SMTL ID : 5gmh.1

Crystal structure of monkey TLR7 in complex with R848

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 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.2: 9 residues within 4Å: Chain B: 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.3: 5 residues within 4Å: Chain B: N.47, V.70, E.71, S.109, Q.129 No protein-ligand interaction detected (PLIP)

2 x RX8: 1-[4-amino-2-(ethoxymethyl)-1H-imidazo[4,5-c]quinolin-1-yl]-2-methylpropan-2-ol(Non-covalent)

RX8.4: 15 residues within 4Å: Chain A: T.510, D.533, L.535, G.562, I.563, T.564 Chain B: Y.242, F.327, F.329, Q.332, V.333, Y.334, V.359, F.386 Ligands: SO4.13 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:T.510, B:F.327, B:F.329, B:F.386 Hydrogen bonds: A:D.533, A:T.564, A:T.564 Water bridges: A:D.533, B:N.243 pi-Stacking: B:Y.334, B:F.386, B:F.386 RX8.29: 12 residues within 4Å: Chain A: F.327, F.329, V.333, Y.334, V.359, F.386 Chain B: T.510, D.533, L.535, G.562, I.563, T.564 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:T.510, A:F.327, A:F.329, A:F.329, A:V.359, A:F.386, A:F.386 Hydrogen bonds: B:D.533, B:T.564 Water bridges: A:N.243 pi-Stacking: A:Y.334, A:F.386, A:F.386

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 9 PLIP interactions: 9 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.468, A:S.468 NAG.6: 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.7: 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 Water bridges: A:R.592 NAG.8: 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.9: 6 residues within 4Å: Chain A: N.391, S.393, K.396, Q.492, H.493 Ligands: SO4.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.391, A:K.396, A:K.396, A:Q.492 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.11: 4 residues within 4Å: Chain A: K.306, G.309, D.310, N.339 No protein-ligand interaction detected (PLIP) NAG.30: 7 residues within 4Å: Chain B: S.468, C.469, S.479, K.480, N.501, Y.524, D.526 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.524 Hydrogen bonds: B:C.469, B:S.479, B:D.526, B:D.526 NAG.31: 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:S.537, B:N.568 NAG.32: 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.33: 5 residues within 4Å: Chain B: N.391, S.393, K.396, Q.492, H.493 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.391, B:S.393, B:K.396, B:K.396, B:Q.492 NAG.34: 3 residues within 4Å: Chain B: G.309, D.310, N.339 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.339

28 x SO4: SULFATE ION(Non-functional Binders)

SO4.12: 1 residues within 4Å: Chain A: R.286 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain A: T.510, L.535, H.536 Chain B: Y.334 Ligands: RX8.4 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain A: K.364, S.365, N.391, M.394 Ligands: NAG.9 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain A: H.536, S.537, T.538, M.566 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain A: I.41, P.42, T.43 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain A: R.762, V.793 Chain B: R.762 Ligands: SO4.35 Ligand excluded by PLIP SO4.18: 5 residues within 4Å: Chain A: K.396, Q.397, F.398, K.399, R.400 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: G.39, G.40, R.65 Ligand excluded by PLIP SO4.20: 9 residues within 4Å: Chain A: C.161, Y.162, D.191, N.192, N.193, N.212, N.213, M.214, Y.446 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain A: R.354, V.403, D.405, V.437, Y.470 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain A: N.705, Y.729 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain A: K.471, Y.472, R.523 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain A: R.714, K.736, R.762 Chain B: R.762 Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain A: S.85, K.86, S.87 Chain B: S.641, F.642, K.666 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain A: Q.474, K.498, E.521 Ligand excluded by PLIP SO4.27: 1 residues within 4Å: Chain A: R.728 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain A: K.185, V.186, T.206, E.207 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain B: R.714, K.736 Ligands: SO4.17 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain B: R.286, K.289 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain B: L.535, H.536, S.537, T.538 Ligand excluded by PLIP SO4.38: 6 residues within 4Å: Chain A: S.641, F.642, K.666 Chain B: S.85, K.86, S.87 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain B: Q.474, K.498, E.521 Ligand excluded by PLIP SO4.40: 5 residues within 4Å: Chain B: K.396, Q.397, F.398, K.399, R.400 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain B: K.471, Y.472, R.523 Ligand excluded by PLIP SO4.42: 9 residues within 4Å: Chain B: P.60, F.63, H.64, R.99, S.100, F.101, S.102, G.103, L.104 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain B: I.41, P.42, T.43, R.65 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain B: R.335, A.336, S.337 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain B: T.510, L.535, H.536 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Structural Analysis Reveals that Toll-like Receptor 7 Is a Dual Receptor for Guanosine and Single-Stranded RNA. Immunity (2016)

Release Date

2016-11-02

Peptides

Toll-like receptor 7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Toll-like receptor 7

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