Polymer entities

Fitzgerald, P. M. D.; Westbrook, J. D.; Bourne, P. E.; McMahon, B.; Watenpaugh, K. D.; Berman, H. M.

doi:10.1107/97809553602060000738

International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

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International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 175-176

Section 3.6.7.3.2. Polymer entities

P. M. D. Fitzgerald,^a ^* J. D. Westbrook,^b P. E. Bourne,^c B. McMahon,^d K. D. Watenpaugh^e and H. M. Berman^f

^a Merck Research Laboratories, Rahway, New Jersey, USA,^bProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA,^cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,^dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,^eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and ^fProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA
Correspondence e-mail: paula_fitzgerald@merck.com

3.6.7.3.2. Polymer entities

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The data items in these categories are as follows:

(a) ENTITY_POLY [Scheme scheme130]

(b) ENTITY_POLY_SEQ [Scheme scheme131]

The bullet ( $[\bullet]$ ) indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. The arrow ( $[\rightarrow]$ ) is a reference to a parent data item.

The polymer type, sequence length and information about any nonstandard features of the polymer may be specified using data items in the ENTITY_POLY category. The sequence of monomers in each polymer entity is given using data items in the ENTITY_POLY_SEQ category. The relationships between categories describing polymer entities are shown in Fig. 3.6.7.6, which also shows how the information describing the polymer is linked to the coordinate list in the ATOM_SITE category and to the full chemical description of each monomer or nonstandard monomer in the CHEM_COMP category.

Figure 3.6.7.6 | top | pdf |

The family of categories used to describe polymer chemical entities. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet ( $[\bullet]$ ). Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.

Non-polymer entities are treated as individual chemical components, in the same way in which monomers within a polymer are treated as individual chemical components. They may be fully described in the CHEM_COMP group of categories (Example 3.6.7.7).

Example 3.6.7.7. An example of both polymer and non-polymer entities in a drug–DNA complex (NDB DDF040) described with data items in the ENTITY, ENTITY_KEYWORDS, ENTITY_NAME_COM, ENTITY_POLY and ENTITY_POLY_SEQ categories (Narayana et al., 1991).

[Scheme scheme132]

Data items in the ENTITY_POLY category can be used to give the number of monomers in the polymer and to assign the type of the polymer as one of the set of types polypeptide(D), polypeptide(L), polydeoxyribonucleotide, polyribonucleotide, polysaccharide(D), polysaccharide(L) or other. Details of deviations from a standard type may be given in _entity_poly.type_details.

In some cases, the polymer is best described as one of the standard types even if it contains some nonstandard features. Flags are provided to indicate the presence of three types of nonstandard features. The presence of chiral centres other than those implied by the assigned type is indicated by assigning a value of yes to the data item _entity_poly.nstd_chirality. A value of yes for _entity_poly.nstd_linkage indicates the presence of monomer-to-monomer links different from those implied by the assigned type and a value of yes for _entity_poly.nstd_monomer indicates the presence of one or more nonstandard monomer components.

Data items in the ENTITY_POLY_SEQ category describe the sequence of monomers in a polymer. By including _entity_poly_seq.mon_id in the category key, it is possible to allow for sequence heterogeneity by allowing a given sequence number to be correlated with more than one monomer ID. Sequence heterogeneity is shown in the example of crambin in Section 3.6.3.

References

Narayana, N., Ginell, S. L., Russu, I. M. & Berman, H. M. (1991). Crystal and molecular structure of a DNA fragment: d(CGTGAATTCACG). Biochemistry, 30, 4449–4455.Google Scholar

International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 175-176