Data Exploration Services

New graphics summarize ligand quality assessments. A) The slider graphic on the Structure Summary page for the PDB structure of a SARS-CoV-2 papain-like proteinase of 7JIR indicates the fitting quality of the ligand of interest. Clicking on the bar will take the user to the Ligands tab for more information about this ligand in this particular entry and across the archive.

More than 70% of PDB structures are complexed with small molecule ligands. These complexes represent a range of "quality" in terms of how well the atomic coordinates are supported by experimental data, and how well the ligand 3D structure agrees with known chemistry (e.g., bond lengths, bond angles).

New ligand structure quality assessment metrics are accessible from Structure Summary pages for PDB structures determined by X-ray crystallography. Correlated quality indicators (e.g., RSR, RSCC) have been aggregated into a ranking score that can be used for comparison across the archive.

Quality information for Ligand/s Of Interest is indicated by a slider bar on the Structure Summary page for a PDB structure (e.g.,7JIR). Clicking on the bar representing the ligand returns the Ligands tab, which provides more information about this ligand in this particular entry and for the top five "high quality" instances in the archive.

The new indicators allow any user to quickly review ligand structure quality and unambiguously select the CCD ligand (or ligands) in a particular PDB structure that will best serve their research or teaching interests.

Detailed documentation about this feature is available; for more information about small molecule ligand validation:

• Enhanced Validation of Small-Molecule Ligands and Carbohydrates in the Protein Data Bank (2021) Structure 29: 393-400.e391 doi:10.1016/j.str.2021.02.004
• Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop (2016) Structure 24:502-508 doi:10.1016/j.str.2016.02.017

Method-specific Validation Task Forces have been convened by the wwPDB to collect recommendations and develop consensus on additional validation that should be performed, and to identify software applications to perform validation tasks.

The “Display Results as” menu manages the search results data type presented.

Search results can be returned and displayed as different data types: Structures, Polymer Entities, Non-polymer Entities, Assemblies, or Molecular Definitions.

The Non-polymer Entities option will return small chemicals (enzyme cofactors, ligands, ions, etc) defined by a non-polymer type in the data file. Each non-polymer Entity is assigned an ID containing the PDB ID and entity ID, e.g., 4HHB_3. This option may be useful for exploring small molecules in their macromolecular context, e.g., covalently bound ligands.

The Molecular Definitions option will return components as defined in theChemical Component Dictionary (CCD) andBiologically Interesting molecule Reference Dictionary (BIRD). Each definition listed links to the summary page for the component. The set of molecular definitions can be exported in .sdf and .mol2 file formats.

Related Advanced Search help documentation is available.

RCSB PDB has integrated 3D structural information with glycosylation resources to promote interactions between the glycoscience and PDB communities.
Relevant PDB structures are now linked to individual data in

• GlyTouCan: the international glycan structure repository
• GlyCosmos: portal aiming to integrate the glycosciences with the life sciences, consisting of Standards, Repositories and Data Resources, providing information about genes, proteins, lipids, pathways and diseases.
• GlyGen: data integration and dissemination project for carbohydrate and glycoconjugate related data integrated from multiple international data sources

Data are accessible from individual Structure Summary pages.

This work builds upon other new improved features for exploring carbohydrate data in the PDB.

Genome View provides a graphical summary of the correspondences between PDB entity sequences and reference genomes.
From an entry's Structure Summary page, use the Genome tab to access

• Chromosome region where the PDB entity is located
• DNA frame that codifies the PDB entity
• Genome positions that encode each single residue

In addition to entity sequences, Genome View also includes alignments between the genome and the UniProt and NCBI sequences associated with the PDB entity. Alignment data is collected using the RCSB PDB 1D Coordinate Server API. Visit the related Help Documentation for more information on the Gene View resource.

Alignment data is collected using theRCSB PDB 1D Coordinate Server API. Visit the related Help Documentation for more information on the Gene View resource.

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