- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.5: 3 residues within 4Å:- Chain A: G.145, H.146, N.171
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.171
NAG.6: 4 residues within 4Å:- Chain B: G.145, H.146, K.148, N.171
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:K.148, B:K.148
NAG.7: 2 residues within 4Å:- Chain C: F.48, N.98
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:F.48
- Hydrogen bonds: C:N.98
NAG.13: 2 residues within 4Å:- Chain D: F.48, N.98
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)
LP4.8: 15 residues within 4Å:- Chain A: R.262
- Chain C: I.47, Y.49, F.60, Y.86, F.88, I.101, S.102, F.103, S.104, F.135
- Ligands: LP5.9, DAO.10, MYR.11, KDO.12
13 PLIP interactions:11 interactions with chain C, 2 interactions with chain A- Hydrophobic interactions: C:I.47, C:Y.49, C:F.60, C:F.88, C:I.101, C:I.101, C:F.135
- Hydrogen bonds: C:S.102, C:S.102, C:S.104, C:S.104
- Salt bridges: A:R.262, A:R.262
LP4.14: 15 residues within 4Å:- Chain B: R.262
- Chain D: L.45, I.47, F.60, Y.86, F.88, I.101, S.102, F.103, S.104, F.105
- Ligands: LP5.15, DAO.16, MYR.17, KDO.18
13 PLIP interactions:11 interactions with chain D, 2 interactions with chain B- Hydrophobic interactions: D:L.45, D:I.47, D:F.60, D:F.60, D:F.88, D:I.101, D:F.103
- Hydrogen bonds: D:S.102, D:S.102, D:S.104, D:S.104
- Salt bridges: B:R.262, B:R.262
- 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)
LP5.9: 18 residues within 4Å:- Chain B: S.413, Q.434, E.437, F.438
- Chain C: I.36, L.38, I.64, V.66, L.71, R.74, F.105, K.106, I.108, F.110, F.135
- Ligands: LP4.8, DAO.10, MYR.11
18 PLIP interactions:14 interactions with chain C, 4 interactions with chain B- Hydrophobic interactions: C:I.36, C:L.38, C:I.64, C:V.66, C:L.71, C:F.105, C:F.105, C:F.105, C:F.110, C:F.110, C:F.135, B:F.438, B:F.438
- Hydrogen bonds: C:K.106, C:K.106, C:K.106, B:S.413, B:Q.434
LP5.15: 15 residues within 4Å:- Chain A: S.413, Q.434, E.437, F.438
- Chain D: V.66, L.71, R.74, F.105, K.106, I.108, F.110, F.135
- Ligands: LP4.14, DAO.16, MYR.17
16 PLIP interactions:13 interactions with chain D, 3 interactions with chain A- Hydrophobic interactions: D:V.66, D:L.71, D:F.105, D:F.105, D:F.105, D:I.108, D:F.110, D:F.110, D:F.135, A:F.438
- Hydrogen bonds: D:K.106, D:K.106, D:K.106, D:I.108, A:S.413, A:Q.434
- 2 x DAO: LAURIC ACID(Non-covalent)
DAO.10: 11 residues within 4Å:- Chain C: L.38, L.62, I.64, R.74, E.76, F.110, Y.115, I.137
- Ligands: LP4.8, LP5.9, MYR.11
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:L.38, C:L.62, C:I.64, C:F.110, C:Y.115, C:I.137
DAO.16: 7 residues within 4Å:- Chain D: L.62, R.74, Y.115, I.137
- Ligands: LP4.14, LP5.15, MYR.17
4 PLIP interactions:4 interactions with chain D- Hydrophobic interactions: D:L.62, D:Y.115, D:Y.115, D:I.137
- 2 x MYR: MYRISTIC ACID(Non-covalent)
MYR.11: 6 residues within 4Å:- Chain C: I.47, F.60, E.76
- Ligands: LP4.8, LP5.9, DAO.10
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:I.47, C:F.60, C:F.60
MYR.17: 9 residues within 4Å:- Chain D: I.30, I.47, F.60, L.62, E.76, Y.86
- Ligands: LP4.14, LP5.15, DAO.16
5 PLIP interactions:5 interactions with chain D- Hydrophobic interactions: D:I.30, D:I.47, D:F.60, D:L.62
- Hydrogen bonds: D:Y.86
- 2 x KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid(Non-covalent)
KDO.12: 3 residues within 4Å:- Chain A: Y.294, K.339
- Ligands: LP4.8
No protein-ligand interaction detected (PLIP)KDO.18: 4 residues within 4Å:- Chain B: Y.294, K.339
- Chain D: K.106
- Ligands: LP4.14
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: B:Y.294, D:K.106
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ohto, U. et al., Structural analyses of human Toll-like receptor 4 polymorphisms D299G and T399I. J.Biol.Chem. (2012)
- Release Date
- 2012-10-17
- Peptides
- Toll-like receptor 4: AB
Lymphocyte antigen 96: CD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 4 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)
- 2 x KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ohto, U. et al., Structural analyses of human Toll-like receptor 4 polymorphisms D299G and T399I. J.Biol.Chem. (2012)
- Release Date
- 2012-10-17
- Peptides
- Toll-like receptor 4: AB
Lymphocyte antigen 96: CD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D