Non-Standard Residue

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:

SEP and TPO in 1bkx
1MA, 2MG, 5MC, 5MU, 7MG, H2U, M2G, OMC, OMG, PSU, and YG in 1evv
MSE in 2ab5

Although phosphoserine and phosphothreonine are given as non-standard residues SEP and TPO in 1bkx, and alternative convention may also be followed. For example, phosophserine and phosphothreonine in 1apm are given as standard residues SER and THR in ATOM records plus PO3 groups 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.

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