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Literature summary for 2.3.2.12 extracted from

  • Ge, X.; Roux, B.
    Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials (2010), J. Mol. Recognit., 23, 128-141.
    View publication on PubMed

Inhibitors

Inhibitors Comment Organism Structure
sparsomycin binds to 50S bacterial ribosomal subunit. Calculated binding free energy is about -6 kcal/mol. In the simulation protocol, restraining potentials are activated for the orientational and translational movements of the ligand relative to the binding site when it is decoupled from the binding pocket, and then released once the ligand fully interacts with the rest of the system. The number of water molecules in the binding pocket is allowed to fluctuate dynamically in response to the ligand during the calculations Haloarcula marismortui

Organism

Organism UniProt Comment Textmining
Haloarcula marismortui
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