- 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
- 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)
- 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.
- 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
- 8 x SO4: SULFATE ION(Non-functional Binders)
- 8 x OLB: (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)
- 3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 1 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)
- 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.