SMTL ID : 6lvy.1

Crystal structure of TLR7/Cpd-2 (SM-360320) 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: 9 residues within 4Å: Chain A: C.161, Y.162, P.166, C.167, Y.168, V.169, S.170, N.193, M.214 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)

2 x EWU: 6-azanyl-2-(2-methoxyethoxy)-9-(phenylmethyl)-7H-purin-8-one(Non-covalent)

EWU.3: 13 residues within 4Å: Chain A: T.510, D.533, L.535, G.562, I.563, T.564 Chain B: F.327, F.329, V.333, Y.334, V.359, T.384, F.386 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.334, B:Y.334, B:V.359, A:L.535 pi-Stacking: B:F.386, B:F.386 Hydrogen bonds: A:D.533, A:D.533, A:T.564, A:T.564 Water bridges: A:D.533 EWU.17: 12 residues within 4Å: Chain A: F.329, Q.332, V.333, Y.334, V.359, F.386 Chain B: T.510, D.533, L.535, G.562, I.563, T.564 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.535, A:Y.334, A:Y.334, A:V.359 Hydrogen bonds: B:D.533, B:T.564, B:T.564 pi-Stacking: A:F.386, A:F.386

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

NAG.4: 7 residues within 4Å: Chain A: S.468, C.469, S.479, K.480, N.501, Y.524, D.526 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.524 Hydrogen bonds: A:C.469, A:S.479, A:D.526 NAG.5: 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.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: 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.8: 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.9: 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.10: 3 residues within 4Å: Chain A: K.306, G.309, N.339 No protein-ligand interaction detected (PLIP) NAG.18: 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.19: 5 residues within 4Å: Chain B: I.26, N.47, V.70, E.71, S.109 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.71, B:S.109, B:S.109 NAG.20: 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

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

SO4.11: 5 residues within 4Å: Chain A: L.363, K.364, S.365, N.391, M.394 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.363, A:S.365, A:N.391 SO4.12: 5 residues within 4Å: Chain A: L.535, H.536, S.537, T.538, M.566 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.537, A:T.538 Salt bridges: A:H.536 SO4.13: 2 residues within 4Å: Chain A: P.42, T.43 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.43, A:T.43, A:R.65 SO4.14: 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 SO4.15: 6 residues within 4Å: Chain A: S.85, K.86, S.87 Chain B: S.641, F.642, K.666 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.641, B:S.641, A:S.85, A:K.86, A:S.87 Salt bridges: B:K.666 SO4.16: 3 residues within 4Å: Chain A: Q.474, K.498, E.521 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.474 Salt bridges: A:K.498 SO4.21: 6 residues within 4Å: Chain A: S.641, F.642, K.666 Chain B: S.85, K.86, S.87 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.86, B:S.87, B:S.87, A:S.641 Salt bridges: A:K.666 SO4.22: 4 residues within 4Å: Chain B: H.536, S.537, T.538, M.566 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.537, B:S.537, B:T.538 Salt bridges: B:H.536 SO4.23: 3 residues within 4Å: Chain B: R.335, A.336, S.337 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.336, B:S.337 SO4.24: 2 residues within 4Å: Chain B: R.286, K.289 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.286, B:K.289

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
A

B
B

Toll-like receptor 7

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