SMTL ID : 5z15.1

Crystal structure of human TLR8 in complex with CU-CPT9c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 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, H.442, S.443, N.444, F.445, Y.446 Ligands: MAN.8 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: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 6 residues within 4Å: Chain A: K.454, C.457, S.467, N.489, Y.512, D.514 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.454 NAG-NAG.5: 8 residues within 4Å: Chain B: I.453, K.454, C.457, D.465, S.467, N.489, Y.512, D.514 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.454

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: 11 residues within 4Å: Chain A: K.454, Q.456, Y.512, T.516, D.538, S.540, V.566, N.568, E.590, V.592, R.621 No protein-ligand interaction detected (PLIP)

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: 14 residues within 4Å: Chain B: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, D.295, 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: 11 residues within 4Å: Chain B: K.454, Q.456, Y.512, T.516, V.536, D.538, S.540, V.566, N.568, E.590, V.592 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.536 Hydrogen bonds: B:Y.512

2 x 7VL: 4-(7-chloranylquinolin-4-yl)-2-methyl-phenol(Non-covalent)

7VL.7: 15 residues within 4Å: Chain A: F.472, F.473, A.496, Q.497, V.498 Chain B: F.239, Y.326, I.327, K.328, G.329, S.330, G.354, V.356, I.381, F.383 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:F.473, A:F.473, A:A.496, B:Y.326, B:K.328, B:V.356, B:I.381, B:F.383 pi-Stacking: A:F.473, B:Y.326, B:F.383 Hydrogen bonds: B:G.329 7VL.12: 14 residues within 4Å: Chain A: F.239, F.324, Y.326, I.327, K.328, G.329, S.330, I.381, F.383 Chain B: F.472, F.473, A.496, Q.497, V.498 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.239, A:F.324, A:Y.326, A:K.328, A:I.381, A:F.383, A:F.383, B:F.472, B:F.472, B:F.473, B:F.473, B:A.496 Hydrogen bonds: A:G.329, A:S.330 pi-Stacking: A:Y.326, B:F.473

1 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.8: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.1 No protein-ligand interaction detected (PLIP)

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

NAG.9: 5 residues within 4Å: Chain A: L.345, S.346, R.348, P.372, N.373 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.372 Hydrogen bonds: A:R.348, A:R.348 NAG.10: 3 residues within 4Å: Chain A: K.586, V.589, N.618 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.618, A:N.618 NAG.11: 5 residues within 4Å: Chain A: N.634, F.656, N.658, T.660, L.661 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.656 Hydrogen bonds: A:N.634, A:N.658, A:T.660 NAG.13: 4 residues within 4Å: Chain B: K.565, K.586, V.589, N.618 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.565

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, Z. et al., Inhibition of Toll-like Receptor 8 by Specifically Targeting a Unique Allosteric Site and Locking Its Resting State. To Be Published

Release Date

2018-07-04

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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