- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.70 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 7 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.8: 2 residues within 4Å:- Chain A: C.255, N.282
No protein-ligand interaction detected (PLIP)NAG.9: 2 residues within 4Å:- Chain A: L.441, N.467
2 PLIP interactions:2 interactions with chain A- Water bridges: A:N.467, A:N.467
NAG.10: 2 residues within 4Å:- Chain B: E.46, N.96
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:E.46, B:N.96
NAG.15: 2 residues within 4Å:- Chain C: E.46, N.96
No protein-ligand interaction detected (PLIP)NAG.20: 1 residues within 4Å:- Chain D: N.467
No protein-ligand interaction detected (PLIP)- 2 x LP4: 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose(Non-covalent)
LP4.11: 15 residues within 4Å:- Chain A: K.238
- Chain B: I.28, I.34, V.43, V.45, F.47, L.56, Y.84, I.99, P.100, F.101, S.102
- Ligands: LP5.12, DAO.13, MYR.14
11 PLIP interactions:9 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:I.28, B:V.43, B:V.45, B:F.47, B:L.56, B:I.99, B:F.101
- Hydrogen bonds: B:S.102, B:S.102
- Water bridges: A:K.238
- Salt bridges: A:K.238
LP4.16: 13 residues within 4Å:- Chain C: I.34, V.43, L.56, L.76, Y.84, I.99, P.100, F.101, S.102
- Chain D: K.238
- Ligands: LP5.17, DAO.18, MYR.19
8 PLIP interactions:1 interactions with chain D, 7 interactions with chain C- Salt bridges: D:K.238
- Hydrophobic interactions: C:I.34, C:V.43, C:L.56, C:L.76, C:I.99
- Hydrogen bonds: C:S.102, C:S.102
- 2 x LP5: (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE(Non-covalent)
LP5.12: 19 residues within 4Å:- Chain B: I.34, V.64, L.69, R.72, F.103, E.104, G.105, I.106, F.108, P.109, C.115
- Chain D: S.388, R.409, E.412, F.413, S.414
- Ligands: LP4.11, DAO.13, MYR.14
15 PLIP interactions:5 interactions with chain D, 10 interactions with chain B- Hydrophobic interactions: D:F.413, B:I.34, B:L.69, B:F.103, B:F.103, B:F.108, B:F.108
- Hydrogen bonds: D:S.388, D:S.388, D:R.409, D:R.409, B:E.104, B:E.104, B:I.106
- Water bridges: B:R.72
LP5.17: 16 residues within 4Å:- Chain A: S.388, R.409, F.413, S.414
- Chain C: L.69, R.72, F.103, E.104, G.105, I.106, F.108, P.109, F.133
- Ligands: LP4.16, DAO.18, MYR.19
15 PLIP interactions:12 interactions with chain C, 3 interactions with chain A- Hydrophobic interactions: C:L.69, C:F.103, C:F.103, C:I.106, C:F.108, C:F.108, C:F.133, C:F.133, A:F.413
- Hydrogen bonds: C:E.104, C:E.104, C:E.104, C:I.106, A:S.388, A:R.409
- 2 x DAO: LAURIC ACID(Non-covalent)
DAO.13: 7 residues within 4Å:- Chain B: L.60, I.62, E.74, F.108, Y.113
- Ligands: LP4.11, LP5.12
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:L.60, B:I.62, B:I.62, B:F.108, B:Y.113
DAO.18: 8 residues within 4Å:- Chain C: L.60, I.62, R.72, E.74, Y.113
- Ligands: LP4.16, LP5.17, MYR.19
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:L.60, C:I.62, C:Y.113
- 2 x MYR: MYRISTIC ACID(Non-covalent)
MYR.14: 7 residues within 4Å:- Chain B: I.28, F.58, F.129, L.131, F.133
- Ligands: LP4.11, LP5.12
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:I.28, B:F.129, B:L.131, B:F.133
- Hydrogen bonds: A:K.238
MYR.19: 8 residues within 4Å:- Chain C: F.58, E.74, A.117, L.131, F.133
- Ligands: LP4.16, LP5.17, DAO.18
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:F.58, C:F.58, C:E.74, C:A.117, C:L.131, C:F.133
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wang, Y. et al., TLR4/MD-2 activation by a synthetic agonist with no similarity to LPS. Proc.Natl.Acad.Sci.USA (2016)
- Release Date
- 2016-04-27
- Peptides
- Toll-like receptor 4, Variable lymphocyte receptor B chimera: AD
Lymphocyte antigen 96: BC - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
BB
CC
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.70 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 7 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x LP4: 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose(Non-covalent)
- 2 x LP5: (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE(Non-covalent)
- 2 x DAO: LAURIC ACID(Non-covalent)
- 2 x MYR: MYRISTIC ACID(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wang, Y. et al., TLR4/MD-2 activation by a synthetic agonist with no similarity to LPS. Proc.Natl.Acad.Sci.USA (2016)
- Release Date
- 2016-04-27
- Peptides
- Toll-like receptor 4, Variable lymphocyte receptor B chimera: AD
Lymphocyte antigen 96: BC - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
BB
CC
D