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. | ||
In addition to the 20 historically "standard" [[Amino Acids|amino acids]], two additional unusual but genetically encoded amino acids | In addition to the 20 historically "standard" [[Amino Acids|amino acids]], two additional unusual but genetically encoded amino acids have been considered to be "standard" by the [[PDB]] since 2014<ref name="pdb22">[https://www.wwpdb.org/news/news?year=2014#5764490799cccf749a90cddf Announcement: Standardization of Amino Acid Nomenclature], World Wide Protein Data Bank News, January 8, 2014.</ref><ref name="sec">[[1fdo]], released 1997, had selenocysteine 140 in chain A coded as HETATM CSE through the [ftp://snapshots.wwpdb.org/20140102/pub/pdb/data/structures/divided/pdb/fd/pdb1fdo.ent.gz WWPDB snapshot of 2014-01-02], but had it coded aa ATOM SEC in the [ftp://snapshots.wwpdb.org/20141203/pub/pdb/data/structures/divided/pdb/fd/pdb1fdo.ent.gz 2014-12-03 snapshot]. See [[Getting Unremediated PDB Files]].</ref>: [[selenocysteine]] and [[pyrrolysine]]. However, elsewhere these may still be designated as "non-standard". | ||
Examples: | Examples: | ||
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* PSU ([[Pseudouridine]]) and several others in [[tRNA]] | * PSU ([[Pseudouridine]]) and several others in [[tRNA]] | ||
* MSE in [[2ab5]] (see [[Selenomethionine]]) | * MSE in [[2ab5]] (see [[Selenomethionine]]) | ||
* [[Amino_Acids#L-_and_D-Amino_Acids|D-amino acids]], present in >700 entries in the PDB, for example [[5e5t]]. | |||
Although phosphoserine and phosphothreonine are given as non-standard residues SEP and TPO in [[1bkx]], an alternative convention may also be followed. | Although phosphoserine and phosphothreonine are given as non-standard residues SEP and TPO in [[1bkx]], an alternative convention may also be followed. | ||
<!-- 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. | ||
--> | --> | ||
For example, a non-standard phenylethane amino acid sidechain in [[1b07]] is named GLY (GLY 5 on chain C in ATOM records) plus | For example, a non-standard phenylethane amino acid sidechain in [[1b07]] is named GLY (GLY 5 on chain C in ATOM records) plus PYJ (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 | 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 unremediated files can still be obtained, see [[Getting Unremediated PDB Files]]. | ||
{{Template:Chemical Components}} | {{Template:Chemical Components}} | ||