SMTL ID : 3wn4.2 (1 other biounit)

Crystal structure of human TLR8 in complex with DS-877

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(2-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-MAN.1: 14 residues within 4Å: Chain A: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, D.440, H.442, S.443, N.444, F.445, Y.446 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.228, A:Y.269 Hydrogen bonds: A:K.204

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(Post Translational Modification)

NAG-NAG-BMA.2: 11 residues within 4Å: Chain A: S.404, R.450, I.453, K.454, C.457, S.467, L.468, N.489, S.491, Y.512, D.514 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 11 residues within 4Å: Chain A: K.454, Q.456, Y.512, T.516, V.536, D.538, S.540, V.566, N.568, E.590, V.592 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.456, A:Q.456, A:Y.512 Hydrophobic interactions: A:Y.512, A:V.536 Water bridges: A:K.454

1 x D87: 2-butylfuro[2,3-c]quinolin-4-amine(Non-covalent)

D87.4: 5 residues within 4Å: Chain A: F.324, Y.326, Y.331, V.356, F.383 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.324, A:Y.326, A:Y.326, A:V.356, A:V.356, A:F.383 pi-Stacking: A:Y.331, A:F.383, A:F.383

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

NAG.5: 4 residues within 4Å: Chain A: K.41, Y.42, G.63, N.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.66 Water bridges: A:N.66 NAG.6: 4 residues within 4Å: Chain A: H.55, T.57, N.93, T.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.93 NAG.7: 4 residues within 4Å: Chain A: T.179, S.200, S.201, N.225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.200 NAG.8: 4 residues within 4Å: Chain A: L.345, S.346, R.348, N.373 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.348, A:R.348, A:N.373 NAG.9: 5 residues within 4Å: Chain A: E.362, Q.366, M.369, Q.370, N.394 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.366, A:Q.366, A:Q.370, A:N.394 NAG.10: 3 residues within 4Å: Chain A: S.500, N.524, A.525 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.500, A:A.525 Water bridges: A:S.500 NAG.11: 3 residues within 4Å: Chain A: T.529, Q.559, N.560 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.560 NAG.12: 5 residues within 4Å: Chain A: K.565, K.586, S.587, V.589, N.618 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.618 NAG.13: 4 residues within 4Å: Chain A: N.634, L.638, N.658, L.661 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.634, A:N.658

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kokatla, H.P. et al., Structure-based design of novel human Toll-like receptor 8 agonists. Chemmedchem (2014)

Release Date

2014-02-19

Peptides

Toll-like receptor 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Toll-like receptor 8

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