The Protein Data Bank (PDB) is a central resource for discovering and sharing the three-dimensional structures of biological molecules. This lesson introduces what the PDB contains, how its records become publicly available, and how the database developed into an international resource.
The Protein Data Bank is a database of three-dimensional structural data for large biological molecules, especially proteins and nucleic acids. A structure record provides information about the molecule's spatial arrangement, allowing researchers to examine its shape and relationships among its atoms.
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What is the Protein Data Bank?
The PDB is a global archive of three-dimensional structural data for large biological molecules, including proteins and nucleic acids.
What happens after researchers submit a structure?
Expert biocurators review and annotate the entry, while automated checks assess data plausibility. Approved data are made freely available online.
What is the wwPDB?
The Worldwide Protein Data Bank is the international organization whose member centers coordinate PDB deposition, processing, and distribution.
What role did SEARCH play in the PDB's early history?
Developed by Edgar Meyer, SEARCH enabled researchers to access information remotely and helped make the PDB a networked resource.
How do SCOP, CATH, and PDBsum use PDB data?
SCOP and CATH classify protein structures. PDBsum creates graphical overviews of PDB entries, drawing on information from sources such as Gene Ontology.
Quiz questions
What kind of structural information can protein NMR provide to help derive a conformation?Answer: Estimates of distances between pairs of atoms, used as restraints in distance geometry.
What does a four-character PDB ID identify?Answer: A particular structural entry, rather than a unique biological molecule.
Which file format became the PDB archive's standard format in 2014?Answer: mmCIF, the macromolecular Crystallographic Information file format.
What supporting data may accompany an X-ray structure with structure-factor data?Answer: An electron density map that can be viewed alongside the structure.
What do integrative or hybrid structural models combine?Answer: Experimental evidence with structural prediction.
Based on the Wikipedia article Protein Data Bank, licensed CC BY-SA 4.0. Adapted into a summary, flashcards and quizzes.