SMTL ID : 5y3j.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 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, G.178, N.179 No protein-ligand interaction detected (PLIP) NAG.3: 7 residues within 4Å: Chain A: C.157, Y.158, P.162, C.163, G.164, R.165, N.189 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.162 Hydrogen bonds: A:C.163, A:G.164, A:N.189, A:N.189 Water bridges: A:G.164, A:A.166 NAG.4: 2 residues within 4Å: Chain A: S.196, N.221 1 PLIP interactions: 1 interactions with chain A 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 6 PLIP interactions: 6 interactions with chain A Water bridges: A:N.648, A:N.648, A:N.648, A:N.648, A:N.648, A:S.650 NAG.6: 2 residues within 4Å: Chain A: N.492, S.494 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.494, A:S.494 Water bridges: A:N.492, A:Q.495 NAG.7: 2 residues within 4Å: Chain A: N.546, S.548 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.546, A:S.548 Water bridges: A:G.517, A:G.517, A:G.517, A:N.546, A:S.571 NAG.8: 5 residues within 4Å: Chain A: A.670, S.672, N.673, F.694 Ligands: NAG.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.672, A:N.673 Water bridges: A:N.673, A:N.673

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain A: R.541, G.542, S.568, R.569 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.568

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

DT-DC-DG-DC-DA-DC.10: 8 residues within 4Å: Chain A: D.513, Y.515, G.542, V.543, G.544, H.545, R.569, V.570 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
B

Toll-like receptor 9

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