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About PDBsum

Description

The PDBsum is a pictorial database that provides 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.

Search

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, which searches a given string against the TITLE, HEADER, COMPND, SOURCE and AUTHOR records in the PDB. For a fuller description of the options that the text search offers, see here.
  • sequence search, which performs a FASTA search of a given protein sequence against the sequences of all proteins in the PDB. The top hits are listed with links to their PDBsum pages.

Browse

You can also use any of the Browse options given on the PDBsum home page:
  • Highlights - which tabulates some of the extreme structures in the database in terms of age, size, etc
  • List of PDB codes - which lists all entries by their 4-character code
  • Het Groups - lists all Het Groups in the PDB with links to the structures that contain them
  • Ligands - as for Het Groups, but considering each bound molecule as a separate entity (often consisting of several covalently joined Het Groups)
  • Drugs - lists the drug molecules (and neutraceuticals) found in structures of the PDB.
  • Enzymes - lists all enzyme structures in the PDB classed by the hierarchical E.C. numbering scheme. Also known as the Enzyme Structures Database or EC->PDB
  • ProSite - lists all PROSITE sequence patterns and the PDB entries that contain them
  • Pfam - lists the PDB entries containing structural information for any Pfam domain
  • Species - classifies all PDB entries by the source species from which the protein comes

Information presented on the PDBsum pages

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

 

PDBsum publications

Latest reference

de Beer T A P, Berka K, Thornton J M, Laskowski R A (2014). PDBsum additions. Nucleic Acids Res., 42, D292-D296. [PubMed id: 24153109]

Earlier references

Laskowski R A (2009). PDBsum new things. Nucleic Acids Res., 37, D355-D359. [PubMed id: 18996896]
Laskowski R A, Chistyakov V V, Thornton J M (2005). PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res., 33, D266-D268. [PubMed id: 15608193]
Laskowski R A (2001). PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res., 29, 221-222. [PubMed id: 11125097]
Laskowski R A, Hutchinson E G, Michie A D, Wallace A C, Jones M L, Thornton J M (1997). PDBsum: A Web-based database of summaries and analyses of all PDB structures. Trends Biochem. Sci., 22, 488-490. [PubMed id: 9433130]

Related reference

Laskowski R A (2007). Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature. Bioinformatics, 23, 1824-1827. [PubMed id: 17384425]

Credits

The original version of PDBsum (c.1995) was created by:
Roman Laskowski, Gail Hutchinson, Alex Michie, Andrew Wallace, Martin Jones, Andrew Martin, Nick Luscombe, Duncan Milburn, Atsushi Kasuya and Janet Thornton
at the
Structure and Modelling Group, University College London

New version by:
Roman Laskowski and Victor Chistyakov
at the
European Bioinformatics Institute spacer

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