2r04
STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES
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OverviewOverview
X-Ray diffraction data have been obtained for nine related antiviral, agents ("WIN compounds") while bound to human rhinovirus 14 (HRV14). These, compounds can inhibit both viral attachment to host cells and uncoating., To calculate interpretable electron density maps it was necessary to, account for (1) the low (approximately 60%) occupancies of these compounds, in the crystal, (2) the large (up to 7.9 A) conformational changes induced, at the attachment site, and (3) the incomplete diffraction data., Application of a density difference map technique, which exploits the, 20-fold noncrystallographic redundancy in HRV14, resulted in clear images, of the HRV14:WIN complexes. A real-space refinement procedure was used to, fit atomic models to these maps. The binding site of WIN compounds in, HRV14 is a hydrophobic pocket composed mainly from residues that form the, beta-barrel of VP1. Among rhinoviruses, the residues associated with the, binding pocket are far more conserved than external residues and are, mostly contained within regular secondary structural elements. Molecular, dynamics simulations of three HRV14:WIN complexes suggest that portions of, the WIN compounds and viral protein near the entrance of the binding, pocket are more flexible than portions deeper within the beta-barrel.
About this StructureAbout this Structure
2R04 is a Protein complex structure of sequences from Human rhinovirus 10 with W71 as ligand. This structure superseeds the now removed PDB entry 1R04. Full crystallographic information is available from OCA.
ReferenceReference
Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses., Badger J, Minor I, Oliveira MA, Smith TJ, Rossmann MG, Proteins. 1989;6(1):1-19. PMID:2558377
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