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. 2012 Jan;40(Database issue):D461-4.
doi: 10.1093/nar/gkr1162. Epub 2011 Dec 1.

MMDB: 3D structures and macromolecular interactions

Thomas Madej  1 , Kenneth J Addess, Jessica H Fong, Lewis Y Geer, Renata C Geer, Christopher J Lanczycki, Chunlei Liu, Shennan Lu, Aron Marchler-Bauer, Anna R Panchenko, Jie Chen, Paul A Thiessen, Yanli Wang, Dachuan Zhang, Stephen H Bryant
Affiliations

MMDB: 3D structures and macromolecular interactions

Thomas Madej et al. Nucleic Acids Res. 2012 Jan.

Abstract

Close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3D) structure by standard sequence similarity searches. Potentially, a great deal can be learned about proteins or protein families of interest from considering 3D structure, and to this day 3D structure data may remain an underutilized resource. Here we present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically relevant complexes and molecular interactions. MMDB is tightly integrated with NCBI's Entrez search and retrieval system, and mirrors the contents of the Protein Data Bank. It links protein 3D structure data with sequence data, sequence classification resources and PubChem, a repository of small-molecule chemical structures and their biological activities, facilitating access to 3D structure data not only for structural biologists, but also for molecular biologists and chemists. MMDB provides a complete set of detailed and pre-computed structural alignments obtained with the VAST algorithm, and provides visualization tools for 3D structure and structure/sequence alignment via the molecular graphics viewer Cn3D. MMDB can be accessed at http://www.ncbi.nlm.nih.gov/structure.

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Figures

Figure 1.
Figure 1.
Structure summary page for the MMDB entry 88973 with PDB accession 3PO2. This is a structure of yeast RNA Polymerase II complex trapped in the elongation process, and contains polypeptides, nucleic acids and ions. The table of molecules and interactions is truncated in this screenshot, with the sequence annotation view for the first polypeptide in the list expanded to full detail. The colors used to depict 3d Domains in the sequence annotation graphic are independent of the colors used to depict molecules in the interactions schematic. The complete table that is displayed on live structure summary pages provides similar information for each molecule in the structure. The page provides links to the source database (PDB), taxonomy, PubMed, Entrez/Protein, Entrez/Nucleotide, PubChem, IBIS, VAST structure neighbors and the Conserved Domain Database. The interaction schematic shows that only the two largest protein subunits of the complex interact with the nucleic acids (which represent the double-stranded DNA template and the RNA product), and that the smaller protein subunits surround the core of the complex and may interact with both or only one of the two large subunits.
See this image and copyright information in PMC

References

    1. Rose PW, Beran B, Bi C, Bluhm WF, Dimitropoulos D, Goodsell DS, Prlic A, Quesada M, Quinn GB, Westbrook JD, et al. The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res. 2011;39:D392–D401. - PMC - PubMed
    1. Krissinel E, Henrick K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 2007;372:774–797. - PubMed
    1. Wang Y, Addess KJ, Chen J, Geer LY, He J, He S, Lu S, Madej T, Marchler-Bauer A, et al. MMDB: annotating protein sequences with Entrez's 3D-structure database. Nucleic Acids Res. 2007;35:D298–D300. - PMC - PubMed
    1. Shoemaker BA, Zhang D, Thangudu RR, Tyagi M, Fong JH, Marchler-Bauer A, Bryant SH, Madej T, Panchenko AR. Inferred Biomolecular Interaction Server—a web server to analyze and predict protein interacting partners and binding sites. Nucleic Acids Res. 2010;38:D518–D524. - PMC - PubMed
    1. Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH. Cn3D: sequence and structure views for Entrez. Trends Biochem. Sci. 2000;25:300–302. - PubMed

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