- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 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 9JR: 4-azanyl-2-butoxy-8-[[3-(pyrrolidin-1-ylmethyl)phenyl]methyl]-5,7-dihydropteridin-6-one(Non-covalent)
- 12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.4: 8 residues within 4Å:- Chain A: S.407, S.468, C.469, S.479, K.480, N.501, Y.524, D.526
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:Y.524
- Hydrogen bonds: A:S.407, A:C.469, A:S.479, A:K.480, A:N.501, A:D.526, A:D.526
- Water bridges: A:K.480
NAG.5: 4 residues within 4Å:- Chain A: E.632, N.657, T.681, N.705
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:N.657
- Water bridges: A:E.632, A:E.632, A:E.632, A:D.634, A:D.634, A:D.683
NAG.6: 4 residues within 4Å:- Chain A: N.391, S.393, K.396, H.493
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.391, A:K.396, A:K.396
NAG.7: 2 residues within 4Å:- Chain A: N.512, S.514
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:S.514
- Water bridges: A:Q.509, A:N.512, A:N.512, A:E.515, A:E.515
NAG.8: 5 residues within 4Å:- Chain A: S.537, M.566, N.568, K.571, N.572
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:K.571
- Hydrogen bonds: A:S.537, A:S.537, A:T.590
- Water bridges: A:N.568
NAG.9: 3 residues within 4Å:- Chain A: K.306, G.309, N.339
4 PLIP interactions:4 interactions with chain A- Water bridges: A:R.335, A:R.335, A:N.339, A:N.339
NAG.10: 5 residues within 4Å:- Chain A: I.26, N.47, V.70, E.71, S.109
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:I.26
- Hydrogen bonds: A:N.47, A:E.71, A:S.109, A:S.109
NAG.11: 4 residues within 4Å:- Chain A: R.674, R.695, N.698, R.701
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:R.674
- Hydrogen bonds: A:R.695, A:N.698, A:R.701
NAG.21: 5 residues within 4Å:- Chain B: I.26, N.47, V.70, E.71, S.109
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:S.109, B:S.109
NAG.22: 7 residues within 4Å:- Chain B: S.468, C.469, S.479, K.480, N.501, Y.524, D.526
11 PLIP interactions:11 interactions with chain B- Hydrophobic interactions: B:Y.524
- Hydrogen bonds: B:C.469, B:S.479, B:N.501, B:D.526
- Water bridges: B:S.407, B:S.407, B:S.407, B:S.407, B:S.468, B:S.468
NAG.23: 5 residues within 4Å:- Chain B: S.537, M.566, N.568, K.571, S.591
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.537, B:S.537
- Water bridges: B:R.592
NAG.24: 5 residues within 4Å:- Chain B: N.391, S.393, K.396, Q.492, H.493
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:N.391, B:K.396, B:K.396, B:Q.492
- 11 x SO4: SULFATE ION(Non-functional Binders)
SO4.12: 5 residues within 4Å:- Chain A: L.535, H.536, S.537, T.538, M.566
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:S.537, A:S.537
- Water bridges: A:T.538
- Salt bridges: A:H.536
SO4.13: 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
SO4.14: 2 residues within 4Å:- Chain A: P.42, T.43
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:T.43, A:R.65
SO4.15: 5 residues within 4Å:- Chain A: K.396, Q.397, F.398, K.399, R.400
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.399, A:R.400
- Salt bridges: A:R.400
SO4.16: 4 residues within 4Å:- Chain A: K.399, Q.474, K.498, E.521
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:Q.474, A:E.521
- Salt bridges: A:K.399, A:K.498
SO4.17: 6 residues within 4Å:- Chain A: S.85, K.86, S.87
- Chain B: S.641, F.642, K.666
7 PLIP interactions:3 interactions with chain A, 4 interactions with chain B- Hydrogen bonds: A:K.86, A:S.87, A:S.87, B:S.641, B:S.641
- Water bridges: B:K.666
- Salt bridges: B:K.666
SO4.18: 1 residues within 4Å:- Chain A: R.728
4 PLIP interactions:4 interactions with chain A- Water bridges: A:R.728, A:R.728
- Salt bridges: A:K.704, A:R.728
SO4.19: 7 residues within 4Å:- Chain A: E.134, Y.156, S.188, K.190, Y.209, Y.211, Y.449
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:E.134, A:S.188, A:Y.211
- Water bridges: A:E.134, A:Y.211
- Salt bridges: A:K.190
SO4.25: 6 residues within 4Å:- Chain A: S.641, F.642
- Chain B: G.84, S.85, K.86, S.87
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:S.85, B:K.86, B:S.87, A:S.641, A:S.641
SO4.26: 3 residues within 4Å:- Chain B: H.536, S.537, T.538
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:S.537, B:T.538
- Water bridges: B:L.535, B:H.536
- Salt bridges: B:H.536
SO4.27: 3 residues within 4Å:- Chain B: R.335, A.336, S.337
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:A.336, B:S.337, B:S.337
- Water bridges: B:R.335
- Salt bridges: B:R.335
- 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
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 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 9JR: 4-azanyl-2-butoxy-8-[[3-(pyrrolidin-1-ylmethyl)phenyl]methyl]-5,7-dihydropteridin-6-one(Non-covalent)
- 12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 11 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
AB
B