SMTL ID : 4r6a.1

Crystal structure of human TLR8 in complex with Hybrid-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.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 Hydrogen bonds: A:D.440, A:K.204 Hydrophobic interactions: A:L.228, A:Y.269

4 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, Y.512, D.514 Chain B: R.547 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.468 NAG-NAG-BMA.3: 9 residues within 4Å: Chain A: K.454, Q.456, Y.512, D.538, S.540, V.566, N.568, E.590, V.592 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.456, A:K.454, A:Q.456 NAG-NAG-BMA.5: 10 residues within 4Å: Chain B: S.404, R.450, I.453, K.454, C.457, S.467, L.468, N.489, Y.512, D.514 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.450 NAG-NAG-BMA.6: 11 residues within 4Å: Chain B: K.454, Q.456, Y.512, T.516, V.536, D.538, S.540, V.566, N.568, E.590, V.592 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.456, B:K.454, B:Q.456 Hydrophobic interactions: B:Y.512, B:V.536

1 x NAG- NAG- BMA- MAN: 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(Post Translational Modification)

NAG-NAG-BMA-MAN.4: 14 residues within 4Å: Chain B: 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.440, B:K.204, B:H.442 Hydrophobic interactions: B:L.228, B:Y.269

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

NAG.7: 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.8: 4 residues within 4Å: Chain A: S.500, N.524, A.525, S.526 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.525, A:S.526 NAG.9: 4 residues within 4Å: Chain A: K.586, S.587, V.589, N.618 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain A: N.634, N.658, T.660, L.661 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.634 NAG.13: 5 residues within 4Å: Chain B: K.221, G.222, I.224, Q.262, N.263 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.263 NAG.14: 4 residues within 4Å: Chain B: L.345, S.346, R.348, N.373 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.348, B:R.348, B:N.373 NAG.15: 2 residues within 4Å: Chain B: S.500, N.524 5 PLIP interactions: 5 interactions with chain B Water bridges: B:N.524, B:N.524, B:A.525, B:S.526, B:S.526 NAG.16: 2 residues within 4Å: Chain B: Q.559, N.560 No protein-ligand interaction detected (PLIP) NAG.17: 5 residues within 4Å: Chain B: K.565, K.586, S.587, V.589, N.618 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.618 Water bridges: B:N.618 NAG.18: 4 residues within 4Å: Chain B: N.634, F.656, N.658, L.661 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.656 Hydrogen bonds: B:N.634

2 x HB2: 1-(4-amino-2-butyl-1H-imidazo[4,5-c]quinolin-1-yl)-2-methylpropan-2-ol(Non-covalent)

HB2.11: 15 residues within 4Å: Chain A: D.521, D.523, G.550, V.551, T.552 Chain B: F.324, Y.326, I.327, K.328, G.329, S.330, G.354, V.356, F.383, R.407 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.324, B:Y.326, B:Y.326, B:Y.326, B:V.356, A:T.552 pi-Stacking: B:Y.331, B:F.383, B:F.383 Hydrogen bonds: A:D.521, A:T.552 Water bridges: A:D.521 HB2.12: 16 residues within 4Å: Chain A: F.324, Y.326, I.327, G.329, S.330, Y.331, G.354, V.356, I.381, F.383, R.407 Chain B: D.521, D.523, G.550, V.551, T.552 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:T.552, A:F.324, A:Y.326, A:Y.326, A:V.356, A:F.383 Hydrogen bonds: B:D.521, B:T.552 Water bridges: B:D.521, B:D.523, B:T.552 pi-Stacking: A:Y.331, A:F.383, A:F.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ganapathi, L. et al., Hybrid-2: AnImidazoquinoline Dual Toll-like receptor 7/8 Agonist that Potently Activates Cytokine Production by Human Newborn and Adult Leukocytes. To be Published

Release Date

2015-08-26

Peptides

Toll-like receptor 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Toll-like receptor 8

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