Unusual sequence numbering: Difference between revisions

The numbering of protein and nucleic acid sequences is arbitrary in structure files from the [[PDB|World Wide Protein Data Bank]] (PDB). That is, authors are free to number sequences as they wish.

'''Straightforward numbering''' assigns 1 to the amino-terminal amino acid, and counts up sequentially and monotonically to the carboxy-terminal amino acid. An example is [http://firstglance.jmol.org/fg.htm?mol=1pgb 1pgb] ([[1pgb]]). The crystallized protein is numbered 1-56, despite it being a fragment of a [http://www.uniprot.org/uniprot/P06654#sequences 448-residue full length sequence] that begins (after adding an N-terminal Met) at full-length sequence number 228.

Rarely, the insertion codes are in reverse alphabetical order. An example is [http://firstglance.jmol.org/fg.htm?mol=1ucy 1ucy] ([[1ucy]]). Chain L begins with nine amino acids all numbered 1. The insertion codes are in '''reverse-alphabetic order''': 1H, 1G, 1F, ... 1B, 1A, 1, 2, 3 .... In the same chain L are fourteen residues numbered 14. These insertion codes are in '''forward alphabetic order''': 13, 14, 14A, 14B, ... 14L, 14M, 15, 16 .... Chain L also has ten residues numbered 60, with forward-alphabetic insertion codes from A through I, and a few other shorter runs of insertion codes.

It is not uncommon for a surface loop of the crystallized protein to be disordered. Often such loops are [[Intrinsically Disordered Protein|intrinsically disordered]]. The disorder blurs the electron density map for that loop, and the loop residues are not given coordinates in the model: they are missing in the model. However, they were not missing in the crystallized protein. This causes a gap in the sequence numbers in the PDB file. An example is [http://firstglance.jmol.org/fg.htm?mol=2ace 2ace] ([[2ace]]). Residues 485-489 are missing in the 3D crystallographic model due to disorder in the crystal. Also missing are 3 N-terminal, and 2 C-terminal residues.  FirstGlance in Jmol tabulates missing residues, and marks regions of the 3D model where residues are missing with "empty baskets".

Rarely, sequence numbers do not increase monotonically from N to C terminus. An example<ref>Thanks to Rachel Kramer Green of [[RCSB]] for this example.</ref> is [http://firstglance.jmol.org/fg.htm?mol=4zwj 4zwj] ([[4zwj]]). In this chimeric protein, chain A is numbered 1002-1161 continuing 1-326 continuing 2012-2361. That is, there are sudden jumps in numbering of consecutive amino acids: 1161 to 1, and 326 to 2012. At right is an excerpt from the ATOM records of the [[PDB file]] for 4zwj chain A.