SMTL ID : 5zln.1

Crystal structure of mouse TLR9 in complex with two DNAs (CpG DNA and TCGCCA DNA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

DT-DC-DG-DC.1: 22 residues within 4Å: Chain A: D.234, H.235, A.236, Y.320, K.322, K.323, V.324, S.325, F.326, A.327, F.350, R.352, F.377 Chain B: D.510, Y.512, G.539, I.540, G.541, H.542, R.566, V.567 Ligands: NAG-NAG.11 Protein-ligand interaction information (PLIP) not available DT-DC-DG-DC.2: 23 residues within 4Å: Chain A: D.510, Y.512, G.539, I.540, G.541, H.542, R.566, V.567 Chain B: D.234, H.235, A.236, Y.320, R.321, K.322, K.323, V.324, S.325, F.326, A.327, F.350, R.352, F.377 Ligands: NAG-NAG.6 Protein-ligand interaction information (PLIP) not available

2 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.3: 9 residues within 4Å: Chain A: Y.154, P.158, C.159, T.160, G.161, N.185, L.206, I.241, E.242 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.241 NAG-NAG-BMA.4: 3 residues within 4Å: Chain A: S.259, H.260, N.284 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.222

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

NAG-NAG.5: 5 residues within 4Å: Chain A: S.276, Q.280, N.303, Q.306, N.307 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.543, S.545, S.568 Ligands: DT-DC-DG-DC.2 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain A: F.643, T.669, N.670 Chain D: G.3, C.4 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain A: S.685, N.707, S.709, H.710, V.730, D.732 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: S.259, H.260, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain B: S.276, Q.280, N.303, Q.306, N.307 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain A: K.323 Chain B: N.543, S.545, S.568 Ligands: DT-DC-DG-DC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.323 NAG-NAG.12: 5 residues within 4Å: Chain A: F.83 Chain B: F.643, N.670 Chain C: G.3, C.4 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain B: S.685, N.707, S.709, H.710, D.732 No protein-ligand interaction detected (PLIP)

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

NAG.14: 2 residues within 4Å: Chain A: P.252, N.275 No protein-ligand interaction detected (PLIP) NAG.19: 6 residues within 4Å: Chain B: Y.154, C.159, T.160, G.161, N.185, L.206 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.159, B:T.160 NAG.20: 2 residues within 4Å: Chain B: P.252, N.275 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.275

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

SO4.15: 4 residues within 4Å: Chain A: R.328, H.330, N.355, Y.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.355 Salt bridges: A:R.328, A:H.330 SO4.16: 4 residues within 4Å: Chain A: Q.245, K.246, S.247, H.249 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.246, A:S.247 Salt bridges: A:K.246, A:H.249 SO4.17: 3 residues within 4Å: Chain A: R.92, L.95, R.98 4 PLIP interactions: 4 interactions with chain A Water bridges: A:L.95, A:R.98 Salt bridges: A:R.92, A:R.98 SO4.18: 2 residues within 4Å: Chain A: R.312, K.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.312 Water bridges: A:K.313 Salt bridges: A:K.313 SO4.21: 4 residues within 4Å: Chain B: Q.245, K.246, S.247, H.249 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.246, B:S.247 Salt bridges: B:H.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishida, H. et al., Structural basis for species-specific activation of mouse Toll-like receptor 9. FEBS Lett. (2018)

Release Date

2018-04-25

Peptides

Toll-like receptor 9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Toll-like receptor 9