Renumbering PDB files: Difference between revisions
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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 atoms|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. | 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 atoms|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. | Below are servers that will re-number atomic coordinate files. | ||
==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. | |||
