SMTL ID : 2a0z.1

The molecular structure of toll-like receptor 3 ligand binding domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

5 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: 2 residues within 4Å: Chain A: E.12, N.31 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: T.22, Q.23, V.24, P.46, N.49 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: R.230, N.231, M.257, Y.281 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.226, T.227, W.252, N.254 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.270, F.293, S.294, H.295 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

NAG-NAG-BMA.4: 2 residues within 4Å: Chain A: N.244, W.275 No protein-ligand interaction detected (PLIP)

2 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

NAG-NAG-FUC.7: 4 residues within 4Å: Chain A: N.377, E.378, E.402 Ligands: SO4.14 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.9: 4 residues within 4Å: Chain A: P.459, S.460, N.486, K.510 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.510

1 x NAG- NAG- BMA- MAN- BMA: alpha-D-mannopyranose-(1-3)-[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-MAN-BMA.8: 7 residues within 4Å: Chain A: E.342, S.366, N.392, K.395, D.416, Y.441 Ligands: GLC.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.395

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

NAG-NDG.10: 2 residues within 4Å: Chain A: R.614, N.615 No protein-ligand interaction detected (PLIP)

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

NAG.11: 2 residues within 4Å: Chain A: E.150, N.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.150, A:N.175

2 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.12: 7 residues within 4Å: Chain A: T.394, D.416, G.418, Y.441, S.443 Ligands: NAG-NAG-BMA-MAN-BMA.8, NAG-NAG-BMA-MAN-BMA.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.416, A:S.443, A:S.443 GLC.13: 4 residues within 4Å: Chain A: Y.535, K.538, E.559, K.562 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.538

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

SO4.14: 2 residues within 4Å: Ligands: NAG-NAG-FUC.7, NAG-NAG-FUC.7 No protein-ligand interaction detected (PLIP) SO4.15: 4 residues within 4Å: Chain A: Y.305, N.307, H.338, N.340 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.305, A:N.340 Water bridges: A:Y.362 Salt bridges: A:H.338 SO4.16: 4 residues within 4Å: Chain A: R.467, N.494, Q.517, H.518 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.494, A:N.494, A:Q.517 Water bridges: A:R.467, A:R.467, A:N.547 Salt bridges: A:R.467, A:H.518

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.17: 2 residues within 4Å: Chain A: R.304, C.335 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bell, J.K. et al., The molecular structure of the Toll-like receptor 3 ligand-binding domain. Proc.Natl.Acad.Sci.USA (2005)

Release Date

2005-08-02

Peptides

Toll-like receptor 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Toll-like receptor 3