SMTL ID : 7wv5.1

ectoTLR3-poly(I:C)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

8 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: 4 residues within 4Å: Chain A: K.177, N.229, M.255, Y.279 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.279 NAG-NAG.2: 2 residues within 4Å: Chain A: T.225, N.252 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.268, H.293 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: P.457, S.458, N.484, K.508 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: K.177, N.229, M.255, Y.279 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.279 NAG-NAG.7: 2 residues within 4Å: Chain B: T.225, N.252 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: N.268, H.293 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: P.457, S.458, N.484, K.508 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA.4: 10 residues within 4Å: Chain A: E.340, S.364, N.390, T.392, K.393, V.412, D.414, Y.439 Chain C: C.16, C.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.393 NAG-NAG-BMA-BMA.9: 10 residues within 4Å: Chain B: E.340, S.364, N.390, T.392, K.393, V.412, D.414, Y.439 Chain D: I.15, I.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.393

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

NAG.11: 2 residues within 4Å: Chain A: E.148, N.173 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.148 NAG.12: 2 residues within 4Å: Chain A: N.375, E.376 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.376 NAG.13: 1 residues within 4Å: Chain A: N.613 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.613 NAG.14: 1 residues within 4Å: Chain A: N.639 No protein-ligand interaction detected (PLIP) NAG.15: 4 residues within 4Å: Chain A: N.242, T.243, L.246, W.273 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.246 Hydrogen bonds: A:N.242 NAG.16: 2 residues within 4Å: Chain B: E.148, N.173 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.148 NAG.17: 2 residues within 4Å: Chain B: N.375, E.376 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.376 NAG.18: 1 residues within 4Å: Chain B: N.613 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.613 NAG.19: 1 residues within 4Å: Chain B: N.639 No protein-ligand interaction detected (PLIP) NAG.20: 4 residues within 4Å: Chain B: N.242, T.243, L.246, W.273 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.246 Hydrogen bonds: B:N.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lim, C.S. et al., TLR3 forms a highly organized cluster when bound to a poly(I:C) RNA ligand. Nat Commun (2022)

Release Date

2022-11-16

Peptides

Toll-like receptor 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Toll-like receptor 3

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