- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-dimer
- Ligands
- 4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 11 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.5: 6 residues within 4Å:- Chain A: S.468, C.469, S.479, N.501, Y.524, D.526
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:Y.524
- Hydrogen bonds: A:C.469, A:S.479, A:N.501, A:D.526
- Water bridges: A:S.407, A:S.407, A:S.407, A:S.407, A:S.468, A:S.468
NAG.6: 5 residues within 4Å:- Chain A: N.391, S.393, K.396, Q.492, H.493
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:N.391, A:K.396, A:K.396, A:Q.492
NAG.7: 3 residues within 4Å:- Chain A: K.306, G.309, N.339
1 PLIP interactions:1 interactions with chain A- Water bridges: A:N.339
NAG.8: 6 residues within 4Å:- Chain A: S.537, M.566, N.568, K.571, T.590, S.591
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.537, A:S.537
NAG.9: 4 residues within 4Å:- Chain A: R.674, R.695, N.698, R.701
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:R.674
- Hydrogen bonds: A:R.674, A:R.695, A:N.698, A:R.701
NAG.10: 2 residues within 4Å:- Chain A: N.512, S.514
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.512, A:S.514
NAG.17: 6 residues within 4Å:- Chain B: S.468, C.469, S.479, N.501, Y.524, D.526
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:Y.524
- Hydrogen bonds: B:S.407, B:S.407, B:C.469, B:S.479, B:N.501, B:D.526, B:D.526
NAG.18: 4 residues within 4Å:- Chain B: S.537, M.566, N.568, S.591
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.537, B:N.568
- Water bridges: B:N.568
NAG.19: 3 residues within 4Å:- Chain B: K.306, G.309, N.339
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:K.306
NAG.20: 4 residues within 4Å:- Chain B: N.391, S.393, K.396, H.493
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:N.391, B:K.396, B:K.396
NAG.21: 2 residues within 4Å:- Chain B: N.512, S.514
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:N.512, B:S.514
- 2 x 9K3: 1-{4-amino-2-[(ethylamino)methyl]-1H-imidazo[4,5-c]quinolin-1-yl}-2-methylpropan-2-ol(Non-covalent)
9K3.11: 13 residues within 4Å:- Chain A: T.510, D.533, L.535, G.562, I.563, T.564
- Chain B: F.329, V.333, Y.334, V.359, F.386, K.410
- Ligands: SO4.15
15 PLIP interactions:9 interactions with chain B, 6 interactions with chain A- Hydrophobic interactions: B:F.329, B:F.329, B:V.359, B:F.386, B:F.386, A:T.510
- Water bridges: B:N.243, A:D.533
- pi-Stacking: B:Y.334, B:F.386, B:F.386
- Hydrogen bonds: A:D.533, A:G.562, A:T.564, A:T.564
9K3.22: 14 residues within 4Å:- Chain A: F.327, F.329, Q.332, V.333, Y.334, V.359, F.386
- Chain B: T.510, D.533, L.535, G.562, I.563, T.564
- Ligands: SO4.25
12 PLIP interactions:8 interactions with chain A, 4 interactions with chain B- Hydrophobic interactions: A:F.327, A:F.329, A:V.359, A:F.386, B:T.510
- Water bridges: A:N.243
- pi-Stacking: A:Y.334, A:F.386, A:F.386
- Hydrogen bonds: B:D.533, B:G.562, B:T.564
- 8 x SO4: SULFATE ION(Non-functional Binders)
SO4.12: 3 residues within 4Å:- Chain A: H.536, S.537, T.538
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.537, A:T.538
- Salt bridges: A:H.536
SO4.13: 3 residues within 4Å:- Chain A: I.41, P.42, T.43
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:T.43, A:T.43
SO4.14: 4 residues within 4Å:- Chain A: K.364, S.365, N.391, M.394
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.365, A:N.391
SO4.15: 5 residues within 4Å:- Chain A: T.510, L.535, H.536
- Chain B: Y.334
- Ligands: 9K3.11
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:T.510, A:T.510
- Salt bridges: A:H.536
SO4.16: 3 residues within 4Å:- Chain A: R.714, K.736, R.762
3 PLIP interactions:3 interactions with chain A- Salt bridges: A:R.714, A:K.736, A:R.762
SO4.23: 5 residues within 4Å:- Chain A: S.641, F.642
- Chain B: S.85, K.86, S.87
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:K.86, B:S.87, B:S.87, A:S.641
SO4.24: 4 residues within 4Å:- Chain B: L.535, H.536, S.537, T.538
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:S.537, B:S.537, B:T.538
- Salt bridges: B:H.536
SO4.25: 4 residues within 4Å:- Chain B: T.510, L.535, H.536
- Ligands: 9K3.22
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:T.510
- Salt bridges: B:H.536
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhang, Z. et al., Structural Analyses of Toll-like Receptor 7 Reveal Detailed RNA Sequence Specificity and Recognition Mechanism of Agonistic Ligands. Cell Rep (2018)
- Release Date
- 2019-01-30
- Peptides
- Toll-like receptor 7: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
BB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-dimer
- Ligands
- 4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 11 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x 9K3: 1-{4-amino-2-[(ethylamino)methyl]-1H-imidazo[4,5-c]quinolin-1-yl}-2-methylpropan-2-ol(Non-covalent)
- 8 x SO4: SULFATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhang, Z. et al., Structural Analyses of Toll-like Receptor 7 Reveal Detailed RNA Sequence Specificity and Recognition Mechanism of Agonistic Ligands. Cell Rep (2018)
- Release Date
- 2019-01-30
- Peptides
- Toll-like receptor 7: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
BB
A