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1QPI biounits

Comments on biological units for the PDB entry 1QPI

The entry 1QPI contains 1 protein chain: A, and 2 DNA chains: M and N. The length of two DNA chains are identical (15 nucleotide residues), their sequences are similar (differ in 3 positions of 15). All correspondent atoms of two chains have identical coordinates (for example, the atom #1565, which is N4 of cytosine 1 of the chain M has the same coordinates x=6.999, y=1.132, z=44.427 as the atom #1870, which is O4 of thymine 1 of the chain N). All atoms of the chain N have alter codes "A", and all atoms of the chain M have alter codes "B". All DNA atoms have occupancy 0.5.

To generate a biological unit, the authors of the entry suggest to apply a two-fold symmetry transform to all chains A, M, and N. As a result, the original copy of the DNA chain M becomes complementary to the symmetric copy of the chain N (and vice versa). In our opinion, working with the resulting file is unconvinient because of superimposition of chains M and N. That is why for the entry we made a biological unit having occupancy of all atoms equal to 1 and no alter codes.

The biounit (BEL1) includes: in the model 1 the protein chain A and the DNA chain M, both in the original position; in the model 2 the protein chain A and the DNA chain N, both in the position obtained by applying the symmetry transform.