PDBrenum

PDBrenum renumbers residues and residue-specific annotations in PDB files to match UniProt sequence numbering for consistent, residue-level structure analyses.

Key Features:

• UniProt alignment: Renumbers PDB residues to UniProt sequence numbers to standardize residue indexing.
• SIFTS mapping: Uses the Sequence ID Tracing Service (SIFTS) from PDBe to establish correspondence between PDB entries and UniProt identifiers.
• Formats output: Writes renumbered structures in mmCIF and legacy PDB formats.
• Assembly handling: Produces renumbered files for asymmetric unit and biological assembly representations.
• Input identifiers: Accepts PDB entry codes and UniProt identifiers (e.g., P04637 for p53_HUMAN) to locate mappings.
• Residue annotations: Applies renumbering to coordinate fields and other residue-specific information within PDB entries.
• Structure-method compatibility: Supports structures determined by X-ray crystallography, nuclear magnetic resonance, and cryo-electron microscopy.
• Implementation: Implemented as a Python3 application for programmatic renumbering.
• Numbering discrepancy handling: Addresses inconsistencies such as inclusion or exclusion of N-terminal signal peptides or initiating methionines.

Scientific Applications:

• Comparative structure-function analysis: Enables direct residue-level comparisons across PDB entries by standardizing numbering to UniProt.
• Mapping variants and PTMs: Facilitates mapping of mutations and post-translational modifications from PDB coordinates to UniProt positions.
• Integration with UniProt annotations: Supports integration of structural data with UniProt and SIFTS annotations for cross-database analyses.

Methodology:

PDBrenum uses PDBe SIFTS mappings to link PDB residues to UniProt sequences, applies those mappings to renumber coordinates and residue-specific fields, and writes renumbered mmCIF and legacy PDB files for asymmetric units and biological assemblies; it is implemented in Python3.