Composition of PDB entry and biounits

The section contains PDB files and information about chains of macromolecules in it. The files are asymmetric unit (PDB entry) and biological unit (Biounits). In case when structure is solved with NMR we cut it on single models and each model is present as Model file. Some structures have features, such as duplication of atoms or two or more variants of the structure posed in one coordinate space, that make it difficult to analyze them by standard tools. We revise those structures and put the information in special files called as "bel files", for example 1qpi.bel1.pdb. Each file is available for downloading and visualizing in Jmol.

We use this files for calculating hydrogen bonds, water bridges, hydrophobic interactions, identification of Pfam domains, etc. However, we use only one file from presented in this section. If structure is solved with NMR method and has a multimodel file, we use the first model only, if the method is X-RAY and the complex has corrected "bel file" we use it, if there is no "bel file", then we use the first biological unit. In consequence this selected file is called the actual unit.

Interaction service is available for the "actual unit". This service allows a user to visualize each individual bond in structure and to download datasets of Hbonds, water bridges, and hydrophobic clusters.

http://npidb.belozersky.msu.ru/img/npidb_help/composition_of_biounits_1.png