Renumbering PDB files: Difference between revisions
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==PDBrenum== | ==PDBrenum== | ||
[http://dunbrack3.fccc.edu/PDBrenum/ PDBrenum] is a server that renumbers atomic coordinate files to match the numberings in the corresponding [http://uniprot.org UniProt] entries. PDBrenum will process both [[PDB format]] and [[mmCIF format]] atomic coordinate files. | [http://dunbrack3.fccc.edu/PDBrenum/ PDBrenum] is a server that renumbers atomic coordinate files to match the numberings in the corresponding [http://uniprot.org UniProt] entries. PDBrenum will process both [[PDB file format]] and [[atomic coordinate file|mmCIF file format]] atomic coordinate files. | ||
Revision as of 00:19, 28 March 2021
Chemical groups (residues) in atomic coordinate files (PDB files) are numbered. For polymers (protein, DNA, RNA), the amino acid and nucleotide groups are given sequence numbers. For non-polymer groups (hetero groups in PDB terminology), the numbers are arbitrary. The wwPDB allows arbitrary numbering of polymer sequences. See examples at Unusual sequence numbering. Discrepancies in numbering are confusing and frustrating when comparing structures of similar macromolecules.
One of many examples is comparison of the structures of a bacterial cytochrome, OmcS. 6ef8 and 6nef are cryo-EM structures of the same cytochrome, mature length 407 amino acids (after removal of the N-terminal signal peptide, length 25 amino acids). 6ef8 is numbered 1-407, while the same residues in 6nef are numbered 26-432.
Below are servers that will re-number atomic coordinate files.
PDBrenumPDBrenum
PDBrenum is a server that renumbers atomic coordinate files to match the numberings in the corresponding UniProt entries. PDBrenum will process both PDB file format and mmCIF file format atomic coordinate files.