SMTL ID : 4q35.1

Structure of a membrane protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

hetero-1-1-mer

Ligands

6 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)

C8E.1: 14 residues within 4Å: Chain A: Y.112, Q.116, V.117, L.119, W.125, T.133, N.134, V.135, Y.140, M.142, M.154, Q.156, N.160, T.163 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.112, A:Y.112, A:V.117, A:T.133 Hydrogen bonds: A:T.133, A:Q.156, A:N.160, A:T.163 C8E.2: 8 residues within 4Å: Chain A: A.687, G.701, A.702, Y.703, S.715, M.716, L.717, Y.732 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.703, A:L.717 Water bridges: A:S.715 C8E.3: 8 residues within 4Å: Chain A: R.161, P.253, N.254, M.255, Y.278, L.279, S.280 Ligands: C8E.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.278, A:Y.278 Hydrogen bonds: A:R.161 C8E.7: 4 residues within 4Å: Chain A: I.616, S.617, W.620, I.642 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.620, A:W.620, A:I.642 Water bridges: A:S.617 C8E.9: 6 residues within 4Å: Chain A: Y.656, S.683, Y.705, T.707, N.708 Ligands: LDA.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.656, A:S.683, A:T.707 Water bridges: A:N.708 C8E.11: 15 residues within 4Å: Chain A: N.254, Y.278, L.279, S.280, Q.281, A.282, W.315, H.317, F.327, N.328, V.329, S.360, V.361 Ligands: C8E.3, LDA.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.282, A:W.315, A:F.327, A:V.361 Hydrogen bonds: A:S.280, A:Q.281

7 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.4: 4 residues within 4Å: Chain A: Y.514, V.558, Y.583, F.585 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.558, A:Y.583, A:F.585 LDA.5: 13 residues within 4Å: Chain A: Y.140, M.142, R.145, Q.146, F.170, H.189, A.196, V.220, G.221, D.222, G.760, L.761, S.762 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.140, A:F.170, A:F.170, A:H.189, A:A.196 Hydrogen bonds: A:G.760 LDA.6: 4 residues within 4Å: Chain A: W.311, Y.331, K.333, F.359 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.311, A:K.333 LDA.8: 4 residues within 4Å: Chain A: I.626, S.638, Y.656 Ligands: C8E.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.626, A:Y.656 LDA.10: 6 residues within 4Å: Chain A: V.430, L.432, A.455, T.456, H.457, N.479 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.430, A:L.432, A:A.455 LDA.12: 2 residues within 4Å: Chain A: W.325 Ligands: LDA.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.325, A:W.325 LDA.13: 7 residues within 4Å: Chain A: Q.281, A.282, M.321, F.327, V.361 Ligands: C8E.11, LDA.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.282, A:F.327, A:F.327, A:V.361

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

SO4.14: 4 residues within 4Å: Chain A: R.224, R.225, S.226, R.277 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.225, A:S.226 Salt bridges: A:R.224, A:R.277 SO4.15: 1 residues within 4Å: Chain A: R.774 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:D.67, A:R.774, A:R.774 Salt bridges: A:R.774 SO4.16: 3 residues within 4Å: Chain A: Y.644, R.646, R.650 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.644 Water bridges: A:Y.644 Salt bridges: A:R.646, A:R.650 SO4.17: 2 residues within 4Å: Chain A: R.619, R.646 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.619, A:R.646 SO4.18: 2 residues within 4Å: Chain A: R.326 Chain B: P.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.328 Water bridges: A:N.328 Salt bridges: A:R.326 SO4.19: 3 residues within 4Å: Chain A: R.645, D.647, E.648 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.648 Water bridges: A:R.645, A:N.782 Salt bridges: A:R.645 SO4.20: 2 residues within 4Å: Chain A: K.155, R.157 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.155, A:R.157 SO4.21: 4 residues within 4Å: Chain A: L.174, R.696, S.723, C.724 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.177, A:S.177, A:C.724 Water bridges: A:S.723 Salt bridges: A:R.696 SO4.22: 4 residues within 4Å: Chain B: V.104, R.106, R.132, Q.136 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.136 Water bridges: B:F.105, B:R.106, B:R.139, B:R.139 Salt bridges: B:R.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiao, S. et al., Structural basis for lipopolysaccharide insertion in the bacterial outer membrane. Nature (2014)

Release Date

2014-06-25

Peptides

LPS-assembly protein LptD: A
LPS-assembly lipoprotein LptE: 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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LPS-assembly protein LptD

LPS-assembly lipoprotein LptE