The present study was conducted to identify the binding interaction between the rho B protein with Actinomycin D compound isolated from Streptomyces parvulus SDMRI – 3 isolated from Punnakayal mangrove ecosystem of tuticoirn found to be an efficient producer of bioactive compound. The most identical sequences were determined by BLASTP analysis of target sequences of the DNA dependent RNA polymerase from Bacillus cereus, Escherichia coli, Enterobacter aerogenes, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus against the PDB database. Docking interactions indicated that Actinomycin D has a significant interaction with Staphylococcus aureus rho B. In Pseudomonas aeruginosa, has less docking score. The docking score varies between -7.1652 to -9.2351 kJ/mol. The docking interactions proposed that Actinomycin D isolated compound from novel actinomycetes strain Streptomyces parvulus SDMRI -3 has good interaction with rho B protein of Bacillus cereus, Escherichia coli, Enterobacter, and Klebsiella pneumoniae via two bonded interactions and four non-bonded interactions, the current study found that the sediments of the Punnakayal mangrove habitat contain potential antibiotic generating bioactive Actinomycetes. Streptomyces parvulus SDMRI - 3 was found as a novel Actinomycete strain and registered in the GenBank with this Accession No. KF818457. Actinomycin D is chemical compound isolated from the novel strain having strong interactions with rho B protein from Staphylococcus aureus. This isolate is a natural source of the medicinal chemical actinomycin D, which is useful in the development of innovative medications for humans.

Homology modeling, Actinomycin D, Streptomyces Parvulus, rpo B protein, Docking