Macromolecular Structure Databases - Essays in Bioinformatics - page 144

Nucleotide consisting of the PDB code followed by the letter designating that
chain (e.g., 1B8GA, 3TATB, 1MUHB).
x Each 3D Domain identified in an MMDB record is assigned a unique integer
identifier that is appended to the Accession number of the chain to which it
belongs (e.g., 1B8G A 2). This new Accession number becomes its identifier in
Entrez 3D Domains. New 3D Domain identifiers are assigned whenever a new
MMDB-ID is assigned.
x For conserved domains, the Accession number is based on the source database:
Pfam: pfam00049
SMART: smart00078
CD: cd00101
COG: COG5641
Appendix 2: Example query: finding and viewing structural data of a protein
Finding the Structure of a Protein. Suppose that we are interested in the biosynthesis of
aminocyclopropanes and would like to find structural information on important active
site residues in any available aminocyclopropane synthases. To begin, we would go to the
Structure main page and enter “aminocyclopropane synthase” in the Search box. Pressing
Enter displays a short list of structures, one of which is 1B8G, 1-aminocyclopropane-1-
carboxylate synthase. Perhaps we would like to know the species from which this protein
was derived. Selecting the Taxonomy link to the right shows that this protein was derived
from Malux x domestica , or the common apple tree. Going back to the Entrez results page
and selecting the PDB code (1B8G) opens the Structure Summary page for this record.
The species is again displayed on this page, along with a link to the Journal of Molecular
Biology article describing how the structure was determined. We immediately see from
this page that this protein appears as a dimer in the structure, with each chain having
three 3D domains, as identified by VAST. In addition, CD-Search has identified an
“aminotran_1_2” CD in each chain. Now we are ready to view the 3D structure.
Viewing the 3D Structure. Once we have found the Structure Summary page,
viewing the 3D structure is straightforward. To view the structure in Cn3D, we simply
select the View 3D Structure button. The default view is to show helices in green, strands
in brown, and loops in blue. This color scheme is also reflected in the
Sequence/Alignment Viewer.
Locating an Active Site. Upon inspecting the structure, we immediately notice that
a small molecule is bound to the protein, likely at the active site of the enzyme. How do
we find out what that molecule is? One easy way is to return to the Structure Summary
page and select the link to the PDB code, which takes us to the PDB Structure Explorer
page for 1B8G. Quickly, we see that pyridoxal-5 ƍ -phosphate (PLP) is a HET group, or
heterogen, in the structure. Our interest piqued, we would now like to know more about
the structural domain containing the active site. Returning to Cn3D, we manipulate the
structure so that PLP is easily visible and then use the mouse to double-click on any PLP
atom. The molecule becomes selected and turns yellow. Now from the Show/Hide menu,
we choose Select by distance and Residues only and enter 5 Angstroms for a search
radius. Scanning the Sequence/Alignment Viewer, we see that seven residues are now