Information Technology Reference
In-Depth Information
3.7 The Distinction between 3D Domains and CDs
The term “domain” refers in general to a distinct functional and/or structural unit of a
protein. Each polypeptide chain in MMDB is analyzed for the presence of two classes of
domains, and it is important for users to understand the difference between them. One
class, called 3D Domains, is based solely on similar, compact substructures, whereas the
second class, called Conserved Domains (CDs), is based solely on conserved sequence
motifs. These two classifications often agree, because the compact substructures within a
protein often correspond to domains joined by recombination in the evolutionary history
of a protein. Note that CD links can be identified even when no 3D structures within a
family are known. Moreover, 3D Domain links may also indicate relationships either to
structures not included in CDD entries or to structures so distantly related that no
significant similarity can be found by sequence comparisons.
4. Finding and Viewing Structures
For an example query on finding and viewing structures, see Appendix 2.
4.1 Why Would I Want to Do This?
x To determine the overall shape and size of a protein
x To locate a residue of interest in the overall structure
x To locate residues in close proximity to a residue of interest
x To develop or test chemical hypotheses regarding an enzyme mechanism
x To locate or predict possible binding sites of a ligand
x To interpret mutation studies
x To find areas of positive or negative charge on the protein surface
x To locate particularly hydrophobic or hydrophilic regions of a protein
x To infer the 3D structure and related properties of a protein with unknown
structure from the structure of a homologous protein
x To study evolutionary processes at the level of molecular structure
x To study the function of a protein
x To study the molecular basis of disease and design novel treatments
4.2 How to Begin
The first step to any structural analysis at NCBI is to find the structure records for the
protein of interest or for proteins similar to it. One may search MMDB directly by
entering search terms such as PDB code, protein name, author, or journal in the Entrez
Structure
Search
box on the Structure homepage
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. Alternative points of entry are shown
below.
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[http://www.ncbi.nlm.nih.gov/Structure]
