SMTL ID : 5wyz.1

Crystal structure of human TLR8 in complex with CU-CPT9b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

1 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: 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 Hydrogen bonds: A:D.440, A:K.204, A:H.442 Hydrophobic interactions: A:L.228, A: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: 10 residues within 4Å: Chain A: R.450, I.453, K.454, C.457, D.465, S.467, N.489, S.491, Y.512, D.514 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 9 residues within 4Å: Chain B: I.453, K.454, C.457, D.465, S.467, N.489, S.491, Y.512, D.514 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.512, A:V.536 Water bridges: A:K.454, A:Y.512

2 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

NAG-NAG-BMA-MAN.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 NAG-NAG-BMA-MAN.6: 10 residues within 4Å: Chain B: K.454, Q.456, Y.512, T.516, D.538, S.540, V.566, N.568, E.590, V.592 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.454, B:Y.512

2 x 7VF: 4-(3-methyl-4-oxidanyl-phenyl)quinolin-7-ol(Non-covalent)

7VF.7: 16 residues within 4Å: Chain A: F.472, F.473, A.496, Q.497, V.498, Y.545 Chain B: F.239, Y.326, I.327, K.328, G.329, S.330, G.354, V.356, I.381, F.383 16 PLIP interactions: 7 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:F.239, B:Y.326, B:V.356, B:I.381, A:F.472, A:F.473, A:F.473, A:A.496, A:Y.545 Hydrogen bonds: B:G.329, B:S.330, A:V.498 pi-Stacking: B:Y.326, A:F.473 Water bridges: A:Q.497, A:Q.497 7VF.11: 17 residues within 4Å: Chain A: F.239, F.324, Y.326, I.327, K.328, G.329, S.330, G.354, V.356, I.381, F.383 Chain B: F.472, F.473, A.496, Q.497, V.498, Y.545 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.472, B:F.473, B:F.473, B:A.496, B:Y.545, A:F.239, A:F.324, A:Y.326, A:V.356 Hydrogen bonds: B:V.498, A:G.329 Water bridges: B:Q.497 pi-Stacking: B:F.473, A:Y.326

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

NAG.8: 4 residues within 4Å: Chain A: L.345, S.346, R.348, N.373 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.348, A:R.348, A:N.373 NAG.9: 3 residues within 4Å: Chain A: K.586, V.589, N.618 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.565, A:K.565, A:N.618, A:N.618 NAG.10: 5 residues within 4Å: Chain A: N.634, L.638, N.658, T.660, L.661 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.658 NAG.12: 4 residues within 4Å: Chain B: K.586, S.587, V.589, N.618 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S. et al., Small-molecule inhibition of TLR8 through stabilization of its resting state. Nat. Chem. Biol. (2018)

Release Date

2017-12-13

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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