SMTL ID : 3w3g.1

Crystal structure of human TLR8 (unliganded form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

5 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.1: 13 residues within 4Å: Chain A: 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 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.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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.450 NAG-NAG-BMA.3: 11 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, R.621 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.456, A:Q.456 Hydrophobic interactions: A:V.536 NAG-NAG-BMA.5: 12 residues within 4Å: Chain B: S.404, R.450, I.453, K.454, C.457, D.465, S.467, L.468, N.489, S.491, Y.512, D.514 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.450, B:K.454 Water bridges: B:R.450 NAG-NAG-BMA.6: 9 residues within 4Å: Chain B: 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:Q.456, B:Y.512 Hydrophobic interactions: B:V.536, B:V.566

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.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 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.228, B:Y.269 Hydrogen bonds: B:K.204, B:H.442

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

NAG.7: 4 residues within 4Å: Chain A: L.345, S.346, R.348, N.373 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.348, A:R.348 NAG.8: 2 residues within 4Å: Chain A: S.500, N.524 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.500, A:N.524 NAG.9: 5 residues within 4Å: Chain A: E.362, Q.366, M.369, Q.370, N.394 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.366, A:N.394 Water bridges: A:E.362 NAG.10: 5 residues within 4Å: Chain A: K.565, K.586, S.587, V.589, N.618 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.565, A:N.618 NAG.11: 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.12: 3 residues within 4Å: Chain A: S.526, T.529, N.560 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.526, A:T.529, A:N.560 NAG.14: 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 Water bridges: B:N.373 NAG.15: 2 residues within 4Å: Chain B: S.500, N.524 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.500, B:S.500, B:N.524 NAG.16: 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.17: 5 residues within 4Å: Chain B: E.362, Q.366, M.369, Q.370, N.394 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.366, B:Q.370, B:N.394

1 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.13: 6 residues within 4Å: Chain A: L.555, L.583, L.591, F.593, I.612, F.613 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.583, A:L.591 Water bridges: A:L.583, A:I.612

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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