SMTL ID : 3ciy.1

Mouse Toll-like receptor 3 ectodomain complexed with double-stranded RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.41 Å

Oligo State

homo-dimer

Ligands

4 x NAG- NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NDG.1: 6 residues within 4Å: Chain C: R.174, Q.225, N.226, T.251, Q.252, Y.276 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.251, C:Y.276 Hydrogen bonds: C:R.174, C:N.226, C:N.226 NAG-NDG.4: 1 residues within 4Å: Chain C: N.372 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.372 NAG-NDG.8: 5 residues within 4Å: Chain D: Q.225, N.226, T.251, Q.252, Y.276 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.226 Hydrophobic interactions: D:T.251, D:Q.252, D:Y.276 NAG-NDG.11: 2 residues within 4Å: Chain D: N.372, E.373 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.372, D:E.373

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-MAN.2: 1 residues within 4Å: Chain C: N.249 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-FUC.3: 1 residues within 4Å: Chain C: N.265 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN-MAN.5: 7 residues within 4Å: Chain A: U.15, U.16 Chain C: D.337, S.361, N.387, K.390, D.411 No protein-ligand interaction detected (PLIP)

2 x NAG- NDG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NDG-BMA.6: 2 residues within 4Å: Chain C: N.398, Q.424 No protein-ligand interaction detected (PLIP) NAG-NDG-BMA.13: 2 residues within 4Å: Chain D: N.398, Q.424 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.398, D:Q.424

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.7: 3 residues within 4Å: Chain C: P.454, S.455, N.481 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain D: P.454, N.481 No protein-ligand interaction detected (PLIP)

1 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(Post Translational Modification)

NAG-NAG-BMA.9: 2 residues within 4Å: Chain D: W.247, N.249 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUL: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-FUL.10: 4 residues within 4Å: Chain D: N.265, R.286, S.288, P.289 No protein-ligand interaction detected (PLIP)

1 x NAG- NDG- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NDG-MAN-MAN-MAN.12: 6 residues within 4Å: Chain B: A.17 Chain D: D.337, S.361, N.387, D.411, Y.436 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.361, D:D.411, D:D.411, D:Y.436

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

NAG.15: 5 residues within 4Å: Chain C: H.18, I.19, D.21, P.41, N.44 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.41 Hydrogen bonds: C:I.19, C:N.44 NAG.16: 2 residues within 4Å: Chain C: E.145, N.170 No protein-ligand interaction detected (PLIP) NAG.17: 4 residues within 4Å: Chain D: H.18, I.19, P.41, N.44 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.19, D:N.44 NAG.18: 1 residues within 4Å: Chain D: N.170 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L. et al., Structural basis of toll-like receptor 3 signaling with double-stranded RNA. Science (2008)

Release Date

2008-05-06

Peptides

Toll-like receptor 3: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

Toll-like receptor 3

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