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URL: http://www.ebi.ac.uk/pdbsum
Proper Citation: PDBsum (RRID:SCR_006511)
Description: Pictorial database of an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of their interactions. Extensive use is made of the freely available RasMol molecular graphics program to view the molecules and their interactions in 3D. Entries are accessed either by their 4-character PDB code, or by one of the two search boxes provided on the PDBsum home page: text search or sequence search. The information given on each PDBsum entry is spread across several pages, as listed below and accessible from the tabs at the top of the page. Only the relevant tabs will be present on any given page. * Top page - summary information including thumbnail image of structure, molecules in structure, enzyme reaction diagram (where relevant), GO functional assignments, and selected figures from key reference * Protein - wiring diagram, topology diagram(s) by CATH domain, and residue conservation (where available) * DNA/RNA - DNA/RNA sequence and NUCPLOT showing interactions made with protein * Ligands - description of bound molecule and LIGPLOT showing interactions made with protein * Prot-prot - schematic diagrams of any protein-protein interfaces and the residue-residue interactions made across them * Clefts - listing of top ten clefts in the surface of the protein, listed by volume with any bound ligands shown * Links - links to external databases Additionally, it accepts users'''' own PDB format files and generates a private set of analyses for each uploaded structure.
Abbreviations: PDBsum
Resource Type: d spatial image, data or information resource, analysis service resource, service resource, production service resource, database, data analysis service
Defining Citation: PMID:18996896, PMID:15608193, PMID:11125097, PMID:9433130
Keywords: 3d structure, protein, molecule, structure, protein chain, dna, ligand, metal ion, interaction, gold standard
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Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
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