Non-Standard Residue: Difference between revisions
Eric Martz (talk | contribs) linked HETATM |
Eric Martz (talk | contribs) linked HETATM |
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<!-- REMEDIATED TO SEP, TPO: For example, phosophserine and phosphothreonine in [[1apm]] are given as standard residues SER and THR in ATOM records plus PO3 groups in HETATM records. | <!-- REMEDIATED TO SEP, TPO: For example, phosophserine and phosphothreonine in [[1apm]] are given as standard residues SER and THR in ATOM records plus PO3 groups in HETATM records. | ||
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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). | 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]]. | 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]] | See also [[Standard Residues]] | ||
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