Unusual sequence numbering: Difference between revisions
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The numbering of protein and nucleic acid sequences is arbitrary in structure files from the [[PDB|World Wide Protein Data Bank]] (PDB). | The numbering of protein and nucleic acid sequences is arbitrary in structure files from the [[PDB|World Wide Protein Data Bank]] (PDB). | ||
'''Straightforward numbering''' assigns 1 to the amino-terminal amino acid, and counts up monotonically to the carboxy-terminal amino acid. An example is [http://firstglance.jmol.org/fgij/fg.htm?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. | '''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/fgij/fg.htm?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. | ||
Below are some examples of '''unusual sequence numbering'''. The 3D structures of these PDB entries are not shown here. To explore them in 3D, the links below will display them in [[FirstGlance in Jmol]] (link with arrow) or in Proteopedia (link in parentheses). | Below are some examples of '''unusual sequence numbering'''. The 3D structures of these PDB entries are not shown here. To explore them in 3D, the links below will display them in [[FirstGlance in Jmol]] (link with arrow) or in Proteopedia (link in parentheses). | ||