- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 4 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG-NAG.3: 9 residues within 4Å:- Chain A: I.453, K.454, C.457, S.467, L.468, N.489, S.491, Y.512, D.514
1 PLIP interactions:1 interactions with chain A- Water bridges: A:R.450
NAG-NAG.6: 10 residues within 4Å:- Chain B: R.450, I.453, K.454, C.457, S.467, L.468, N.489, S.491, Y.512, D.514
1 PLIP interactions:1 interactions with chain B- Water bridges: B:N.517
- 2 x URI: URIDINE(Non-covalent)
URI.7: 12 residues within 4Å:- Chain A: Y.326, K.328, G.329, Y.331, V.356, F.383, R.407
- Chain B: V.498, D.521, D.523, V.551, T.552
8 PLIP interactions:3 interactions with chain B, 5 interactions with chain A- Hydrogen bonds: B:D.521, B:D.523, B:T.552, A:G.329, A:R.407
- Hydrophobic interactions: A:F.383
- pi-Stacking: A:Y.331, A:F.383
URI.14: 12 residues within 4Å:- Chain A: V.498, D.521, D.523, V.551, T.552
- Chain B: Y.326, K.328, G.329, Y.331, V.356, F.383, R.407
8 PLIP interactions:5 interactions with chain B, 3 interactions with chain A- Hydrophobic interactions: B:F.383
- Hydrogen bonds: B:G.329, B:R.407, A:D.521, A:D.523, A:T.552
- pi-Stacking: B:Y.331, B:F.383
- 10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.8: 3 residues within 4Å:- Chain A: R.348, P.372, N.373
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.373
NAG.9: 3 residues within 4Å:- Chain A: S.500, N.524, A.525
No protein-ligand interaction detected (PLIP)NAG.10: 3 residues within 4Å:- Chain A: H.55, N.93, T.95
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.93
NAG.11: 3 residues within 4Å:- Chain A: T.529, Q.559, N.560
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.560
NAG.12: 4 residues within 4Å:- Chain A: K.586, S.587, V.589, N.618
No protein-ligand interaction detected (PLIP)NAG.15: 4 residues within 4Å:- Chain B: L.345, S.346, R.348, N.373
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:R.348, B:R.348, B:N.373
NAG.16: 3 residues within 4Å:- Chain B: S.500, N.524, A.525
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:A.525
- Water bridges: B:A.525
NAG.17: 4 residues within 4Å:- Chain B: S.526, T.529, Q.559, N.560
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:N.560
NAG.18: 5 residues within 4Å:- Chain B: T.562, K.586, S.587, V.589, N.618
No protein-ligand interaction detected (PLIP)NAG.19: 4 residues within 4Å:- Chain B: N.634, N.658, T.660, L.661
1 PLIP interactions:1 interactions with chain B- Water bridges: B:N.634
- 2 x UCG: 3'-O-[(R)-{[(2R,3aR,4R,6R,6aR)-6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-hydroxy-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]uridine 5'-(dihydrogen phosphate)(Non-covalent)
UCG.13: 15 residues within 4Å:- Chain A: K.292, V.293, E.318, I.319, D.321, R.348, H.351, R.353, N.378, H.447, F.448, T.449, R.450, P.451, L.452
15 PLIP interactions:15 interactions with chain A- Hydrophobic interactions: A:I.319
- Hydrogen bonds: A:E.318, A:E.318, A:R.348, A:R.353, A:N.378, A:L.452
- Water bridges: A:E.297, A:S.323
- Salt bridges: A:D.321, A:H.447
- pi-Stacking: A:H.351, A:H.447
- pi-Cation interactions: A:H.351, A:H.447
UCG.20: 14 residues within 4Å:- Chain B: K.292, V.293, E.318, I.319, D.321, R.348, H.351, R.353, H.447, F.448, T.449, R.450, P.451, L.452
13 PLIP interactions:13 interactions with chain B- Hydrophobic interactions: B:I.319
- Hydrogen bonds: B:E.318, B:E.318, B:R.353, B:L.452
- Water bridges: B:H.351, B:N.444
- Salt bridges: B:D.321, B:H.447
- pi-Stacking: B:H.351, B:H.447
- pi-Cation interactions: B:H.351, B:H.447
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Tanji, H. et al., Toll-like receptor 8 senses degradation products of single-stranded RNA. Nat.Struct.Mol.Biol. (2015)
- Release Date
- 2015-01-14
- Peptides
- Toll-like receptor 8: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 4 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x URI: URIDINE(Non-covalent)
- 10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x UCG: 3'-O-[(R)-{[(2R,3aR,4R,6R,6aR)-6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-hydroxy-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]uridine 5'-(dihydrogen phosphate)(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Tanji, H. et al., Toll-like receptor 8 senses degradation products of single-stranded RNA. Nat.Struct.Mol.Biol. (2015)
- Release Date
- 2015-01-14
- Peptides
- Toll-like receptor 8: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B