Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5661_Библиотеки_им_академика_М_И_Перельмана

Peptide-based chromophores provide a more complex example. In proteins, chromophores typically comprise three amino acids condensed into one molecule. In the CCD component, the one-letter code lists all amino acids that make up the chromophore. For example, the CCD denition for the chromophore CR2, which comprises the amino acids GLY-TYR-GLY and has the corresponding one-letter code GYG.

The PDB archive also contains examples of complex ligands, which comprise combinations of amino acid and amino acid-like components. These peptide-like molecules commonly possess important biological functions, such as antibiotic or inhibitory activity, however, a description of their global chemistry does not t within the classic PDB denitions of polymers and ligands. Therefore, to support the curation of this important class of molecules, their chemical and biological descrip­tions are described in a separate dictionary. The “Peptide Reference Dictionary” (PRD) resource [30] provides a standardized framework for these denitions so that each PRD entity can be described in a way that outlines both its subcomponent composition and global characteristics. These PRD denitions are stored in the wwPDB Biologically Interesting Molecule Reference Dictionary (BIRD) (https:// www.wwpdb.org/data/bird).

subcomponent-specic data, which would otherwise not be possible. Links to PRD denition les can be found on relevant PDB entry pages and references to key PRD identiers (ID, name, type, and function) are stored in PDB entry PDBx/mmCIF les under the pdbx_molecule_features category (Figure 5.2).

The most common ligand-associated annotations found in PDB entry les refer to intermolecular bonding. These refer to all nonstandard linkages between and among polymer components and CCD ligands. This information was historically found in PDB-format LINK, SSBOND, and CONECT records, however, the current PDBx/mmCIF archive format provides additional data, including leaving group information, atomic descriptions, and author numbering for up to three chemical component partners per interaction [9]. At present, to ensure standardization across the whole PDB archive, all link records and bonding distances are calculated and validated during the biocuration process [31]. The PDBx/mmCIF dictionary cur­rently supports covalent, hydrogen, covalent–metal, and disulde-bond interaction “types” [32] (Figure 5.3).

The most recent development concerning PDB ligand denitions relates to the annotation of polymeric carbohydrates [33]. These new “branched poly­mer” descriptions (entity_type item “branched”) are composed of multiple and sequential CCD monosaccharides. The description of polymeric carbohydrates is outlined within the PDBx/mmCIF model le for a given PDB entry, under the new pdbx categories entity_branch, entity_branch_descriptor, entity_branch_link, entity_branch_list, and branch_scheme (Figure 5.4a). Whilst chemically distinct