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 Plasmodium
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Graphical Structure Summaries Molecular Modeling Database (MMDB) Structure Summaries and Vector Alignment Search Tool (VAST) reports now use graphical overviews to depict macromolecular chains, domains, and regions of structural alignment to other proteins. An MMDB Structure Summary for the Klenow fragment of DNA Polymerase I in complex with a short piece of single-stranded DNA is given in Figure 1. 
Figure 1: Structure summary for MMDB structure 11885, derived from PDB record 1D8Y: DNA polymerase I complexed with DNA. Protein and nucleotide chains as well as 3D domain and Conserved Domain assignments are represented by clickable colored bars. Graphical Overviews The graphical overview of Figure 1 consists of two blocks; one for the protein chains represented in the structure file, and another for the nucleotide chain. The first block is comprised of three tiers of colored bars, the first of which, labeled “ Protein”, indicates that the structure contains a single protein chain of 605 amino acids. The next tier, labeled “3d-Domains”, includes seven colored bars showing the disposition of the 3D domains assigned by NCBI on the basis of structural compactness. Five 3D domains have been detected with the first beginning at the amino terminal end of the protein chain, labeled “1”, and the last ending at the carboxy-terminal end, labeled “3”. Note that 3D domains “3” and “4” are comprised of two discontiguous segments of sequence within the amino-acid chain and are therefore shown using two separate bars each. The domain color scheme used in the Structure Summary follows that used by Cn3D, NCBI’s macromolecular structure viewer, when structures are viewed and colored by “Domain” so that the two-dimensional depiction of the structure in the Structure Summary is easily correlated with its 3D representation. The “CDs” tier shows the mapping of Conserved Domains detected within the protein via a Reverse-PSI BLAST comparison to NCBI’s Conserved Domain Database (CDD). Although Conserved Domain definitions are based on sequence alignments and 3D domain assignments are based on structural compactness, there is often a good correspondence between the two, as can be seen in Figure 1 by the superposition of 3D domain “1” and the 3'  5'exonuclease Conserved Domain.Links from the Structure Summary Each colored bar in a tier is a link to further structural information. Clicking on the bar labeled “Chain A” leads to the VAST 3D neighbor report from which structural alignments can be downloaded and viewed using Cn3D. The 3D domain bar labeled “ 1” is a link to the VAST 3D neighbors report for the first 3D domain, the 3' 5' exonuclease domain, shown
in Figure 3. The CDD bar labeled “3_5_exonuclease” leads to
a report showing CDD sequence alignments which also include the “query” sequence;
in this case, the sequence of 1D8Y, chain A. “Protein” and “Nucleotide” links
to the left of the bars lead to Entrez nucleotide and protein sequence
records, respectively.Clicking on the “View 3D Structure” button in the Structure Summary shown in Figure 1 invokes Cn3D to display the structure shown in Figure 2 in which the 3' 5' exonuclease domain is shown with
cylinders representing alpha helices. The structure is colored by domain
so that
the color-scheme matches that used in the graphical domain bars shown
in the Structure Summary report of Figure 1.Explore the NCBI structure database at:
 Figure 2: Cn3D rendering of DNA polymerase I. The 3'  5' exonuclease domain, to the left, is shown using “3D objects” to highlight helices and strands. The other four domains are shown in a “tube-worm” representation. The single-stranded DNA is shown in a space-filled representation, as is the phosphate group appearing in the cleft between the “fingers” and “thumb” domains of the enzyme. 
Figure 3: VAST 3D neighbor report for 3D domain “1” corresponding to the 3' 5'
exonuclease Conserved Domain of DNA polymerase I. The portions of each 3D neighbor
aligning with 3D
domain “1” are indicated graphically. Links from the aligned-region
bars display the detailed structural alignment and 3D superposition.
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