SMTL ID : 6lw0.1

Crystal structure of TLR7/Cpd-6 (DSR-139293) complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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)

NAG-NAG.1: 8 residues within 4Å: Chain A: C.161, Y.162, 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, P.166, C.167, Y.168, V.169, S.170, N.193, M.214 No protein-ligand interaction detected (PLIP)

11 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 6 residues within 4Å: Chain A: S.468, C.469, S.479, N.501, Y.524, D.526 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.524 Hydrogen bonds: A:C.469, A:S.479, A:D.526, A:D.526 NAG.4: 4 residues within 4Å: Chain A: Q.509, N.512, S.514, E.515 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.509, A:N.512, A:E.515 NAG.5: 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.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: 5 residues within 4Å: Chain A: S.537, N.568, K.571, N.572, S.591 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.537, A:S.537, A:N.568 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.674, A:R.695, A:N.698 NAG.9: 4 residues within 4Å: Chain A: E.632, N.657, T.681, N.705 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.632, A:N.657, A:T.681 NAG.18: 7 residues within 4Å: Chain B: S.468, C.469, S.479, N.501, S.503, Y.524, D.526 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.524 Hydrogen bonds: B:C.469, B:S.479, B:D.526 NAG.19: 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.20: 8 residues within 4Å: Chain B: S.537, M.566, N.568, K.571, N.572, T.590, S.591 Ligands: SO4.22 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.571 Hydrogen bonds: B:S.537, B:S.537 NAG.21: 5 residues within 4Å: Chain B: F.485, Q.509, N.512, S.514, E.515 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.509, B:S.514, B:S.514

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

SO4.10: 5 residues within 4Å: Chain A: L.535, H.536, S.537, T.538, M.566 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.537, A:S.537 SO4.11: 7 residues within 4Å: Chain A: S.85, K.86, S.87 Chain B: S.641, F.642, K.666, S.667 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.641, A:K.86, A:S.87, A:S.87 SO4.12: 2 residues within 4Å: Chain A: R.728, K.754 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.728, A:K.754 SO4.13: 8 residues within 4Å: Chain A: Y.211, S.235, H.276, R.445, Y.446, D.447, K.448, Y.449 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.212, A:D.447, A:K.448 Water bridges: A:S.235 Salt bridges: A:H.276 SO4.14: 7 residues within 4Å: Chain A: E.134, Y.156, S.188, K.190, Y.209, Y.211, Y.449 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.134, A:S.188, A:Y.211 Water bridges: A:E.134 Salt bridges: A:K.190 SO4.15: 5 residues within 4Å: Chain A: L.257, Q.258, I.259, H.282, W.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.257, A:I.259 SO4.16: 2 residues within 4Å: Chain A: Q.474, K.498 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.474 Salt bridges: A:K.498 SO4.22: 4 residues within 4Å: Chain B: H.536, S.537, T.538 Ligands: NAG.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.537, B:T.538 SO4.23: 7 residues within 4Å: Chain A: S.641, F.642, K.666, S.667 Chain B: 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 Salt bridges: A:K.666 SO4.24: 9 residues within 4Å: Chain B: Y.211, N.212, S.235, H.276, R.445, Y.446, D.447, K.448, Y.449 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.446, B:D.447, B:K.448 Water bridges: B:S.235 Salt bridges: B:H.276 SO4.25: 2 residues within 4Å: Chain B: R.531, H.556 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.556, A:N.529 Salt bridges: B:R.531, B:H.556 SO4.26: 6 residues within 4Å: Chain B: Y.156, S.188, K.190, Y.209, Y.211, Y.449 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.188 Salt bridges: B:K.190

2 x EX0: 2-ethoxy-8-(5-fluoranylpyridin-3-yl)-9-[[4-[[(1S,4S)-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]methyl]phenyl]methyl]purin-6-amine(Non-covalent)

EX0.17: 14 residues within 4Å: Chain A: F.329, Q.332, V.333, Y.334, V.359, F.386, K.388, K.410 Chain B: T.510, D.533, L.535, G.562, I.563, T.564 14 PLIP interactions: 5 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:T.510, B:L.535, A:F.329, A:Y.334, A:Y.334, A:V.359, A:V.359, A:F.386, A:K.410 Hydrogen bonds: B:D.533, B:T.564, B:T.564 pi-Stacking: A:F.386, A:F.386 EX0.27: 13 residues within 4Å: Chain A: Q.509, T.510, D.533, L.535, G.562, I.563, T.564 Chain B: Q.332, Y.334, V.359, F.386, K.388, K.410 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:T.510, A:L.535, B:Y.334, B:V.359, B:F.386, B:F.386 Hydrogen bonds: A:D.533, A:T.564, B:Y.334 pi-Stacking: B:F.386

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tojo, S. et al., Structural analysis reveals TLR7 dynamics underlying antagonism. Nat Commun (2020)

Release Date

2020-11-11

Peptides

Toll-like receptor 7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Toll-like receptor 7

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