Structural
Databases
1. PDB
2. CATH
3. NDB
4. SCOP
5. MMDB
Protein Data Bank (PDB)
PDB
• PDB identification code
4-character identifier also called PDB ID
• [0—9][A—Z or 0—9] [A—Z or 0—9] [A—Z or 0—9].
e.g., 1LYZ (hen’s egg-white lysozyme)
• Enter the identification code into the PDB ID box and hit the Explore button.
• The Structure Explore page for this entry is returned.
• If the PDB ID is not known, clicking Search Lite opens the query page.
• Enter the keyword (name of ligand/biomacromolecule or author) and
click the Search button.
• In the advanced search, clicking Search Field opens the
query form (Figure ).
• Construct combination of your query options including
• PDB ID,
• citation author,
• chain type (for protein, enzyme, carbohydrate, DNA or RNA),
• Compound information,
• PDB header, and
• experimental technique used.
• Clicking the Search button returns you to the search page with a list of
hits from which you select the desired entry to access the Summary
information of the selected molecule.
• From the Summary information, the user can choose one of many
options including
• View Structure,
• Download/Display File,
• Structural Neighbors (links to CATH, CE, PSSP, SCOP and VAST),
• Geometry, or
• equence Details.
• Select Download/Display File, then choose PDB text and PDB non
compression format to retrieve the pdb file in text format.
• To view the structure online, select View Structure followed by
choosing one of the 3D display options.
• The display can be saved as [Link]/[Link].
• The Structure Neighbors provide links to
• CATH (fold classification by domain),
• CE (representative structure comparison, structure alignments,
structure superposition tool),
• FSSP (fold tree, domain dictionary, sequence neighbors,
structure superposition),
• SCOP (Class, fold, superfamily, and family classification), and
• VAST (representative structure comparison, structure
alignments, structure superposition tool).
• The Geometry option provides tables of
• Dihedral angles,
• bond angles, and
• bond lengths.
Nucleic Acid Database (NDB)
• The structural information about nucleic acids can be obtained from PDB or Nucleic Acid
Database (NDB) at [Link]
• On the NDB home page, choose Search Nucleic acid database search Quick search to open the
search form for the database (Figure 12.4).
• Activate Classification list box (listing of the database by classes: DNA, DNA/RNA, Peptide
nucleic acid, Peptide nucleic acid/DNA, Protein/DNA, Protein/RNA, Ribosome, Ribozyme, RNA,
and tRNA).
• Highlight the desired class, and click the Execute Selection button to open a list of database for
the class.
• Highlight an entry and click the Display Selection button.
• An information page providing NDB ID, Compound name, Sequence, Citation, Crystal
information, Coordinates, and Views is returned.
• Click the link, coordinates for the asymmetric unit to open the coordinate file and save it as
[Link].
Molecular modeling database
(MMDB)
• Molecular modelling database (MMDB) of Entrez is a subset of 3D structures from
PDB recorded in asn.1 format (Wang et. al., 2002).
• The database that provides the link between 3D structures and sequences can be
accessed at http:// [Link]/Entrez/[Link].
• Enter author’s last name or text words/ keywords (e.g., zinc finger, DNA protein
complex, or topoisomerase) or PDB ID (if it is known) and click the Search or Go
button.
• A list of hits is returned.
• Select the desired entries and then click the PDB ID to receive the MMDB Structure
summary (Figure 12.3).
• Choose options (radios) to view or save the structure file as structure.
• cgi (Cn3D), structure. In (KineMage), or [Link] (RasMol).
• Sequence similarities or structure similarities can be
viewed/saved by clicking the respective chain designation
of Sequence neighbours or Structure neighbours.
• This returns the sequence display summary or VAST
structure neighbours, respectively.
CATH
SCOP