Non-Standard Residue: Difference between revisions
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Any residue of protein or nucleic acid that is not included in the list of [[Standard Residues]] is considered ''Non-Standard''. The atomic coordinates for atoms in non-standard residues are given in records of type HETATM in the PDB file format. | Any residue of protein or nucleic acid that is not included in the list of [[Standard Residues]] is considered ''Non-Standard''. The atomic coordinates for atoms in non-standard residues are given in records of type [[HETATM]] in the PDB file format. | ||
Examples: | Examples: | ||
Revision as of 05:51, 26 December 2009
Any residue of protein or nucleic acid that is not included in the list of Standard Residues is considered Non-Standard. The atomic coordinates for atoms in non-standard residues are given in records of type HETATM in the PDB file format.
Examples:
Although phosphoserine and phosphothreonine are given as non-standard residues SEP and TPO in 1bkx, an alternative convention may also be followed. For example, a non-standard phenylethane amino acid sidechain in 1b07 is named GLY (GLY 5 on chain C in ATOM records) plus PYL (sequence number 1005 in chain C in HETATM records).
The former scheme of designating modified standard nucleotides with plus signs (+A, +C, +G, +I, +T, +U) was discontinued in the PDB remediation project, effective August 1, 2007. The unremdiated files can still be obtained, see Getting Unremediated PDB Files.
See also Standard Residues