: 12 residues within 4Å: Chain A: T.285, F.351, V.355, S.360, F.363, L.366, A.367, S.370, L.405, C.406, V.409, W.413 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.351, A:V.355, A:F.363, A:W.413 Hydrogen bonds: A:S.370, A:S.370 MPG.2: 15 residues within 4Å: Chain A: T.15, K.18, G.52, V.53, F.60, N.61, N.134, F.221, M.224, Q.267, A.271, Y.353, I.356, Y.364 Ligands: MPG.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.53, A:F.60, A:N.61, A:I.356 Hydrogen bonds: A:T.15, A:K.18, A:Q.267, A:Q.267 Water bridges: A:K.141, A:K.141, A:N.149 Salt bridges: A:K.18 MPG.3: 6 residues within 4Å: Chain A: G.20, L.23, L.24, K.27, V.31, L.322 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.23, A:K.27, A:L.322 MPG.4: 11 residues within 4Å: Chain A: Q.46, T.49, V.50, L.54, A.57, F.91, T.222, A.225, L.226, S.229 Ligands: MPG.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.54, A:T.222, A:A.225, A:L.226 Hydrogen bonds: A:Q.46 MPG.5: 8 residues within 4Å: Chain A: G.22, R.45, I.48, T.49, L.180, I.183, S.260 Ligands: MPG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.49 MPG.6: 14 residues within 4Å: Chain A: I.19, L.23, I.261, S.262, A.264, Y.265, F.268, V.312, L.323, L.324, S.325, F.335, L.339 Ligands: MPG.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.19, A:L.23, A:I.261, A:A.264, A:Y.265, A:Y.265, A:F.268, A:L.323, A:L.323, A:F.335, A:L.339 Hydrogen bonds: A:S.325 MPG.7: 12 residues within 4Å: Chain A: L.232, D.263, Q.267, K.345, Y.349, G.352, Y.353, Y.364, Q.371, Y.402 Ligands: MPG.2, MPG.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.232, A:Y.349, A:Y.353, A:Y.364

1 x LOP: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE(Non-covalent)

LOP.8: 13 residues within 4Å: Chain A: L.302, A.306, S.309, F.310, W.313, A.336, W.337, L.339, V.343, L.344, M.396, I.400, F.403 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.302, A:W.313, A:W.313, A:W.313, A:A.336, A:L.339, A:V.343, A:V.343, A:L.344, A:I.400, A:F.403, A:F.403

5 x OCT: N-OCTANE(Non-covalent)

OCT.9: 5 residues within 4Å: Chain A: A.86, M.87, F.91, W.210 Ligands: OCT.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.91, A:W.210 OCT.10: 4 residues within 4Å: Chain A: G.20, A.21, L.158, V.161 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.158, A:V.161 OCT.11: 4 residues within 4Å: Chain A: P.208, S.209, W.210 Ligands: OCT.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.208, A:W.210 OCT.12: 1 residues within 4Å: Chain A: L.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.9 OCT.13: 3 residues within 4Å: Chain A: M.128, G.129, W.132 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:M.128, A:W.132, A:W.132, A:W.132

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

CL.14: 2 residues within 4Å: Chain A: I.269, V.301 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Ligands: ZN.17 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: Y.66, Q.217, K.220 Ligands: ZN.17 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.15: 2 residues within 4Å: Chain A: K.287, R.416 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.287, A:R.416 SO4.16: 2 residues within 4Å: Chain A: R.316, R.332 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.316 Salt bridges: A:R.332

1 x ZN: ZINC ION(Non-covalent)

ZN.17: 3 residues within 4Å: Chain A: K.358 Ligands: CL.18, CL.19 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Le Bas, A. et al., Structure of WzxE the lipid III flippase for Enterobacterial Common Antigen polysaccharide. Open Biology (2025)

Release Date

2025-01-22

Peptides

Lipid III flippase: A
NB10 Nanobody: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Lipid III flippase

NB10 Nanobody

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