Non-Standard Residue: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Jaime Prilusky, Eric Martz, Wayne Decatur

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-Any residue not included in the list of [[Standard Residues]] is considered ''Non-Standard''.
+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 &quot;standard&quot; [[Amino Acids|amino acids]], two additional unusual but genetically encoded amino acids have been considered to be &quot;standard&quot; 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 &quot;non-standard&quot;.
 Examples:
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 * SEP and TPO in [[1bkx]]
 * 1MA, 2MG, 5MC, 5MU, 7MG, H2U, M2G, OMC, OMG, PSU, and YG in [[1evv]]
-* MSE in [[2ab5]]
+* PSU ([[Pseudouridine]]) and several others in [[tRNA]]
+* 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.
+<!-- 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 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 unremediated files can still be obtained, see [[Getting Unremediated PDB Files]].
+{{Template:Chemical Components}}
+==See Also==
+*[[Standard Residues]]
+*[[Amino Acids]]
+*[[Hetero atoms]]
+*[[Alternate locations]]
+*[[Ligand]]
+*[[tRNA]]
+[[Category:Topic Page]]
-Note: 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.
+==References==
+<references />