Unusual sequence numbering

From Proteopedia

Revision as of 18:47, 4 December 2017

The numbering of protein and nucleic acid sequences is arbitrary in structure files from the World Wide Protein Data Bank (PDB). Here are some examples. These PDB entries are not shown here. To explore these, the links below will display them in FirstGlance in Jmol (link with arrow) or in Proteopedia (link in parentheses).

Numbering Does Not Start With One

Multiple Residues with the Same Number

Insertion Codes

Sometimes the residues of a protein are numbered according to a different reference sequence. When there are insertions relative to the reference sequence, the additional residues may all be given the same sequence number, but marked with alphabetic insertion codes. This is frequently done in antibodies, where the reference sequence is the germline sequence, but the antibody has been somatically mutated, especially in complementarity-determining region (CDR) 3. An example is 1igy (1igy). Five residues in chain B all have sequence number 82. They are distinguished by insertion codes: 82, 82A, 82B, 82C. At right is this part of the PDB file.

Insertion Codes In Reverse

Rarely, the insertion codes are in reverse alphabetical order. An example is

Not Monotonic

Rarely, sequence numbers do not increase monotonically from N to C terminus. An example^[1] is 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. Here is an excerpt from the ATOM records of the PDB file for 4zwj chain A:

References

1. ↑ Thanks to Rachel Kramer Green of RCSB.org for this example.