RCSB PDB's Comparison Tool calculates pairwise sequence (blast2seq, Needleman-Wunsch, and Smith-Waterman) and structure alignments (FATCAT, CE, Mammoth, TM-Align, TopMatch).
Comparisons can be made for any protein in the PDB archive and for customized or local files not in the PDB.
Special features include support for both rigid-body and flexible alignments and detection of circular permutations.
The Jmol Symmetry view highlights global, local, and helical symmetry among subunits. The view displays the symmetry axes, a polyhedron
that reflects the symmetry, and a color scheme that emphasizes the symmetry.
PDB ID: 4HHB
PDB ID: 1STP
PDB ID: 1IFD
Structure Summary pages provide access to information about structure quality.
The slider graphic compares important global quality indicators for a given structure with the PDB archive. Global percentile ranks (black vertical boxes) are calculated with respect to all X-ray structures available prior to 2011.
Resolution-specific percentile ranks (white vertical boxes) are calculated considering entries with similar resolution.
This graphic is from the wwPDB Validation Report, which provides a more detailed assessment of the quality of a structure and highlights specific concerns.
These reports were created using the recommendations of wwPDB Validation Task Forces. The full wwPDB Validation Report PDF is available for download. PDFs of Ramachandran plots (created by MolProbity) are provided to offer an independent method to evaluate the conformational quality of protein structures.
For examples, view the Structure Summary pages for 1CBS
(1.8Å structure of a small protein and a ligand, an entry with better overall quality relative to all X-ray structures)
and 1FCC (a 3.2Å structure with worse overall quality relative to all
Map genomic location to protein sequence and 3D structure.
A list of links provide access to external websites related to macromolecular structure.
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