Standard Residues: Difference between revisions
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''Standard residues'' ([[Amino Acids|standard amino acids]] and nucleotides) are defined in the [[PDB files|PDB data file format]], and have record type ATOM in PDB-format atomic coordinate files. Standard residues are: | ''Standard residues'' ([[Amino Acids|standard amino acids]] and nucleotides) are defined in the [[PDB files|PDB data file format]], and have record type ATOM in PDB-format atomic coordinate files. Standard residues are: | ||
* The [[Amino Acids| | * The [[Amino Acids|22 standard amino acids]], plus ambiguous residue codes ASX, GLX, and undetermined UNK. In 2014, the [[PDB]] added genetically encoded proteogenic [[Amino Acids|SEC (U) and PYL (O)]] as "standard"<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>. | ||
* | * Eleven standard nucleotides A, C, G, I, U, DA, DC, DG, DI, DT, and DU<ref name="du">In December, 2019, there are over 80 entries in the Protein Data Bank containing deoxyribo-U ("DU"), and over 250 containing ribo-T. However, note that the PDB does not use "T" to designate ribo-T, but rather 5MU for 5-methyl uridine. 5-methyl-uracil is thymine.</ref>, plus N for an unknown nucleotide. (I is inosine.) The PDB [http://www.wwpdb.org/documentation/file-format-content/format33/sect4.html#HET provides this list under HET]. Note that the PDB does not use "T" to designate ribo-thymidine, but rather 5MU for 5-methyl uridine<ref name="du" />. | ||
The distinction between ribonucleotides (A, C, G, I | The distinction between ribonucleotides (A, C, G, I, U) and deoxyribonucleotides (DA, DC, DG, DI, DT, DU<ref name="du" />) was first made when the PDB was remediated, effective August 1, 2007. The unremediated files can still be obtained, see [[Getting Unremediated PDB Files]]. | ||
Note that, in [[Jmol]], A, C, G, I, T, U select nucleotides in either DNA or RNA for backward compatibility, while DA, DC, DG, DI, DT, and DU select only DNA nucleotides. You can select RNA nucleotides with e.g. "(A, U) and RNA". | Note that, in [[Jmol]], A, C, G, I, T, U select nucleotides in either DNA or RNA for backward compatibility, while DA, DC, DG, DI, DT, and DU select only DNA nucleotides. You can select RNA nucleotides with e.g. "(A, U) and RNA", or by enclosing the single-letter nucleotide names in brackets, e.g. "([A],[C],[G],[I],[U])". | ||
{{Template:Chemical Components}} | {{Template:Chemical Components}} | ||
==See also== | ==See also== | ||
*[[Amino Acids]] | |||
*[[Alternate locations]] | |||
*[[Non-Standard Residues]] | *[[Non-Standard Residues]] | ||
*[[HETATM]] ([[Hetero atoms]]) | *[[HETATM]] ([[Hetero atoms]]) | ||
*[[tRNA]] | *[[tRNA]] | ||
[[Category:Topic Page]] | [[Category:Topic Page]] | ||
==Notes & References== | |||
<references /> | |||