SMTL ID : 5y3m.1

Crystal structure of bovine TLR9 in complex with two DNAs (CpG DNA and TCGTTT DNA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x DT- DC- DG- DT: DNA (5'-D(*TP*CP*GP*T)-3')(Non-covalent)

DT-DC-DG-DT.1: 22 residues within 4Å: Chain A: D.238, H.239, A.240, Y.324, H.325, K.326, K.327, V.328, S.329, F.330, A.331, F.354, R.356, F.381 Chain D: D.512, Y.514, G.541, V.542, G.543, H.544, R.568, V.569 Protein-ligand interaction information (PLIP) not available DT-DC-DG-DT.2: 23 residues within 4Å: Chain A: D.512, Y.514, G.541, V.542, G.543, H.544, R.568, V.569 Chain D: D.238, H.239, A.240, Y.324, H.325, K.326, K.327, V.328, S.329, F.330, A.331, F.354, R.356, F.381 Ligands: NAG.4 Protein-ligand interaction information (PLIP) not available

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

NAG.3: 6 residues within 4Å: Chain A: C.157, C.163, P.164, R.165, N.189, R.245 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.163 NAG.4: 3 residues within 4Å: Chain A: N.545, S.547 Ligands: DT-DC-DG-DT-DT.2 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Water bridges: D:K.327 Hydrogen bonds: A:N.545, A:S.547 NAG.5: 5 residues within 4Å: Chain A: L.451, N.452, Q.477, R.502, V.503 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.503 NAG.6: 2 residues within 4Å: Chain A: N.491, S.493 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.493, A:S.493 NAG.7: 6 residues within 4Å: Chain A: S.687, S.688, N.709, S.711, I.732, D.734 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.732 Hydrogen bonds: A:S.687, A:S.688, A:S.711, A:D.734 NAG.8: 6 residues within 4Å: Chain D: C.157, C.163, P.164, R.165, N.189, R.245 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:C.163, D:R.245 NAG.9: 2 residues within 4Å: Chain D: N.360, Q.364 No protein-ligand interaction detected (PLIP) NAG.10: 5 residues within 4Å: Chain A: F.87 Chain D: P.623, N.647, S.649, S.650 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:F.87 Hydrogen bonds: D:N.647 NAG.11: 3 residues within 4Å: Chain D: G.516, N.545, S.547 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.547 NAG.12: 3 residues within 4Å: Chain D: N.491, G.492, S.493 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.493

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: AD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

Toll-like receptor 9

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