SMTL ID : 5awa.1

Crystal structure of human TLR8 in complex with MB-568

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA-MAN-MAN.1: 15 residues within 4Å: Chain A: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, D.295, D.440, H.442, S.443, N.444, F.445, Y.446 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.269 Hydrogen bonds: A:K.204 NAG-NAG-BMA-MAN-MAN.11: 15 residues within 4Å: Chain B: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, D.295, D.440, H.442, S.443, N.444, F.445, Y.446 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.269 Hydrogen bonds: B:K.204

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.2: 11 residues within 4Å: Chain A: S.404, I.453, K.454, C.457, S.467, L.468, N.489, S.491, Y.512, D.514 Chain B: R.547 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 11 residues within 4Å: Chain A: R.547 Chain B: S.404, I.453, K.454, C.457, S.467, L.468, N.489, S.491, Y.512, D.514 No protein-ligand interaction detected (PLIP)

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: 10 residues within 4Å: Chain A: K.454, Q.456, Y.512, T.516, D.538, S.540, V.566, N.568, E.590, V.592 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.456, A:K.454, A:Q.456, A:Y.512 NAG-NAG-BMA.13: 10 residues within 4Å: Chain B: K.454, Q.456, Y.512, T.516, D.538, S.540, V.566, N.568, E.590, V.592 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.456, B:K.454, B:Q.456

2 x M8D: 5-[[3-(aminomethyl)phenyl]methyl]-3-pentyl-quinolin-2-amine(Non-covalent)

M8D.4: 12 residues within 4Å: Chain A: G.329, S.330, Y.331, V.356, I.381, F.383, R.407 Chain B: D.521, D.523, G.550, V.551, T.552 13 PLIP interactions: 2 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:D.521, B:T.552 Hydrophobic interactions: A:Y.331, A:Y.331, A:Y.331, A:V.356, A:V.356, A:I.381, A:F.383, A:F.383 pi-Stacking: A:Y.331, A:F.383, A:F.383 M8D.14: 12 residues within 4Å: Chain A: D.521, D.523, G.550, V.551, T.552 Chain B: G.329, S.330, Y.331, V.356, I.381, F.383, R.407 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.331, B:Y.331, B:Y.331, B:V.356, B:V.356, B:I.381, B:F.383, B:F.383 pi-Stacking: B:Y.331, B:F.383, B:F.383 Hydrogen bonds: A:D.521, A:D.523, A:T.552

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

NAG.5: 2 residues within 4Å: Chain A: S.500, N.524 No protein-ligand interaction detected (PLIP) NAG.6: 5 residues within 4Å: Chain A: L.345, S.346, R.348, P.372, N.373 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.372 Hydrogen bonds: A:R.348, A:R.348, A:N.373 NAG.7: 4 residues within 4Å: Chain A: K.586, S.587, V.589, N.618 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.618 Water bridges: A:N.618, A:N.618 NAG.8: 4 residues within 4Å: Chain A: K.221, Q.262, N.263, N.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.287 NAG.9: 3 residues within 4Å: Chain A: T.529, Q.559, N.560 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.560 Water bridges: A:Q.559 NAG.10: 5 residues within 4Å: Chain A: N.634, L.638, F.656, N.658, L.661 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain B: S.500, N.524 No protein-ligand interaction detected (PLIP) NAG.16: 5 residues within 4Å: Chain B: L.345, S.346, R.348, P.372, N.373 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.372 Hydrogen bonds: B:R.348, B:R.348, B:N.373 NAG.17: 4 residues within 4Å: Chain B: K.586, S.587, V.589, N.618 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.618 Water bridges: B:N.618, B:N.618 NAG.18: 4 residues within 4Å: Chain B: K.221, Q.262, N.263, N.287 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.287 NAG.19: 3 residues within 4Å: Chain B: T.529, Q.559, N.560 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.560 Water bridges: B:Q.559 NAG.20: 5 residues within 4Å: Chain B: N.634, L.638, F.656, N.658, L.661 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beesu, M. et al., Structure-based Design of Human TLR8-specific Agonists with Augmented Potency and Adjuvanticity. To Be Published

Release Date

2016-07-20

Peptides

Toll-like receptor 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Toll-like receptor 8

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