Welcome to RNAP3D!

RNA polymerase (RNAP), the enzyme for transcription, becomes an attractive target in drug design due to its ubiquitous existence and function throughout life. Structural differences in RNAP of virus, prokaryote, archaea and eukaryote allow specific drugs to target microbial and viral RNAP without any interaction with our own. RNAP3D is a freely accessible and user-friendly database of RNAP structure and related reference.RNAP3D is designed to compile detailed results of the structure of RNAP, presented in a dynamic manner that allows users to view the visualized structure of RNA polymerase as well as their binding ligands. And it is connected to other resources, including PDB, PubMed and UNIPROT, to provide multi-faceted views of polymerase knowledge. In order to enable insights into the difference of structure, we also include analyzing information on overall structure and sequence diversity. This resource can assist for drug design, targeting by transcription factor analog, biologics and other small molecules, and fundamental research into RNAP structures.

RNAP entries

1.Browse by organism.On the “Organism" page,users can browse the database by clicking the species image of interest.

2.Browse by type.On the “Home" page,users can browse the database by clicking the types image of interest.For example, users can retrieve the detailed RNAP I information through the following steps:Eukarytoes -> RNAP I -> PDB.

3.Browse by Taxonomy.On the “RNAP structures" page,users can browse the database by clicking the taxonomy image of interest.

4.RNAP structural information.Users can browse “RNA Polymearase Viewer” page by clicking PDB id,and then display different formats according to their interests. In addition,users can select ligands or residues of different subunits to view their interactions. Users can also click PDB code to view detailed information in PDB database. Alternatively, users can download the PDB file of the polymerase.

Ligands

1.Browse by PDB.Users can click PDB id and select the ligand of interest.

2.Browse by organism.On the “mall-molecule RNA inhibitors” page,users can browse the database by clicking the species image of interest.Users can select the organisms of interest to view all its inhibitors, and click the Ligands interaction button to view the interactions of inhibitors in proteins.The ID and PDB are linked to relative pages in PDB.

Analyzing information on overall structure and sequence diversity

Users can learn about the diversity and conservation of RNA polymerases through the "Structure Home" page and "Sequence Home" page.

Search

1.To browse the detailed information of any specific RNAP, users can specify the organism,PDB, name and so on in "Search" page.