SMTL ID : 3w3l.2 (1 other biounit)

Crystal structure of human TLR8 in complex with Resiquimod (R848) crystal form 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 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

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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.456, A:K.454, A:Q.456, A:Y.512 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 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.228, B:Y.269 Hydrogen bonds: 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 Hydrophobic interactions: B:V.536 Water bridges: B:Y.512

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.2: 9 residues within 4Å: Chain A: S.404, R.450, K.454, C.457, S.467, L.468, N.489, Y.512, D.514 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.450 Water bridges: A:S.491, A:N.517 NAG-NAG-BMA.5: 9 residues within 4Å: Chain B: S.404, 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:N.517

7 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.656 Hydrogen bonds: A:N.634, A:N.658, A:N.658 NAG.9: 3 residues within 4Å: Chain A: R.348, P.372, N.373 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.373 NAG.10: 4 residues within 4Å: Chain A: K.586, S.587, V.589, N.618 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.618 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: 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 NAG.18: 4 residues within 4Å: Chain B: K.586, S.587, V.589, N.618 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.618 Water bridges: B:K.565, B:K.565, B:K.565

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

RX8.11: 15 residues within 4Å: Chain A: D.521, D.523, G.550, V.551, T.552 Chain B: F.324, Y.326, I.327, S.330, Y.331, G.354, V.356, F.383, R.407 Ligands: SO4.13 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.324, B:Y.326, B:Y.326, B:V.356, B:V.356 Water bridges: B:G.329 pi-Stacking: B:Y.331, B:F.383, B:F.383 Hydrogen bonds: A:D.521, A:D.523, A:T.552, A:T.552 RX8.15: 17 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 Ligands: SO4.14 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.324, A:Y.326, A:V.356 Water bridges: A:G.329 pi-Stacking: A:Y.331, A:F.383, A:F.383 Hydrogen bonds: B:D.521, B:D.523, B:T.552, B:T.552

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

SO4.12: 2 residues within 4Å: Chain A: K.677, R.701 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.677, A:R.701 SO4.13: 2 residues within 4Å: Chain A: D.523 Ligands: RX8.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.523 SO4.14: 2 residues within 4Å: Chain A: Y.331 Ligands: RX8.15 No protein-ligand interaction detected (PLIP) SO4.19: 3 residues within 4Å: Chain B: K.655, K.677, R.701 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.655, B:K.677, B:R.701

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
B

B
C

Toll-like receptor 8

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