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

International Tables for Crystallography (2006). Vol. G, ch. 3.6, pp. 168-169

Section 3.6.7.1.4. Alternative conformations

P. M. D. Fitzgerald,a* J. D. Westbrook,b P. E. Bourne,c B. McMahon,d K. D. Watenpaughe and H. M. Bermanf

aMerck 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

3.6.7.1.4. Alternative conformations

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The data items in these categories are as follows:

(a) ATOM_SITES_ALT [Scheme scheme92]

(b) ATOM_SITES_ALT_ENS [Scheme scheme93]

(c) ATOM_SITES_ALT_GEN [Scheme scheme94]

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.

Biological macromolecules are often very flexible, and as the resolution of a structure determination increases, it becomes increasingly possible to model reliably the alternative conformations that the structure adopts. Typically, partial occupancies are assigned to atom sites within the alternative conformations to indicate the relative frequency of occurrence of each conformation. It can, however, be difficult to deduce the possible different conformations of the whole structure from inspection of the atom-site occupancies alone. For instance, a segment of protein main chain might adopt one of three slightly different conformations, and within each conformation a particular side chain might adopt one of two possible conformations, one of which sterically distorts an adjacent residue sequence, while the other does not. The data model in the mmCIF dictionary allows these kinds of correlations in positions to be described.

The relationships between the categories used to describe alternative conformations are shown in Fig. 3.6.7.1[link].

In the core CIF dictionary, alternative conformations are indicated by using the _atom_site.disorder_assembly and *.disorder_group data items. Aliases to these data items are present in the mmCIF dictionary, but it is not intended that they should be used to describe disorder in a macromolecular structure.

The model for describing alternative conformations in mmCIF uses the ATOM_SITES_ALT family of categories. Ensembles of correlated alternative conformations can be identified using the category ATOM_SITES_ALT_ENS. Each ensemble is generated from one or more of the alternative conformations given in the list of alternative sites in the ATOM_SITES_ALT category. Data items in the ATOM_SITES_ALT_GEN category explicitly tie together the alternative conformations that contribute to each ensemble. Finally, the atoms in each alternative conformation are identified in the ATOM_SITE category by the data item _atom_site.label_alt_id.

The current version of the mmCIF dictionary cannot be used to describe an NMR structure determination completely. However, an mmCIF can be used to store the multiple models usually used to describe a structure determined by NMR using the data items in these categories.

Example 3.6.7.3[link] is a simplified version of the example given in the mmCIF dictionary (see Fig. 3.6.7.2[link]).

[Figure 3.6.7.2]

Figure 3.6.7.2 | top | pdf |

Alternative conformations in an HIV-1 protease structure (PDB 5HVP) to be described with data items in the ATOM_SITES_ALT, ATOM_SITES_ALT_ENS and ATOM_SITES_ALT_GEN categories. (a) Complete structure, (b) ensemble 1, (c) ensemble 2.

Example 3.6.7.3. Alternative conformations in an HIV-1 protease structure (PDB 5HVP) described with data items in the ATOM_SITES_ALT, ATOM_SITES_ALT_ENS and ATOM_SITES_ALT_GEN categories.

[Scheme scheme95]








































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