Computational protocol: Small-molecule inhibition of TLR8 through stabilization of itsresting state

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Protocol publication

[…] Diffraction dataset was collected on beamline PF-AR NE3A (Ibaraki, Japan), PF BL-5A (Ibaraki, Japan), and SPring-8 BL41XU (Hyogo, Japan) under cryogenic condition at 100 K. The wavelength was set to 1.0000 Å. The dataset was processed using the HKL2000 package or iMOSFM. hTLR8/CU-CPT structures were determined by the molecular replacement method using the Molrep program with the unliganded hTLR8 structure (PDB ID: 3W3G) as a search model. The model was further refined with stepwise cycles of manual model building using the COOT program and restrained refinement using REFMAC until the R factor was converged. CU-CPT compounds, N-glycans, and water molecules were modeled into the electron density maps at the latter cycles of the refinement. The quality of the final structure was validated with the PDB validation server (http://wwpdb-validation.wwpdb.org/). The favored and the allowed regions in the Ramachandran plot were 94 % and 6 % for TLR8/CU-CPT8m, and 94 % and 5 % for TLR8/CU-CPT9b. The statistics of the data collection and refinement are summarized in . The figures representing structures were prepared with PyMOL (http://www.pymol.org) or CueMol (http://www.cuemol.org). Coordinates and structure factor have been deposited in the Protein Data Bank with PDB ID 5WYX (TLR8/CU-CPT8m), and 5WYZ (TLR8/CU-CPT9b). […]

Pipeline specifications

Software tools Molrep, Coot, PyMOL, CueMol
Databases wwPDB
Application Protein structure analysis
Organisms Bacteria, Homo sapiens