PCDB

PCDB catalogs conformational variability of proteins observed in crystallographic structures to enable analysis of protein dynamics and structure–function relationships.

Key Features:

• Compilation of Crystallographic Structures: Aggregates all available crystallographic structures of each protein across different experimental conditions to represent alternative conformations.
• Conformational Diversity Measurement: Quantifies conformational diversity using the maximum root-mean-square deviation (RMSD) between deposited structures for each domain.
• CATH Classification Integration: Organizes and extracts structures according to the CATH (Class, Architecture, Topology, Homologous superfamily) classification system.
• Cross-Linking with Additional Information: Links structural entries to protein function, ligand presence, mutations, active site details, and organism taxonomy.
• Extensive Database Content: Contains 7,989 domains from 4,171 proteins encompassing 36,581 structures, with a recorded maximum RMSD of 26.7 Å and an average of 4.5 structures per domain.

Scientific Applications:

• Protein Dynamics and Flexibility: Enables exploration of how proteins alter conformations under different conditions to study flexibility and dynamic behavior.
• Structural Biology Research: Supports analyses of protein folding, stability, and conformational changes associated with biological processes using crystallographic data.
• Drug Discovery and Development: Informs identification of potential binding sites and assessment of how ligands or mutations affect protein structure relevant to drug design.
• Evolutionary Studies: Facilitates evolutionary analyses by combining structural diversity data with organism taxonomy to trace functional and structural changes across species.

Methodology:

Aggregates crystallographic structures per protein/domain, organizes and extracts structures using the CATH classification, computes maximum RMSD between deposited structures for each domain, and associates structures with annotations for function, ligands, mutations, active sites, and taxonomy.