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. 2005 Jan 1;33(Database issue):D266-8.
doi: 10.1093/nar/gki001.

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids

Roman A Laskowski  1 , Victor V Chistyakov, Janet M Thornton
Affiliations

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids

Roman A Laskowski et al. Nucleic Acids Res. .

Abstract

PDBsum is a database of mainly pictorial summaries of the 3D structures of proteins and nucleic acids in the Protein Data Bank. Its pages aim to provide an at-a-glance view of the contents of every 3D structure, plus detailed structural analyses of each protein chain, DNA-RNA chain and any bound ligands and metals. In the past year, the database has been significantly improved, in terms of both appearance and new content. Moreover, it has moved to its new address at http://www.ebi.ac.uk/thornton-srv/databases/pdbsum.

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Figures

Figure 1
Figure 1
Diagram showing the reaction catalysed by enzymes of class E.C.2.6.1.16—the glucosamine 6-phosphate synthases. The diagram is taken from the PDBsum page for 1gdo, where the bound ligand—an l-glutamate—corresponds to one of the enzyme's products and is highlighted with a blue border in the diagram. Clicking on the highlighted molecule goes to the corresponding ligand page.
Figure 2
Figure 2
Surface of the glucosamine 6-phosphate synthase structure (PDB code 1gdo) coloured by residue conservation: red and pink for the most highly conserved regions, and blue for the most variable. The bound ligand—an l-glutamate—can be seen in spacefill representation within the highly conserved binding pocket. Also bound are an acetate ion and a sodium ion (green sphere).
Figure 3
Figure 3
Example of one of the PDBsum highlights listings, here showing the top five structures in terms of the highest quoted resolution.
See this image and copyright information in PMC

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References

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