SMTL ID : 4r0a.1

Crystal structure of human TLR8 in complex with uridine mononucleoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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 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-MAN-MAN.12: 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 Hydrophobic interactions: B:L.228, B:Y.269 Hydrogen bonds: B:K.204, B:H.442

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 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.491 NAG-NAG.13: 10 residues within 4Å: Chain A: R.547 Chain B: S.404, I.453, K.454, C.457, S.467, L.468, N.489, Y.512, D.514 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.491

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.14: 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 URI: URIDINE(Non-covalent)

URI.4: 13 residues within 4Å: Chain A: Y.326, I.327, K.328, G.329, Y.331, V.356, F.383, R.407 Chain B: V.498, D.521, D.523, V.551, T.552 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:D.521, B:D.521, B:D.523, B:T.552, A:G.329, A:R.407 Hydrophobic interactions: A:F.383 Water bridges: A:S.330, A:S.330 pi-Stacking: A:Y.331, A:F.383 URI.15: 13 residues within 4Å: Chain A: V.498, D.521, D.523, V.551, T.552 Chain B: Y.326, I.327, K.328, G.329, Y.331, V.356, F.383, R.407 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.383 Hydrogen bonds: B:G.329, B:R.407, A:D.521, A:D.523, A:T.552 Water bridges: B:S.330, B:S.330, A:T.552, A:T.552 pi-Stacking: B:Y.331, B:F.383

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

NAG.5: 3 residues within 4Å: Chain A: N.58, E.59, Q.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.58, A:E.59 NAG.6: 2 residues within 4Å: Chain A: H.55, N.93 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.93 NAG.7: 4 residues within 4Å: Chain A: Q.117, N.138, T.140, E.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.117, A:T.140, A:E.142 NAG.8: 5 residues within 4Å: Chain A: S.200, S.201, R.203, I.224, N.225 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.224 Hydrogen bonds: A:R.203 NAG.9: 3 residues within 4Å: Chain A: S.500, N.524, S.526 No protein-ligand interaction detected (PLIP) NAG.10: 5 residues within 4Å: Chain A: K.565, K.586, S.587, V.589, N.618 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.565, A:N.618, A:N.618 Water bridges: A:K.565 NAG.11: 4 residues within 4Å: Chain A: N.634, F.656, N.658, L.661 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.656 Water bridges: A:N.634 NAG.16: 3 residues within 4Å: Chain B: N.58, E.59, Q.62 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.58, B:E.59, B:E.59 NAG.17: 2 residues within 4Å: Chain B: H.55, N.93 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.93 NAG.18: 4 residues within 4Å: Chain B: Q.117, N.138, T.140, E.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.117, B:E.142 NAG.19: 5 residues within 4Å: Chain B: S.200, S.201, R.203, I.224, N.225 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.224 Hydrogen bonds: B:R.203 NAG.20: 3 residues within 4Å: Chain B: S.500, N.524, S.526 No protein-ligand interaction detected (PLIP) NAG.21: 5 residues within 4Å: Chain B: K.565, K.586, S.587, V.589, N.618 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.565, B:N.618, B:N.618 Water bridges: B:K.565 NAG.22: 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 Water bridges: B:N.634

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanji, H. et al., Toll-like receptor 8 senses degradation products of single-stranded RNA. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-01-14

Peptides

Toll-like receptor 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Toll-like receptor 8

Related Entries With Identical Sequence