11 Questions
What is the format of the PDB ID?
4 alphanumeric characters
What would happen if you were to open a PDB file without a proper tool?
The file will be read as a text file
What is the purpose of databases like SCOP, HSSP, and CATH?
To classify and analyze protein structures
What type of file extension do atomic coordinate files have?
.pdb
What is the purpose of molecular graphics visualization tools?
To view and manipulate 3D protein structures
What is the primary function of the Nucleic Acid Structure Database (NDB)?
To perform searches based on annotations relating to sequence, structure, and function
What is the name of the international repository of macromolecular structure data established in 1972?
Protein Databank (PDB)
What method is used to determine the structural information of a protein?
Both X-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy
What type of information can be found in a PDB file?
Data collected, molecule name, primary and secondary structure, ligand, atomic coordinates, crystallographic structure factors, and NMR experimental data
Who maintains the Protein Data Bank (PDB)?
Worldwide Protein Data Bank
What can be done with the information available in the PDB?
All of the above
Study Notes
Protein Databank (PDB)
- Established in 1972 at Brookhaven National Laboratory (BNL)
- Sole international repository of macromolecular structure data
- Moved to Research Collaboratory for Structural Bioinformatics (http://www.rcsb.org)
Nucleic Acid Structure Database (NDB)
- Contains information about experimentally-determined nucleic acids and complex assemblies
- Allows searches based on annotations relating to sequence, structure, and function
- Enables downloading, analysis, and learning about nucleic acids (http://ndbserver.rutgers.edu/)
Protein Structure Database
- Contains information about 3D structure of proteins
- PDB files contain experimentally-determined 3D structures of biological macromolecules
- Structural information can be determined by X-ray crystallography or Nuclear Magnetic Resonance (NMR) spectroscopy methods
Features of PDB
- Allows searching for information regarding structure, sequence, function, and visualization
- Enables downloading and assessing molecules
- PDB files contain data collected, molecule name, primary and secondary structure, ligand, atomic coordinates, crystallographic structure factors, and NMR experimental data
Data Submission and Access
- Data submitted by scientists from all over the world
- Maintained by Worldwide Protein Data Bank
- All data in PDB are accessible to the public
- Each entry in PDB is provided with a unique identification number called the PDB ID (4-letter alphanumeric code)
Derived Databases
- Structural Classification of Proteins (SCOP) groups different protein structures
- Homology-Derived Secondary Structure of Proteins (HSSP) provides 3D-structure and 1D-sequence of proteins
- CATH classifies protein structures according to their evolution
Protein Visualization Tools
- Required to view and manipulate 3D structures encoded by PDB files (.pdb)
- Enables visualization of molecules from various perspectives
This quiz covers the importance of structural databases in molecular biology, focusing on the Protein Databank (PDB) and the Nucleic Acid Structure Database (NDB).
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