MMDB: annotating protein sequences with Entrez's 3D-structure database

Wang, Yanli; Addess, Kenneth J.; Chen, Jie; Geer, Lewis Y.; He, Jane; He, Siqian; Lu, Shennan; Madej, Thomas; Marchler-Bauer, Aron; Thiessen, Paul A.; Zhang, Naigong; Bryant, Stephen H.

Using the table view with this example, one may notice that several related structures are complexes of the same protein with different drugs/inhibitors, e.g. structures with PDB codes 1O86 (11), 1UZF (12) and 1UZE (12) . Clicking on the graphical alignment footprint of 1O86, a human ACE enzyme in complex with lisinopril, one can see a text representation of the corresponding BLAST alignment, and a Cn3D view of the alignment can be launched by clicking on 'Get 3D Structure data' (Figure 3 ). One may see that the query protein is highly similar in sequence to the human ACE enzyme, as identical residue pairs are colored red by default. The sequence identity across the aligned region is 82%, and it Figure 1 . Non-identical protein sequences in Entrez have been classified into groups linked to related structures, at various levels of sequence similarity. Sequence identity is calculated from the BLAST alignments, and here only those neighbor relationships are listed that produce an aligned footprint of 50 residues or more. The analysis also excludes protein sequences which have been directly obtained from MMDB. Forty-eight percent of sequences in Entrez protein have at least one structure neighbor with an extensive alignment footprint and at least 30% identical residues. appears that the core of the structure is mostly formed by residues conserved between the two aligned rows, while non-conserved residues are mainly located on the structure's surface.