SMTL ID : 3wn4.1 (1 other biounit)

Crystal structure of human TLR8 in complex with DS-877

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

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

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 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.228, A:Y.269 Hydrogen bonds: A:K.204 NAG-NAG-BMA-MAN-MAN.14: 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:K.204

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, S.491, Y.512, D.514 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 11 residues within 4Å: Chain A: K.454, Q.456, Y.512, T.516, V.536, D.538, S.540, V.566, N.568, E.590, V.592 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.456, A:Q.456, A:Y.512 Hydrophobic interactions: A:Y.512, A:V.536 Water bridges: A:K.454 NAG-NAG-BMA.15: 11 residues within 4Å: Chain B: S.404, R.450, I.453, K.454, C.457, S.467, L.468, N.489, S.491, Y.512, D.514 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 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:Q.456 Hydrophobic interactions: B:Y.512, B:V.536 Water bridges: B:K.454

2 x D87: 2-butylfuro[2,3-c]quinolin-4-amine(Non-covalent)

D87.4: 5 residues within 4Å: Chain A: F.324, Y.326, Y.331, V.356, F.383 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.324, A:Y.326, A:Y.326, A:Y.331, A:V.356, A:V.356, A:F.383, A:F.383, A:F.383, A:F.383 pi-Stacking: A:F.383 D87.17: 5 residues within 4Å: Chain B: F.324, Y.326, Y.331, V.356, F.383 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.324, B:Y.326, B:Y.326, B:Y.331, B:V.356, B:V.356, B:F.383, B:F.383, B:F.383, B:F.383 pi-Stacking: B:F.383

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

NAG.5: 11 residues within 4Å: Chain A: K.41, Y.42, G.63, N.66 Chain B: T.739, T.740, L.742, S.743, H.768, N.770, V.771 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: H.55, T.57, N.93, T.95 Ligand excluded by PLIP NAG.7: 8 residues within 4Å: Chain A: T.179, S.200, S.201, N.225 Chain B: K.586, K.617, N.618 Ligands: NAG.25 Ligand excluded by PLIP NAG.8: 9 residues within 4Å: Chain A: L.345, S.346, R.348, N.373 Chain B: Y.460, G.461, D.484, A.486, K.511 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: E.362, Q.366, M.369, Q.370, N.394 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: S.500, N.524, A.525 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: T.529, Q.559, N.560 Ligand excluded by PLIP NAG.12: 9 residues within 4Å: Chain A: K.565, K.586, S.587, V.589, N.618 Chain B: R.203, Q.266, R.268 Ligands: NAG.20 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.634, L.638, N.658, L.661 Ligand excluded by PLIP NAG.18: 11 residues within 4Å: Chain A: T.739, T.740, L.742, S.743, H.768, N.770, V.771 Chain B: K.41, Y.42, G.63, N.66 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: H.55, T.57, N.93, T.95 Ligand excluded by PLIP NAG.20: 8 residues within 4Å: Chain A: K.586, K.617, N.618 Chain B: T.179, S.200, S.201, N.225 Ligands: NAG.12 Ligand excluded by PLIP NAG.21: 9 residues within 4Å: Chain A: Y.460, G.461, D.484, A.486, K.511 Chain B: L.345, S.346, R.348, N.373 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain B: E.362, Q.366, M.369, Q.370, N.394 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: S.500, N.524, A.525 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: T.529, Q.559, N.560 Ligand excluded by PLIP NAG.25: 9 residues within 4Å: Chain A: R.203, Q.266, R.268 Chain B: K.565, K.586, S.587, V.589, N.618 Ligands: NAG.7 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: N.634, L.638, N.658, L.661 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kokatla, H.P. et al., Structure-based design of novel human Toll-like receptor 8 agonists. Chemmedchem (2014)

Release Date

2014-02-19

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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