SMTL ID : 3w3j.1

Crystal structure of human TLR8 in complex with CL097

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 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: 15 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 Ligands: SO4.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.440, A:K.204, A:H.442 Hydrophobic interactions: A:L.228, A:Y.269 NAG-NAG-BMA-MAN.4: 16 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 Ligands: SO4.32, GOL.33 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

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 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.517, A:N.517, A:N.517 NAG-NAG.5: 8 residues within 4Å: Chain B: K.454, C.457, D.465, S.467, L.468, N.489, Y.512, D.514 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.468

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.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.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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.456, B:K.454, B:Q.456 Hydrophobic interactions: B:V.536

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

NAG.7: 2 residues within 4Å: Chain A: S.500, N.524 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.524, A:N.524, A:S.526, A:S.526 NAG.8: 5 residues within 4Å: Chain A: N.634, F.656, N.658, T.660, 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: 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.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.21: 3 residues within 4Å: Chain B: S.500, N.524, A.525 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.524 Water bridges: B:N.524, B:S.526 NAG.22: 5 residues within 4Å: Chain B: N.634, F.656, N.658, T.660, L.661 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.656 Hydrogen bonds: B:N.634, B:N.658 Water bridges: B:N.658 NAG.23: 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.24: 3 residues within 4Å: Chain B: K.586, S.587, N.618 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.618, B:N.618, B:N.618

2 x C09: 2-(ethoxymethyl)-1H-imidazo[4,5-c]quinolin-4-amine(Non-covalent)

C09.11: 14 residues within 4Å: Chain A: D.521, D.523, G.550, V.551, T.552 Chain B: F.324, Y.326, Y.331, G.354, V.356, I.381, F.383, R.407 Ligands: SO4.13 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:D.521, A:T.552 Water bridges: A:D.521 Hydrophobic interactions: B:F.324, B:Y.326, B:V.356, B:V.356 pi-Stacking: B:Y.331, B:F.383, B:F.383 C09.20: 13 residues within 4Å: Chain A: F.324, Y.326, Y.331, G.354, V.356, F.383, R.407 Chain B: D.521, D.523, G.550, V.551, T.552 Ligands: SO4.25 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:D.521, B:T.552, B:T.552 Water bridges: B:D.521 Hydrophobic interactions: A:F.324, A:Y.326, A:V.356, A:V.356 pi-Stacking: A:Y.331, A:F.383, A:F.383

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

SO4.12: 3 residues within 4Å: Chain A: P.332, Q.333, H.334 Ligand excluded by PLIP SO4.13: 6 residues within 4Å: Chain A: D.523, T.552 Chain B: F.239, K.328, G.329 Ligands: C09.11 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain A: R.268, K.292 Ligand excluded by PLIP SO4.15: 6 residues within 4Å: Chain A: L.109, E.111, E.128, S.130, Y.154, H.442 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain A: S.49, N.71, N.73 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain A: K.655, K.677, R.701 Ligand excluded by PLIP SO4.18: 7 residues within 4Å: Chain A: Y.154, A.156, S.185, S.187, F.206, P.441 Ligands: NAG-NAG-BMA-MAN.1 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: H.704, K.727, T.728 Ligand excluded by PLIP SO4.25: 7 residues within 4Å: Chain A: F.239, Y.326, K.328, G.329 Chain B: D.523, T.552 Ligands: C09.20 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain B: R.268, K.292 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: R.353, H.447, F.448 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain B: K.655, K.677, R.701 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain B: S.49, N.71, N.73, H.74 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain B: S.703, H.704, K.727, T.728, N.730 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain B: R.693, K.717, K.741 Ligand excluded by PLIP SO4.32: 6 residues within 4Å: Chain B: S.185, S.187, F.206, P.441 Ligands: NAG-NAG-BMA-MAN.4, NAG-NAG-BMA-MAN.4 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.33: 4 residues within 4Å: Chain B: N.444, T.449 Ligands: NAG-NAG-BMA-MAN.4, NAG-NAG-BMA-MAN.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.444

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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