SMTL ID : 5az5.1 (1 other biounit)

Crystal structure of human TLR8 in complex with MB-343

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

3 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.295, D.440, H.442, S.443, N.444, F.445, Y.446 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.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.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 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: 12 residues within 4Å: Chain A: S.404, R.450, 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) NAG-NAG.5: 10 residues within 4Å: Chain B: R.450, I.453, K.454, C.457, D.465, S.467, L.468, N.489, Y.512, D.514 No protein-ligand interaction detected (PLIP)

1 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.6: 9 residues within 4Å: Chain B: K.454, Q.456, Y.512, D.538, S.540, V.566, N.568, E.590, V.592 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.456, B:K.454, B:Q.456

2 x MBL: 1-pentyl-4-phenyl-imidazol-2-amine(Non-covalent)

MBL.7: 11 residues within 4Å: Chain A: F.324, Y.326, Y.331, G.354, V.356, I.381, F.383 Chain B: D.521, D.523, G.550, T.552 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:T.552, B:T.552 Salt bridges: B:D.521, B:D.523 Hydrophobic interactions: A:F.324, A:Y.326, A:Y.326, A:Y.326, A:V.356, A:V.356, A:F.383 pi-Stacking: A:Y.331, A:F.383 MBL.11: 12 residues within 4Å: Chain A: V.498, D.521, D.523, G.550, T.552 Chain B: F.324, Y.326, Y.331, G.354, V.356, F.383, R.407 15 PLIP interactions: 6 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:V.498, A:T.552, B:F.324, B:Y.326, B:Y.326, B:V.356, B:V.356, B:F.383, B:F.383 Hydrogen bonds: A:T.552, A:T.552 Salt bridges: A:D.521, A:D.523 pi-Stacking: B:Y.331, B:F.383

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

NAG.8: 3 residues within 4Å: Chain A: N.634, N.658, L.661 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.658 NAG.9: 3 residues within 4Å: Chain A: R.348, P.372, N.373 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.348, A:R.348 NAG.10: 6 residues within 4Å: Chain A: T.562, K.565, K.586, S.587, V.589, N.618 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.565, A:K.586 NAG.12: 4 residues within 4Å: Chain B: N.634, L.638, N.658, L.661 No protein-ligand interaction detected (PLIP) NAG.13: 4 residues within 4Å: Chain B: L.345, S.346, R.348, N.373 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.348, B:R.348, B:N.373 NAG.14: 5 residues within 4Å: Chain B: T.562, K.586, S.587, V.589, N.618 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.618 Water bridges: B:N.618, B:N.618 NAG.15: 3 residues within 4Å: Chain B: T.529, Q.559, N.560 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.529

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanji, H. et al., Crystal structure of human TLR8 in complex with MB-343. To Be Published

Release Date

2016-10-05

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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