SMTL ID : 6lvx.1

Crystal structure of TLR7/Cpd-1 (SM-374527) complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

homo-dimer

Ligands

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.1: 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)

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

EWL.2: 11 residues within 4Å: Chain A: T.510, D.533, L.535, G.562, I.563, T.564 Chain B: F.329, V.333, Y.334, V.359, F.386 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.329, B:Y.334, B:V.359, A:L.535 pi-Stacking: B:F.386, B:F.386 Hydrogen bonds: A:D.533, A:T.564, A:T.564 EWL.14: 13 residues within 4Å: Chain A: F.327, 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 15 PLIP interactions: 6 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:L.535, A:F.327, A:F.329, A:F.329, A:Y.334, A:Y.334, A:V.359, A:V.359, A:F.386 Hydrogen bonds: B:D.533, B:T.564, B:T.564, B:T.564 Water bridges: B:D.533 pi-Stacking: A:F.386

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

NAG.3: 8 residues within 4Å: Chain A: C.161, Y.162, P.166, C.167, Y.168, V.169, S.170, N.193 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.166 Hydrogen bonds: A:C.167, A:Y.168, A:Y.168 NAG.4: 7 residues within 4Å: Chain A: S.468, C.469, S.479, K.480, 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.5: 5 residues within 4Å: Chain A: N.391, S.393, K.396, Q.492, H.493 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.396, A:K.396 NAG.6: 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.7: 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.8: 3 residues within 4Å: Chain A: E.632, N.657, T.681 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.657, A:T.681 NAG.9: 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.15: 7 residues within 4Å: Chain B: S.468, C.469, S.479, K.480, N.501, 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.16: 5 residues within 4Å: Chain B: I.26, N.47, V.70, E.71, S.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.109, B:S.109 NAG.17: 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.18: 3 residues within 4Å: Chain B: S.537, M.566, N.568 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.537, B:S.537

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

SO4.10: 3 residues within 4Å: Chain A: I.41, P.42, T.43 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.43 SO4.11: 5 residues within 4Å: Chain A: K.396, Q.397, F.398, K.399, R.400 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.399, A:R.400 Salt bridges: A:R.400 SO4.12: 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:S.365, A:N.391 SO4.13: 4 residues within 4Å: Chain A: L.535, H.536, S.537, T.538 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.537, A:S.537, A:T.538 Salt bridges: A:H.536 SO4.19: 3 residues within 4Å: Chain B: H.536, S.537, T.538 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.537, B:T.538 Salt bridges: B:H.536 SO4.20: 6 residues within 4Å: Chain A: S.641, F.642, K.666 Chain B: S.85, K.86, S.87 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.641, A:S.641, B:S.85, B:K.86, B:S.87 Salt bridges: A:K.666

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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