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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:13

Protein Organization

Overview
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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Published on: July 16, 2017

PCDB: a database of protein conformational diversity.

Ezequiel I Juritz1, Sebastian Fernandez Alberti, Gustavo D Parisi

  • 1Universidad Nacional de Quilmes, Centro de Estudios e Investigaciones, Roque Saenz Peña 352, Bernal, Argentina.

Nucleic Acids Research
|November 25, 2010
PubMed
Summary

The Protein Conformational Diversity Database (PCDB) quantifies protein flexibility using structural data. It links conformational diversity to protein function, mutations, and taxonomy.

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Last Updated: Jun 6, 2026

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Published on: July 16, 2017

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Proteins exhibit dynamic conformational changes crucial for their function.
  • Understanding protein conformational diversity is key to deciphering biological mechanisms.
  • Existing databases often lack comprehensive data on protein structural variations.

Purpose of the Study:

  • To introduce the Protein Conformational Diversity Database (PCDB).
  • To provide a resource for analyzing protein conformational diversity.
  • To link structural dynamics with functional and biological context.

Main Methods:

  • Compilation of redundant crystallographic structures for each protein domain.
  • Calculation of maximum Root Mean Square Deviation (RMSD) as a measure of conformational diversity.
  • Integration with CATH structural classification and cross-linking with functional data.

Main Results:

  • PCDB currently houses 36,581 structures across 7,989 domains from 4,171 proteins.
  • The maximum recorded conformational diversity (RMSD) is 26.7 Å.
  • On average, each domain is represented by 4.5 different structures.

Conclusions:

  • PCDB offers a valuable resource for studying protein dynamism.
  • The database enables correlation of conformational diversity with protein function, ligands, mutations, and taxonomy.
  • PCDB facilitates deeper insights into structure-function relationships.