- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x G- U- C- C- C: RNA (5'-R(*GP*UP*CP*CP*C)-3')(Non-covalent)
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.5: 7 residues within 4Å:- Chain A: S.468, C.469, S.479, K.480, N.501, Y.524, D.526
7 PLIP interactions:7 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
NAG.6: 6 residues within 4Å:- Chain A: S.537, M.566, N.568, K.571, T.590, S.591
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.537, A:S.537, A:T.590
NAG.7: 4 residues within 4Å:- Chain A: R.674, R.695, N.698, R.701
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:R.674
- Hydrogen bonds: A:R.674, A:R.695, A:N.698, A:R.701
- Water bridges: A:R.674
NAG.8: 3 residues within 4Å:- Chain A: K.306, G.309, N.339
No protein-ligand interaction detected (PLIP)NAG.9: 4 residues within 4Å:- Chain A: N.391, S.393, K.396, H.493
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:N.391, A:K.396, A:K.396
- Water bridges: A:N.391
NAG.10: 5 residues within 4Å:- Chain A: I.26, N.47, V.70, E.71, S.109
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:I.26
- Hydrogen bonds: A:N.47, A:S.109, A:S.109
NAG.11: 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.12: 4 residues within 4Å:- Chain A: E.632, N.657, T.681, N.705
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:N.657, A:T.681
- Water bridges: A:E.632, A:D.634
NAG.26: 6 residues within 4Å:- Chain B: S.468, C.469, S.479, N.501, Y.524, D.526
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:Y.524
- Hydrogen bonds: B:C.469, B:S.479, B:N.501, B:D.526, B:D.526
NAG.27: 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
NAG.28: 5 residues within 4Å:- Chain B: I.26, N.47, V.70, E.71, S.109
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:I.26
- Hydrogen bonds: B:N.47, B:S.109, B:S.109
NAG.29: 5 residues within 4Å:- Chain B: S.537, M.566, N.568, T.590, S.591
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.537, B:S.537, B:T.590
- 2 x IDQ: 1-[[4-(aminomethyl)phenyl]methyl]-2-butyl-imidazo[4,5-c]quinolin-4-amine(Non-covalent)
IDQ.13: 14 residues within 4Å:- Chain A: T.510, D.533, L.535, G.562, I.563, T.564
- Chain B: F.327, F.329, Q.332, V.333, Y.334, V.359, F.386
- Ligands: SO4.22
16 PLIP interactions:10 interactions with chain B, 6 interactions with chain A- Hydrophobic interactions: B:F.327, B:F.329, B:F.329, B:Y.334, B:V.359, B:F.386, A:T.510, A:L.535, A:L.535
- Water bridges: B:Q.332
- pi-Stacking: B:Y.334, B:F.386, B:F.386
- Hydrogen bonds: A:D.533, A:T.564, A:T.564
IDQ.30: 15 residues within 4Å:- Chain A: N.243, 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: SO4.35
14 PLIP interactions:9 interactions with chain A, 5 interactions with chain B- Hydrophobic interactions: A:F.327, A:F.329, A:F.329, A:Y.334, A:F.386, A:F.386, B:T.510, B:L.535, B:L.535
- pi-Stacking: A:Y.334, A:F.386, A:F.386
- Hydrogen bonds: B:D.533, B:T.564
- 17 x SO4: SULFATE ION(Non-functional Binders)
SO4.14: 4 residues within 4Å:- Chain A: H.536, S.537, T.538, M.566
Ligand excluded by PLIPSO4.15: 5 residues within 4Å:- Chain A: K.396, Q.397, F.398, K.399, R.400
Ligand excluded by PLIPSO4.16: 5 residues within 4Å:- Chain A: S.85, K.86, S.87
- Chain B: S.641, K.666
Ligand excluded by PLIPSO4.17: 3 residues within 4Å:- Chain A: I.41, P.42, T.43
Ligand excluded by PLIPSO4.18: 1 residues within 4Å:- Chain A: R.728
Ligand excluded by PLIPSO4.19: 4 residues within 4Å:- Chain A: K.388, K.410
- Chain B: Q.509, T.510
Ligand excluded by PLIPSO4.20: 4 residues within 4Å:- Chain A: K.364, S.365, N.391, M.394
Ligand excluded by PLIPSO4.21: 9 residues within 4Å:- Chain A: Y.211, N.212, S.235, H.276, R.445, Y.446, D.447, K.448, Y.449
Ligand excluded by PLIPSO4.22: 4 residues within 4Å:- Chain A: L.535, H.536
- Chain B: Y.334
- Ligands: IDQ.13
Ligand excluded by PLIPSO4.23: 5 residues within 4Å:- Chain A: R.531, S.555, H.556, Q.559
- Chain B: N.529
Ligand excluded by PLIPSO4.24: 3 residues within 4Å:- Chain A: Q.474, K.498, E.521
Ligand excluded by PLIPSO4.25: 2 residues within 4Å:- Chain A: H.798, T.810
Ligand excluded by PLIPSO4.31: 7 residues within 4Å:- Chain A: S.641, F.642, K.666
- Chain B: S.85, K.86, S.87
- Ligands: G-U-C-C-C.1
Ligand excluded by PLIPSO4.32: 4 residues within 4Å:- Chain B: H.536, S.537, T.538, M.566
Ligand excluded by PLIPSO4.33: 1 residues within 4Å:- Chain B: R.286
Ligand excluded by PLIPSO4.34: 3 residues within 4Å:- Chain B: R.335, A.336, S.337
Ligand excluded by PLIPSO4.35: 4 residues within 4Å:- Chain B: T.510, L.535, H.536
- Ligands: IDQ.30
Ligand excluded by PLIP- 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 2.20 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x G- U- C- C- C: RNA (5'-R(*GP*UP*CP*CP*C)-3')(Non-covalent)
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x IDQ: 1-[[4-(aminomethyl)phenyl]methyl]-2-butyl-imidazo[4,5-c]quinolin-4-amine(Non-covalent)
- 17 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