3DNA in PDB

As mentioned previously, PDB makes use of blocview (part of 3DNA) to generate the simple yet effective images for nucleic-acid-containing structures. That's the connection I knew of between 3DNA and PDB. By pure chance, however, I recently noticed the 3DNA entry in PDB — it is actually a protein structure, completely unrelated to the 3DNA software package!

Just out of curiosity, I browsed the abstract of the Liu et al. article, titled "Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding" [J Mol Biol. 2009 Jan 16;385(2):595-605]. I then downloaded the full PDF version of the paper and read it carefully through. This work studied binding interactions of benzenes with the internal cavity of L99A mutated T4 lysozyme. The authors demonstrated that the center of the phenyl ring can be shifted by more than one angstrom due to different halogen-substitutions (where the 3DNA entry corresponds to C6H5I), and (further) proved the concept that "the protein is flexible and adapts to the size and shape of the ligand". At better than 2.0 Å resolution, they also observed the I...S and I...Se halogen-bonds.

I became interested in this paper not just because of the name of 3DNA, for which a quick browsing over the abstract would be sufficient. This paper also reminded me of an early article I published with the title "Influence of fluorine on aromatic interactions":

Non-covalent interactions between aromatic ligands influence the conformations of metal complexes, and the system [M(OAr)₂L₂] has been used to investigate the difference between phenyl–phenyl, phenyl–pentafluorophenyl and pentafluorophenyl–pentafluorophenyl interactions. X-Ray crystal structures show that pentafluorophenyl groups adopt partially stacked orientations with the two aromatic rings close to parallel and with significant π overlap. In contrast, phenyl groups are skewed away from each other with only edge-to-face contacts. Phenyl–pentafluorophenyl interactions adopt a coplanar fully stacked geometry. These results have been rationalised on the basis of energy calculations (carried out blind) using a variety of empirical models for treating weak non-covalent interactions. The major cause of the different behaviour of the three systems lies in the electrostatic interactions between the π systems.

Knowing of the pattern of a PDB id, — 4 characters long: the first character is a numeral in the range 0-9, while the rest can be either numerals or letters — I played around with some other possible ids with my name initials in it. Indeed I found one, 1XJL, a protein structure of human annexin A2 in the presence of calcium ions. If you are bimolecular structure-oriented, why not have a try with some ids of special meaning to you — you might be related to PDB in some unexpected way!