SMTL ID : 4r07.2 (1 other biounit)

Crystal structure of human TLR8 in complex with ORN06

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-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.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

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(Non-covalent)(Post Translational Modification)

NAG-NAG-BMA.2: 9 residues within 4Å: Chain A: Q.456, Y.512, V.536, D.538, S.540, V.566, N.568, E.590, V.592 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.456, A:Q.456 Hydrophobic interactions: A:V.536 NAG-NAG-BMA.3: 11 residues within 4Å: Chain A: 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.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 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.228, B:Y.269 Hydrogen bonds: B:K.204, B:H.442 Water bridges: B:N.444 NAG-NAG-BMA.5: 8 residues within 4Å: Chain B: 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:Q.456, B:Y.512

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.6: 10 residues within 4Å: Chain B: R.450, I.453, K.454, C.457, S.467, L.468, N.489, S.491, Y.512, D.514 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.450

2 x URI: URIDINE(Non-covalent)

URI.7: 13 residues within 4Å: Chain A: Y.326, K.328, G.329, Y.331, V.356, F.383, R.407 Chain B: V.498, D.521, D.523, G.550, V.551, T.552 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.383 Hydrogen bonds: A:G.329, A:R.407, B:D.521, B:D.521, B:D.523, B:T.552 Water bridges: A:S.330, A:S.330 pi-Stacking: A:Y.331, A:F.383 URI.13: 12 residues within 4Å: Chain A: V.498, D.521, D.523, V.551, T.552 Chain B: Y.326, 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.521, A:D.523, A:D.523, A:T.552 Water bridges: B:S.330, B:S.330 pi-Stacking: B:Y.331, B:F.383

2 x UCG: 3'-O-[(R)-{[(2R,3aR,4R,6R,6aR)-6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-hydroxy-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]uridine 5'-(dihydrogen phosphate)(Non-covalent)

UCG.8: 15 residues within 4Å: Chain A: K.292, V.293, E.318, I.319, D.321, R.348, H.351, R.353, N.378, H.447, F.448, T.449, R.450, P.451, L.452 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.319 Hydrogen bonds: A:E.318, A:R.348, A:R.353, A:N.378, A:L.452 Water bridges: A:K.292, A:S.323, A:H.351, A:I.453 Salt bridges: A:D.321, A:H.447 pi-Stacking: A:H.351, A:H.447 pi-Cation interactions: A:H.351, A:H.447 UCG.14: 15 residues within 4Å: Chain B: K.292, V.293, E.318, I.319, D.321, R.348, H.351, R.353, N.378, H.447, F.448, T.449, R.450, P.451, L.452 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.319 Hydrogen bonds: B:E.318, B:E.318, B:R.353, B:N.378, B:L.452 Water bridges: B:S.323, B:N.444, B:I.453 Salt bridges: B:D.321, B:H.447 pi-Stacking: B:H.351, B:H.447 pi-Cation interactions: B:H.351, B:H.447

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

NAG.9: 6 residues within 4Å: Chain A: E.318, L.345, S.346, R.348, P.372, N.373 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.372 Hydrogen bonds: A:E.318, A:E.318, A:R.348 NAG.10: 3 residues within 4Å: Chain A: S.500, N.524, A.525 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.524, A:N.524, A:A.525 NAG.11: 4 residues within 4Å: Chain A: K.586, S.587, V.589, N.618 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.618, A:N.618 NAG.12: 5 residues within 4Å: Chain A: N.634, L.638, N.658, T.660, L.661 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain B: R.348, P.372, N.373 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.373 NAG.16: 3 residues within 4Å: Chain B: S.500, N.524, S.526 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.526, B:S.526 Water bridges: B:S.500, B:S.500, B:N.524, B:A.525 NAG.17: 5 residues within 4Å: Chain B: T.562, K.586, S.587, V.589, N.618 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain B: Q.262, N.263, N.287 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.287

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
C

B
D

Toll-like receptor 8

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