SMTL ID : 5y3k.1 (1 other biounit)

Crystal structure of horse TLR9 in complex with two DNAs (CpG DNA and GCGCAC DNA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

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: 6 residues within 4Å: Chain A: S.688, R.689, N.710, S.712, V.733, D.735 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: H.146, A.147, N.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.179 NAG.3: 6 residues within 4Å: Chain A: C.157, Y.158, C.163, G.164, R.165, N.189 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.163, A:G.164, A:N.189 NAG.4: 3 residues within 4Å: Chain A: S.196, A.220, N.221 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.220 Hydrogen bonds: A:N.221 NAG.5: 6 residues within 4Å: Chain A: P.624, F.646, N.648, S.650, N.673 Ligands: NAG.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.673 Hydrogen bonds: A:N.648 NAG.6: 2 residues within 4Å: Chain A: N.492, S.494 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.494, A:S.494 NAG.7: 4 residues within 4Å: Chain A: G.517, N.546, S.548 Ligands: DG-DC-DG-DC-DA-DC.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.548 Water bridges: A:N.546 NAG.8: 4 residues within 4Å: Chain A: S.672, N.673, F.694 Ligands: NAG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.672, A:N.673

1 x DG- DC- DG- DC- DA- DC: DNA (5'-D(*GP*CP*GP*CP*AP*C)-3')(Non-covalent)

DG-DC-DG-DC-DA-DC.9: 10 residues within 4Å: Chain A: D.513, Y.515, G.542, V.543, G.544, H.545, N.546, R.569, V.570 Ligands: NAG.7 Protein-ligand interaction information (PLIP) not available

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ohto, U. et al., Toll-like Receptor 9 Contains Two DNA Binding Sites that Function Cooperatively to Promote Receptor Dimerization and Activation. Immunity (2018)

Release Date

2018-04-18

Peptides

Toll-like receptor 9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Toll-like receptor 9

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