SMTL ID : 4r09.2 (1 other biounit)

Crystal structure of human TLR8 in complex with ORN06S

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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-MAN.1: 16 residues within 4Å: Chain A: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, V.293, D.440, H.442, S.443, N.444, F.445, Y.446 Ligands: 06S.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.228, A:Y.269 Hydrogen bonds: A:K.204, A:H.442

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(Non-covalent)

NAG-NAG-BMA.2: 8 residues within 4Å: Chain A: I.453, K.454, C.457, S.467, L.468, N.489, Y.512, D.514 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 14 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 Ligands: 06S.10 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.3: 8 residues within 4Å: Chain A: Q.456, Y.512, D.538, S.540, V.566, N.568, E.590, V.592 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.456 NAG-NAG.5: 9 residues within 4Å: Chain B: 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 B Hydrophobic interactions: B:V.536 Hydrogen bonds: B:Q.456, B:Y.512

2 x 06S: O-[(2R,3S,4R,5R)-5-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-2-({[(S)-({(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-2-[(thiophosphonooxy)methyl]tetrahydrofuran-3-yl}oxy)(sulfanyl)phosphoryl]oxy}methyl)-4-hydroxytetrahydrofuran-3-yl] dihydrogen (S)-phosphorothioate(Non-covalent)

06S.6: 18 residues within 4Å: Chain A: Y.269, K.292, V.293, I.319, D.321, R.348, H.351, R.353, N.378, N.444, H.447, F.448, T.449, R.450, L.452 Ligands: NAG-NAG-BMA-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.269, A:K.292, A:N.378, A:N.444 Salt bridges: A:E.297, A:D.321 pi-Stacking: A:H.351, A:H.447 pi-Cation interactions: A:H.351, A:H.447 06S.10: 16 residues within 4Å: Chain B: Y.269, K.292, V.293, I.319, D.321, H.351, R.353, N.378, N.444, H.447, F.448, T.449, R.450, L.452 Ligands: NAG-NAG-BMA.4, NAG-NAG-BMA.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.292, B:H.351, B:N.378, B:N.444 Salt bridges: B:E.297, B:D.321 pi-Stacking: B:H.351, B:H.447 pi-Cation interactions: B:H.351, B:H.447

2 x UPT: 1-[(2R,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-sulfidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]pyrimidine-2,4(1H,3H)-dione(Non-covalent)

UPT.7: 13 residues within 4Å: Chain A: P.242, F.243, F.298, F.324, R.353, I.381, F.445, Y.446, H.447, F.448 Chain B: I.548, A.549, G.550 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.446 Hydrogen bonds: A:R.353 pi-Stacking: A:F.298 UPT.11: 13 residues within 4Å: Chain A: I.548, A.549, G.550 Chain B: P.242, F.243, F.298, F.324, R.353, I.381, F.445, Y.446, H.447, F.448 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.298, B:Y.446 Hydrogen bonds: B:R.353, B:R.353

2 x URI: URIDINE(Non-covalent)

URI.8: 12 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, V.551, T.552 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.383 Hydrogen bonds: A:G.329, A:R.407, B:D.521, B:T.552 pi-Stacking: A:Y.331, A:F.383 URI.9: 12 residues within 4Å: Chain A: V.498, D.521, D.523, V.551, T.552 Chain B: Y.326, G.329, S.330, Y.331, V.356, F.383, R.407 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.521, A:T.552, A:T.552, B:G.329, B:S.330, B:R.407 Hydrophobic interactions: B:F.383 pi-Stacking: B:Y.331, B:F.383

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

NAG.12: 10 residues within 4Å: Chain B: I.453, K.454, C.457, D.465, S.467, L.468, N.489, S.491, Y.512, D.514 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.454, B:Y.512 Hydrogen bonds: B:K.454, B:S.467, B:N.489, B:D.514

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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