SMTL ID : 3wpc.1

Crystal structure of horse TLR9 in complex with agonistic DNA1668_12mer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 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: 5 residues within 4Å: Chain A: S.688, R.689, N.710, V.733, D.735 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain B: S.688, R.689, N.710, V.733, D.735 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: H.146, G.178, N.179 No protein-ligand interaction detected (PLIP) NAG.4: 7 residues within 4Å: Chain A: C.157, Y.158, P.162, C.163, G.164, R.165, N.189 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.162 Hydrogen bonds: A:C.163, A:G.164, A:N.189 Water bridges: A:A.166 NAG.5: 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.6: 4 residues within 4Å: Chain A: Q.489, N.492, S.494, H.516 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.489, A:S.494, A:S.494 Water bridges: A:N.492 NAG.7: 4 residues within 4Å: Chain A: N.546, S.548, V.570, S.571 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.546, A:S.548 Water bridges: A:N.546, A:S.571 NAG.8: 7 residues within 4Å: Chain A: F.646, A.670, S.672, N.673, F.694 Chain C: A.5, C.6 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:R.53, A:N.673 Hydrophobic interactions: A:F.646 Hydrogen bonds: A:S.672, A:N.673 NAG.10: 4 residues within 4Å: Chain B: H.146, A.147, G.178, N.179 No protein-ligand interaction detected (PLIP) NAG.11: 7 residues within 4Å: Chain B: C.157, Y.158, P.162, C.163, G.164, R.165, N.189 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.162 Hydrogen bonds: B:C.163, B:G.164, B:N.189, B:N.189 Water bridges: B:A.166 NAG.12: 3 residues within 4Å: Chain B: S.196, A.220, N.221 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.220 Hydrogen bonds: B:N.221 NAG.13: 4 residues within 4Å: Chain B: S.263, R.264, G.287, N.288 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.264, B:N.288 Water bridges: B:R.264, B:G.287 NAG.14: 2 residues within 4Å: Chain B: N.492, S.494 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.494, B:S.494 Water bridges: B:Q.489, B:Q.489, B:N.492, B:N.492 NAG.15: 3 residues within 4Å: Chain B: G.517, N.546, S.548 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.546, B:S.548 Water bridges: B:G.517, B:N.546 NAG.16: 6 residues within 4Å: Chain B: F.646, S.672, N.673, F.694 Chain D: A.5, C.6 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.646 Hydrogen bonds: B:S.672, B:N.673

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

SO4.9: 9 residues within 4Å: Chain A: I.211, V.212, T.213, L.214, V.230, N.233, P.252, L.254, S.273 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.212, A:V.230, A:S.273 Water bridges: A:N.233 SO4.18: 7 residues within 4Å: Chain B: I.211, V.212, L.214, V.230, N.233, P.252, S.273 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.273 Water bridges: B:C.234

1 x NA: SODIUM ION(Non-functional Binders)

NA.17: 2 residues within 4Å: Chain B: A.551, T.577 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.577

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 10 residues within 4Å: Chain B: F.700, A.701, A.703, T.704, L.706, R.707, F.724, L.727, S.730, L.731 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.704, B:R.707, B:S.730 Water bridges: B:L.731

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ohto, U. et al., Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9. Nature (2015)

Release Date

2015-02-11

Peptides

Toll-like receptor 9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Toll-like receptor 9

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