SMTL ID : 5awc.2 (1 other biounit)

Crystal structure of human TLR8 in complex with MB-564

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA.1: 13 residues within 4Å: Chain A: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, D.295, H.442, S.443, N.444, F.445 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.228, A:Y.269 Hydrogen bonds: A:K.204, A:H.442 Water bridges: A:N.444 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.4: 13 residues within 4Å: Chain B: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, 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 NAG-NAG-BMA.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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.456, B:K.454, B:Q.456, B:Y.512 Hydrophobic interactions: B:V.536

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: 10 residues within 4Å: Chain A: S.404, I.453, K.454, C.457, S.467, L.468, N.489, Y.512, D.514 Chain B: R.547 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 11 residues within 4Å: Chain B: S.404, I.453, K.454, C.457, D.465, S.467, L.468, N.489, S.491, Y.512, D.514 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain A: S.500, N.524 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.500 NAG.8: 5 residues within 4Å: Chain A: T.562, K.586, S.587, V.589, N.618 No protein-ligand interaction detected (PLIP) NAG.11: 2 residues within 4Å: Chain B: S.500, N.524 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.500 NAG.12: 4 residues within 4Å: Chain B: K.586, S.587, V.589, N.618 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.618

2 x M4D: 5-(4-azanylbutyl)-3-pentyl-quinolin-2-amine(Non-covalent)

M4D.9: 13 residues within 4Å: Chain A: V.498, D.521, D.523, G.550, T.552 Chain B: Y.326, G.329, S.330, Y.331, G.354, V.356, I.381, F.383 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:V.498, A:T.552, B:Y.326, B:Y.326, B:Y.326, B:Y.331, B:Y.331, B:V.356, B:V.356 Hydrogen bonds: A:D.521 pi-Stacking: B:Y.331, B:F.383, B:F.383 M4D.10: 14 residues within 4Å: Chain A: F.324, Y.326, G.329, S.330, Y.331, G.354, V.356, I.381, F.383 Chain B: D.521, D.523, G.550, V.551, T.552 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.324, A:Y.326, A:Y.326, A:Y.331, A:Y.331, A:V.356, A:V.356, B:T.552 pi-Stacking: A:Y.331, A:F.383, A:F.383 Hydrogen bonds: B:D.521, B:D.523, B:T.552

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beesu, M. et al., Structure-based Design of Human TLR8-specific Agonists with Augmented Potency and Adjuvanticity. To Be Published

Release Date

2016-07-20

Peptides

Toll-like receptor 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Toll-like receptor 8

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