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PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences
PLoS One. 2021 ;16(7) :e0253411
PMID: 34228733    PMCID: PMC8259974   
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Abstract
The Protein Data Bank (PDB) was established at Brookhaven National Laboratories in 1971 as an archive for biological macromolecular crystal structures. In mid 2021, the database has almost 180,000 structures solved by X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy, and other methods. Many proteins have been studied under different conditions, including binding partners such as ligands, nucleic acids, or other proteins; mutations, and post-translational modifications, thus enabling extensive comparative structure-function studies. However, these studies are made more difficult because authors are allowed by the PDB to number the amino acids in each protein sequence in any manner they wish. This results in the same protein being numbered differently in the available PDB entries. For instance, some authors may include N-terminal signal peptides or the N-terminal methionine in the sequence numbering and others may not. In addition to the coordinates, there are many fields that contain structural and functional information regarding specific residues numbered according to the author. Here we provide a webserver and Python3 application that fixes the PDB sequence numbering problem by replacing the author numbering with numbering derived from the corresponding UniProt sequences. We obtain this correspondence from the SIFTS database from PDBe. The server and program can take a list of PDB entries or a list of UniProt identifiers (e.g., "P04637" or "P53_HUMAN") and provide renumbered files in mmCIF format and the legacy PDB format for both asymmetric unit files and biological assembly files provided by PDBe.
Notes
1932-6203 Faezov, Bulat Dunbrack, Roland L Jr Orcid: 0000-0001-7674-6667 R35 GM122517/GM/NIGMS NIH HHS/United States Journal Article PLoS One. 2021 Jul 6;16(7):e0253411. doi: 10.1371/journal.pone.0253411. eCollection 2021.