SMTL ID : 3wpf.1

Crystal structure of mouse TLR9 (unliganded form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: S.689, N.711, S.713, H.714, D.736 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.689, A:N.711, A:S.713, A:D.736 NAG.2: 5 residues within 4Å: Chain A: S.280, Q.284, N.307, Q.310, N.311 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.307 Hydrogen bonds: A:S.280, A:N.311, A:N.311 NAG.3: 6 residues within 4Å: Chain A: C.157, Y.158, P.162, C.163, G.165, N.189 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.162 Hydrogen bonds: A:C.163

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

SO4.4: 3 residues within 4Å: Chain A: L.29, K.30, S.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.30, A:S.31 SO4.5: 6 residues within 4Å: Chain A: Y.187, Y.208, N.209, G.232, R.235, I.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.209, A:I.245 Water bridges: A:N.189 Salt bridges: A:R.235 SO4.6: 1 residues within 4Å: Chain A: R.581 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.581 SO4.7: 3 residues within 4Å: Chain A: K.74, Y.111 Ligands: SO4.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.111, A:Y.111 Water bridges: A:S.130 Salt bridges: A:K.74 SO4.8: 5 residues within 4Å: Chain A: N.766, K.769, G.778, R.779, S.780 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.766, A:S.780 Water bridges: A:S.780 Salt bridges: A:K.769, A:R.779 SO4.9: 3 residues within 4Å: Chain A: W.26, S.51, W.75 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.51 SO4.10: 4 residues within 4Å: Chain A: H.55, S.88, C.89, H.90 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.90, A:H.90 Salt bridges: A:H.55 SO4.11: 3 residues within 4Å: Chain A: R.356, N.383, R.405 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.383 Salt bridges: A:R.356, A:R.405 SO4.12: 3 residues within 4Å: Chain A: K.74, N.108 Ligands: SO4.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.108 Water bridges: A:S.110, A:S.110, A:S.128 Salt bridges: A:K.74 SO4.13: 3 residues within 4Å: Chain A: T.7, L.8, R.787 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.7, A:L.8 Salt bridges: A:R.787 SO4.14: 4 residues within 4Å: Chain A: Y.534, N.535, H.564, D.566 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.564 SO4.15: 4 residues within 4Å: Chain A: Q.249, K.250, S.251, H.253 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.250, A:S.251 Salt bridges: A:H.253

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Toll-like receptor 9

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