SMTL ID : 3w3n.1

Crystal structure of human TLR8 in complex with Resiquimod (R848) crystal form 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 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(Post Translational Modification)

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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.228, A:Y.269 Hydrogen bonds: A:K.204, A:H.442 NAG-NAG-BMA-MAN-MAN.3: 10 residues within 4Å: Chain A: K.454, Q.456, Y.512, V.536, 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 Hydrophobic interactions: A:V.536 NAG-NAG-BMA-MAN-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 Hydrophobic interactions: B:L.228, B:Y.269 Hydrogen bonds: B:K.204, B:H.442 NAG-NAG-BMA-MAN-MAN.6: 10 residues within 4Å: Chain B: K.454, Q.456, Y.512, V.536, D.538, S.540, V.566, N.568, E.590, V.592 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.456, B:Q.456, B:Y.512 Hydrophobic interactions: B:V.536

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: 9 residues within 4Å: Chain A: R.450, K.454, C.457, S.467, L.468, N.489, S.491, Y.512, D.514 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.450 Water bridges: A:N.517 NAG-NAG-BMA.5: 12 residues within 4Å: Chain A: R.547 Chain B: R.450, I.453, K.454, C.457, D.465, S.467, L.468, N.489, S.491, Y.512, D.514 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.450, B:R.450

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

NAG.7: 3 residues within 4Å: Chain A: S.500, N.524, A.525 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.525 NAG.8: 4 residues within 4Å: Chain A: N.634, F.656, N.658, L.661 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.656 Hydrogen bonds: A:N.634, A:N.658 NAG.9: 3 residues within 4Å: Chain A: L.345, S.346, N.373 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.373 Water bridges: A:R.348, A:R.348 NAG.10: 5 residues within 4Å: Chain A: E.362, Q.366, M.369, Q.370, N.394 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.366, A:N.394 NAG.11: 5 residues within 4Å: Chain A: T.562, 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.12: 4 residues within 4Å: Chain A: K.41, Y.42, Q.65, N.66 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.65 Hydrogen bonds: A:Q.65, A:N.66 Water bridges: A:Q.65 NAG.16: 3 residues within 4Å: Chain B: S.500, N.524, A.525 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.525 Water bridges: B:N.524 NAG.17: 5 residues within 4Å: Chain B: N.634, F.656, N.658, T.660, L.661 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.656 Hydrogen bonds: B:N.634, B:N.658 NAG.18: 4 residues within 4Å: Chain B: L.345, S.346, R.348, N.373 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.345 Hydrogen bonds: B:R.348, B:N.373 NAG.19: 5 residues within 4Å: Chain B: E.362, Q.366, M.369, Q.370, N.394 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.366, B:N.394 NAG.20: 4 residues within 4Å: Chain B: K.586, S.587, V.589, N.618 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.618, B:N.618 NAG.21: 4 residues within 4Å: Chain B: H.55, T.57, N.93, T.95 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.93 NAG.22: 4 residues within 4Å: Chain B: K.221, Q.262, N.263, N.287 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.263, B:N.287

2 x RX8: 1-[4-amino-2-(ethoxymethyl)-1H-imidazo[4,5-c]quinolin-1-yl]-2-methylpropan-2-ol(Non-covalent)

RX8.13: 14 residues within 4Å: Chain A: D.521, D.523, G.550, V.551, T.552 Chain B: F.324, Y.326, I.327, G.329, S.330, Y.331, G.354, V.356, F.383 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:D.521, A:T.552 Water bridges: A:D.521, A:T.552 Hydrophobic interactions: B:F.324, B:Y.326, B:Y.326, B:V.356 pi-Stacking: B:Y.331, B:F.383, B:F.383 RX8.15: 14 residues within 4Å: Chain A: F.324, Y.326, I.327, G.329, S.330, Y.331, G.354, V.356, F.383 Chain B: D.521, D.523, G.550, V.551, T.552 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:D.521, B:D.523, B:T.552, B:T.552, A:G.329 Hydrophobic interactions: A:F.324, A:Y.326, A:Y.326 pi-Stacking: A:Y.331, A:F.383, A:F.383

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 6 residues within 4Å: Chain A: Q.663, S.686, D.687, F.688, T.689, S.690 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.663, A:S.686, A:S.690

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanji, H. et al., Structural reorganization of the Toll-like receptor 8 dimer induced by agonistic ligands. Science (2013)

Release Date

2013-04-03

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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