SMTL ID : 9g95.1

Lipid III flippase WzxE with NB10 nanobody in outward-facing conformation at 2.7552 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

5 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.351, A:V.355, A:F.363, A:W.413, A:W.413 Hydrogen bonds: A:S.370, A:S.370 MPG.2: 14 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 7 PLIP interactions: 7 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 Salt bridges: A:K.18 MPG.3: 7 residues within 4Å: Chain A: I.19, G.20, L.23, L.24, K.27, V.31 Ligands: OCT.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.19, A:L.23, A:K.27 MPG.4: 10 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.91, A:A.225, A:L.226 Hydrogen bonds: A:Q.46 MPG.5: 6 residues within 4Å: Chain A: G.22, R.45, I.48, T.49, L.180, I.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.49

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

OCT.6: 5 residues within 4Å: Chain A: A.86, M.87, F.91, W.210 Ligands: OCT.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.91, A:W.210 OCT.7: 5 residues within 4Å: Chain A: G.20, A.21, L.158, V.161 Ligands: MPG.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.158, A:V.161 OCT.8: 4 residues within 4Å: Chain A: P.208, S.209, W.210 Ligands: OCT.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.208, A:W.210 OCT.9: 1 residues within 4Å: Chain A: L.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.9, A:L.9 OCT.10: 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

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

SO4.11: 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 SO4.12: 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.13: 3 residues within 4Å: Chain A: K.358 Ligands: CL.14, CL.15 No protein-ligand interaction detected (PLIP)

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

CL.14: 1 residues within 4Å: Ligands: ZN.13 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: K.65, Y.66, Q.217 Ligands: ZN.13 Ligand excluded by 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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