- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x U- U- A- A: RNA (5'-R(P*UP*UP*AP*A)-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)
NAG-NAG.3: 9 residues within 4Å:- Chain A: C.161, Y.162, Y.163, P.166, C.167, Y.168, V.169, S.170, N.193
No protein-ligand interaction detected (PLIP)NAG-NAG.5: 7 residues within 4Å:- Chain B: I.26, N.47, V.70, E.71, K.108, S.109, Q.129
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:K.108
- 1 x NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 9 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.6: 8 residues within 4Å:- Chain A: S.407, S.468, C.469, S.479, K.480, N.501, Y.524, D.526
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:Y.524
- Hydrogen bonds: A:S.407, A:C.469, A:S.479, A:N.501, A:D.526
NAG.7: 5 residues within 4Å:- Chain A: S.537, M.566, N.568, K.571, N.572
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.537, A:S.537
NAG.8: 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.9: 4 residues within 4Å:- Chain A: R.674, R.695, N.698, R.701
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.695, A:N.698, A:R.701
NAG.10: 3 residues within 4Å:- Chain A: E.632, N.657, T.681
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.657
NAG.11: 4 residues within 4Å:- Chain A: N.47, V.70, E.71, S.109
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.47, A:S.109, A:S.109
NAG.12: 3 residues within 4Å:- Chain A: K.306, G.309, N.339
No protein-ligand interaction detected (PLIP)NAG.25: 7 residues within 4Å:- Chain B: S.468, C.469, S.479, K.480, 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.26: 4 residues within 4Å:- Chain B: S.537, M.566, N.568, K.571
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:K.571
- Hydrogen bonds: B:S.537, B:S.537, B:T.590
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.13: 6 residues within 4Å:- Chain A: S.85, K.86, S.87
- Chain B: S.641, K.666
- Ligands: U-U-A-A.2
6 PLIP interactions:3 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:S.641, B:S.641, B:S.641, A:S.85, A:K.86, A:S.87
PO4.27: 7 residues within 4Å:- Chain A: S.641, F.642, K.666
- Chain B: S.85, K.86, S.87
- Ligands: U-U-A-A.1
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:K.86, B:S.87, B:S.87
- Salt bridges: A:K.666
- 13 x SO4: SULFATE ION(Non-functional Binders)
SO4.14: 4 residues within 4Å:- Chain A: L.535, 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
SO4.15: 1 residues within 4Å:- Chain A: R.728
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:R.728
SO4.16: 5 residues within 4Å:- Chain A: L.363, K.364, S.365, N.391, M.394
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:L.363, A:S.365
SO4.17: 5 residues within 4Å:- Chain A: K.396, Q.397, F.398, K.399, R.400
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:Q.397, A:K.399, A:R.400
- Salt bridges: A:R.400
SO4.18: 6 residues within 4Å:- Chain A: Y.156, S.188, K.190, Y.209, Y.211, Y.449
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.188
- Salt bridges: A:K.190
SO4.19: 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
SO4.20: 2 residues within 4Å:- Chain A: I.707, Y.729
No protein-ligand interaction detected (PLIP)SO4.21: 4 residues within 4Å:- Chain A: Q.474, F.496, K.498, E.521
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Q.474, A:E.521
- Salt bridges: A:K.498
SO4.22: 7 residues within 4Å:- Chain A: Y.211, N.212, D.233, H.276, Y.446, D.447, K.448
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:N.212, A:D.447, A:K.448
- Salt bridges: A:H.276, A:K.448
SO4.23: 4 residues within 4Å:- Chain A: R.531, H.556, Q.559
- Chain B: N.529
3 PLIP interactions:1 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:N.529
- Salt bridges: A:R.531, A:H.556
SO4.28: 3 residues within 4Å:- Chain B: H.536, S.537, M.566
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:S.537
SO4.29: 5 residues within 4Å:- Chain B: S.188, K.190, Y.209, Y.211, Y.449
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:S.188, B:Y.211, B:Y.449
- Salt bridges: B:K.190
SO4.30: 8 residues within 4Å:- Chain B: Y.211, D.233, S.235, H.276, Y.446, D.447, K.448, Y.449
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:N.212, B:D.447, B:K.448
- Salt bridges: B:H.276, B:K.448
- 2 x ACK: 2',3'- cyclic AMP(Non-covalent)
ACK.24: 13 residues within 4Å:- Chain A: Y.242, F.329, L.331, Q.332, Y.334, F.386, K.410
- Chain B: T.510, D.533, L.535, G.562, I.563, T.564
8 PLIP interactions:5 interactions with chain A, 3 interactions with chain B- Hydrogen bonds: A:Q.332, A:K.410, B:G.562, B:T.564, B:T.564
- pi-Stacking: A:Y.334, A:F.386, A:F.386
ACK.31: 14 residues within 4Å:- Chain A: T.510, D.533, L.535, G.562, I.563, T.564
- Chain B: Y.242, F.329, L.331, Q.332, Y.334, V.359, F.386, K.410
10 PLIP interactions:7 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:Y.242, B:Q.332, B:Q.332, B:K.410, A:G.562, A:T.564, A:T.564
- pi-Stacking: B:Y.334, B:F.386, B:F.386
- 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 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x U- U- A- A: RNA (5'-R(P*UP*UP*AP*A)-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)
- 1 x NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 9 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
- 13 x SO4: SULFATE ION(Non-functional Binders)
- 2 x ACK: 2',3'- cyclic AMP(Non-covalent)
- 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