SMTL ID : 6lvz.1

Crystal structure of TLR7/Cpd-3 (SM-394830) complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.83 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.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-BMA.2: 8 residues within 4Å: Chain B: C.161, Y.162, P.166, C.167, Y.168, V.169, S.170, N.193 No protein-ligand interaction detected (PLIP)

1 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: 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

11 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.524 Hydrogen bonds: A:S.407, A:S.407, A:C.469, A:S.479, A:D.526, A:D.526 NAG.5: 5 residues within 4Å: Chain A: N.391, S.393, K.396, Q.492, H.493 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.391, A:K.396, A:K.396 NAG.6: 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.7: 5 residues within 4Å: Chain A: S.537, M.566, N.568, K.571, N.572 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.571 Hydrogen bonds: A:S.537, A:S.537 NAG.8: 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.9: 4 residues within 4Å: Chain A: R.674, R.695, N.698, R.701 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.674 Hydrogen bonds: A:R.674, 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: 3 residues within 4Å: Chain A: K.306, G.309, N.339 No protein-ligand interaction detected (PLIP) NAG.19: 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:N.501, B:D.526 NAG.20: 6 residues within 4Å: Chain B: S.537, M.566, N.568, K.571, N.572 Ligands: SO4.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.537, B:S.537 NAG.21: 3 residues within 4Å: Chain B: K.306, G.309, N.339 No protein-ligand interaction detected (PLIP)

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

SO4.12: 4 residues within 4Å: Chain A: L.535, H.536, S.537, T.538 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.537 Salt bridges: A:H.536 SO4.13: 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:K.399, A:R.400 Salt bridges: A:K.399, A:R.400 SO4.14: 5 residues within 4Å: Chain A: S.188, K.190, Y.209, Y.211, Y.449 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.188, A:S.188, A:Y.211 Salt bridges: A:K.190 SO4.15: 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 SO4.16: 7 residues within 4Å: Chain A: R.354, V.379, D.381, V.403, D.405, V.437, Y.470 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.470 Salt bridges: A:R.354 SO4.22: 5 residues within 4Å: Chain B: L.535, H.536, S.537, T.538 Ligands: NAG.20 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.536, B:S.537, B:S.537, B:T.538 SO4.23: 5 residues within 4Å: Chain B: S.188, K.190, Y.209, Y.211, Y.449 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.188, B:Y.211 Salt bridges: B:K.190 SO4.24: 2 residues within 4Å: Chain B: R.531, H.556 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.556 Salt bridges: B:R.531, B:H.556 SO4.25: 3 residues within 4Å: Chain B: R.335, A.336, S.337 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.336, B:S.337, B:S.337

2 x EWX: 6-azanyl-2-(2-methoxyethoxy)-9-(pyridin-3-ylmethyl)-7H-purin-8-one(Non-covalent)

EWX.17: 13 residues within 4Å: Chain A: T.510, D.533, L.535, G.562, I.563, T.564 Chain B: F.327, F.329, Y.334, V.359, T.384, F.386, K.410 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.535, B:Y.334, B:Y.334 Hydrogen bonds: A:D.533, A:D.533, A:T.564 pi-Stacking: B:F.386, B:F.386 EWX.18: 14 residues within 4Å: Chain A: F.329, V.333, Y.334, G.357, V.359, T.384, F.386, K.410 Chain B: T.510, D.533, L.535, G.562, I.563, T.564 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.535, A:Y.334, A:V.359 Hydrogen bonds: B:D.533, B:D.533, B:T.564, B:T.564 pi-Stacking: A:F.386, A: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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