extended-wwPDB-identifier-examples

Example data files depicting extended length CCD names and extended PDB identifiers

As previously anounced, in Future Planning: Entries with extended PDB and CCD ID codes will be distributed in PDBx/mmCIF format only, the wwPDB will need to extend the length of the chemical component database (CCD) identifiers (residue codes) and PDB identifiers as the available pool of codes is used up.

Due to legacy PDB file format limitations, CCD id codes have been limited to three alpha-numeric characters, and PDB codes to four.

As early as Fall 2023, the availabile three character CCD identifiers will be consumed and the wwPDB will need to extend the length.

Existing identifiers will not be extended to the exsting PDB entries, but will only be used for newer CCD and PDB codes.

Within this repository are sample CCD and model files displaying extended length identifiers.

Some examples:

• CCD

  • SEP with CCD identifier changed to BB87Q
  • EPE with CCD identifier changed to 7ZTVU
  • 8B8 with CCD identifier changed to 9QRZS
  • WAS with CCD identifier changed to 9ABCD
  • BMA with CCD identifier changed to 1XAMB
  • DVA with CCD identifier changed to X2AVD

• PRD and PRDCC

  • PRD_999999 with CCD component X2AVD replacing DVA in PRD_000001
  • PRDCC_999999 with CCD component X2AVD replacing DVA in PRD_000001

• Models

  • 7fgz with extended CCD code 7ZTVUreplacing EPE
  • pdb_00017fgz with extended PDB accession code and CCD code 7ZTVU replacing EPE
  • 7xsv with extended CCD code BB87Qreplacing SEP in polymer
  • pdb_00017xsv with extended PDB accession and and CCD code BB87Q replacing SEP in polymer
  • 8eur with extended CCD code 9ABCD replacing WAS
  • 7w41 with extended CCD code 9QRZSreplacing 8B8
  • pdb_00017w41 with extended PDB accession code and CCD code 9QRZS replacing 8B8
  • pdb_00017u1t with extended PDB accession code
  • 1b5f with extended CCD code 1XAMB replacing BMA in branched entities of oligosaccharides
  • pdb_00011b5f with extended PDB accession code and CCD code 1XAMB replacing BMA in branched entities of oligosaccharides
  • 1a7y with extended CCD code X2AVD replacing DVA in the oligopepetide entity PRD_999999
  • pdb_00011a7y with extended PDB accession code and CCD code X2AVD replacing DVA in the oligopepetide entity PRD_999999