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Validation reports contain an assessment of the quality of a structure and highlight specific concerns by considering the coordinates of the model, the experimental data and the fit between the two. Easily interpretable summary information that compares the quality of a model with that of other models in the archive will help users of PDB data to critically assess archived entries and to select the most appropriate structural models for their needs. These reports are developed using the recommendations of thewwPDB Validation Task Forces.
Reports for released entries are available from Structure Summary pages.
Validation reports for manuscript reviewers are created during annotation of deposited structures.
Information and example Validation Reports (at wwpdb.org).
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NOTE Parameters: BLAST method, E-value cutoff: 10.0, Mask Low Complexity: On.
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Drug-Target Complex: Atorvastatin bound to its target HMG-CoA reductase
Drug: Atorvastatin (Lipitor)
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PoseView images are 2D diagrams that show a ligand and interacting residues.
Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions.
Access PoseView images in the Ligand Chemical Component section on an entry's Structure Summary.
Learn more about PoseView.
Provides a graphical summary of a full-length protein sequence from UniProt and how it corresponds to PDB entries. It also loads annotations from external databases (such as Pfam) and homology models information from the Protein Model Portal. Annotations visualizing predicted regions of protein disorder and hydrophobic regions are displayed.
Learn more about Protein Feature View.
This feature is available from the Molecular Description widget on Structure Summary pages and by entering a UniProt ID below.
Illustrates the correspondences between the human genome and 3D structure. All human genes have been mapped to representative PDB structure protein chains (selected from sequence clusters at 40% sequence identity) to show which regions of a gene are available in PDB coordinates.
Learn more about Gene View.
RCSB PDB's Comparison Tool calculates pairwise sequence (blast2seq, Needleman-Wunsch, and Smith-Waterman) and structure alignments (FATCAT, CE, 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 JSmol symmetry display mode (select the Symmetry button) 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.
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.
Mutations in a gene can have profound effects on the function of a protein. This analysis tool highlights the location of a gene location (i.e., the site of a SNP).
A TGT-to-GGT transversion in codon 64 of the BRCA1 gene leads to substitution of glycine for cysteine. This SNP is located on chromosome 17 at genomic coordinate: 43,106,478. The new mapping tool can be used to locate this position on the UniProt sequence and 3D structure.Access the Mapping Tool
EPPIC (Evolutionary Protein-Protein Interface Classifier) provides value-added information about biological assemblies in the PDB. This web server classifies interfaces present in protein crystals to distinguish biological interfaces from crystal contacts. EPPIC Version 3 enumerates all possible symmetric assemblies with a prediction of the most likely assembly based on probabilistic scores from pairwise evolutionary scoring.
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High school students release a PDB structure; PDB versioning; Structure Quality Metrics; Illustrating PDB Structures in the Molecule of the Month style; and more. Fall 2019 Issue