Standard Residues: Difference between revisions
mNo edit summary |
Eric Martz (talk | contribs) No edit summary |
||
| (6 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
''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 | * 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, 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]]. | 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]]. | ||
| Line 11: | Line 11: | ||
==See also== | ==See also== | ||
*[[Amino Acids]] | |||
*[[Alternate locations]] | *[[Alternate locations]] | ||
*[[Non-Standard Residues]] | *[[Non-Standard Residues]] | ||