SMTL ID : 6xlp.1

Structure of the essential inner membrane lipopolysaccharide-PbgA complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x VJ4- VJ1- KDO: 2-deoxy-3-O-[(1R,3R)-1,3-dihydroxytetradecyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-alpha-D-glucopyranose-(6-1)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)]1,5-anhydro-2-deoxy-2-{[(1S,3R)-1-hydroxy-3-(pentanoyloxy)undecyl]amino}-4-O-phosphono-D-glucitol

VJ4-VJ1-KDO.1: 15 residues within 4Å: Chain A: F.184, I.185, H.188, V.189, I.192, W.193, Y.213, M.215, T.216, A.217, R.218, R.219, F.220 Ligands: OLB.16, PG4.19 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:R.219, A:R.219, A:T.216, A:T.216, A:T.216, A:R.218, A:R.219, A:R.219 Hydrophobic interactions: A:F.184, A:I.185, A:H.188, A:V.189, A:V.189, A:I.192, A:A.217, A:F.220, A:F.220, A:F.220 Water bridges: A:R.206, A:Y.213, A:P.214, A:F.220 Salt bridges: A:R.219, A:R.219

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

SO4.2: 5 residues within 4Å: Chain A: R.164, S.165, R.168, R.169 Ligands: OLB.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.164, A:S.165 Salt bridges: A:R.169 SO4.3: 3 residues within 4Å: Chain A: R.170, R.171, R.174 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.170, A:R.171, A:R.174 SO4.4: 2 residues within 4Å: Chain A: R.557, R.565 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.557, A:R.565 SO4.5: 2 residues within 4Å: Chain A: G.262, R.395 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.395 SO4.6: 3 residues within 4Å: Chain A: T.48, T.49, L.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.50 SO4.7: 4 residues within 4Å: Chain A: Q.503, P.511, A.512, R.527 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.503, A:A.512 Water bridges: A:S.513, A:S.513, A:N.523, A:R.527 Salt bridges: A:R.527 SO4.8: 2 residues within 4Å: Chain A: Q.281, S.420 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.281, A:S.420, A:S.420 SO4.9: 3 residues within 4Å: Chain A: W.46, R.53 Ligands: OLB.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.46 Salt bridges: A:R.53

8 x OLB: (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLB.10: 11 residues within 4Å: Chain A: S.20, H.23, L.27, I.30, S.65, F.66, F.69, R.170, R.174, L.180, F.181 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.23, A:L.27, A:I.30, A:F.69, A:L.180, A:F.181, A:F.181 Hydrogen bonds: A:S.20, A:H.23, A:R.174 OLB.11: 7 residues within 4Å: Chain A: A.51, I.54, F.179, V.190, W.193, Y.199 Ligands: OLB.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.51, A:I.54, A:F.179, A:V.190 Water bridges: A:Y.199, A:Y.199 OLB.12: 9 residues within 4Å: Chain A: I.106, E.109, R.113, V.126, E.133, R.136, D.137, L.140, M.141 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.106, A:E.109, A:V.126, A:L.140, A:L.140 Hydrogen bonds: A:E.109 Salt bridges: A:R.113 OLB.13: 10 residues within 4Å: Chain A: W.24, L.27, L.31, F.155, K.162, S.165, L.166, R.169, L.176 Ligands: SO4.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.24, A:L.27, A:L.31, A:L.31, A:F.155, A:L.166, A:L.176 Hydrogen bonds: A:S.165 Salt bridges: A:R.169 OLB.14: 4 residues within 4Å: Chain A: L.50, I.54 Ligands: OLB.11, OLB.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.54 OLB.15: 5 residues within 4Å: Chain A: L.50, R.53, I.54, Y.57 Ligands: OLB.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.54, A:Y.57 Salt bridges: A:R.53 OLB.16: 3 residues within 4Å: Chain A: N.197, L.226 Ligands: VJ4-VJ1-KDO.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.197, A:N.197 OLB.17: 6 residues within 4Å: Chain A: S.38, L.41, F.42, W.46, Y.57 Ligands: SO4.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.41, A:F.42, A:W.46, A:Y.57, A:Y.57 Hydrogen bonds: A:W.46

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.18: 5 residues within 4Å: Chain A: R.218, E.222, L.227, A.229, Q.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.233 PG4.19: 15 residues within 4Å: Chain A: Y.55, S.59, H.63, F.66, S.187, H.188, Q.205, R.206, N.208, L.209, L.211, S.212, Y.213, P.214 Ligands: VJ4-VJ1-KDO.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.63, A:N.208, A:L.209, A:S.212, A:Y.213 Water bridges: A:L.211 PG4.20: 10 residues within 4Å: Chain A: N.119, S.319, D.535, N.536, D.537, T.538, L.539, L.550, N.551, N.552 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.119

1 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.21: 11 residues within 4Å: Chain A: T.71, A.97, G.100, M.101, D.107, H.117, L.118, P.120, W.123, P.210, L.211 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.210 Hydrogen bonds: A:W.123, A:L.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clairfeuille, T. et al., Structure of the essential inner membrane lipopolysaccharide-PbgA complex. Nature (2020)

Release Date

2020-08-26

Peptides

LPS binding protein: 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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LPS binding protein