Validation Services

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).

Check your X-ray, NMR, or EM structures before depositing (standalone server).

Deposit 3D macromolecular structure data to the PDB

Have non-atomic coordinates, multi-scale structures obtained through integrative/hybrid (I/H) methods? Deposit at PDB-Dev which is a prototype deposition and archiving system for structural models obtained through integrative/hybrid (I/H) methods.

Questions about your deposition?

• Deposit FAQ
• Tutorials
• wwPDB Annotation Policies
• wwPDB Processing Procedures

Search by Unreleased & Access New Entries

The PDB archive is updated weekly in two phases

Phase I: Every Saturday by 3:00 UTC, for every new entry, wwPDB website provides sequence(s) (amino acid or nucleotide) for each distinct polymer and, where appropriate, the InChI string(s) for each distinct ligand and the crystallization pH value(s).

Phase II: Every Wednesday by 00:00 UTC, all new and modified data entries will be updated at each of the wwPDB FTP sites.

As of Tue May 17 2022 there are 190639 structures.

• Access new data entries this week
• Search unreleased entries

Search by Drugs & Drug Targets

Drugs & Drug Targets in the PDB have been mapped to DrugBank. They have been made available through the integrated search system. You can find some search examples under the help examples page.

• 

  Drug-Target Complex: Atorvastatin bound to its target HMG-CoA reductase

• 

  Drug: Atorvastatin (Lipitor)

Protein Feature View

Provides a graphical summary of biological and structural protein features of PDB entities and how they correspond to UniProtKB  sequences. It loads features from RCSB PDB webservices and third party resources such as UniProtKB, CATH or SCOPe.

Learn more about  Protein Feature View.

Examples: SARS-CoV-2 spike glycoprotein, H-Ras, and BRCA1

This feature is available in Structure Summary pages and Instance Sequence pages.

Genome View

Illustrates the correspondences between PDB Entity sequences and genomes. When the relationships between PDB Entities and genes are available, PDB Entity sequences are mapped to their genome positions to show which regions of a gene are available in the Entity coordinates.

Learn more about Genome View.

Examples: Breast Cancer 1 (early onset) , SARS-CoV-2 spike glycoprotein and H-Ras (shown image).

This feature is available from the Structure Summary page Genome tab.

Protein Symmetry

The Mol* symmetry display mode (select the Assembly 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.

• Hemoglobin

  

  PDB ID:4HHB

• Streptavidin

  

  PDB ID:1STP

• Inovirus

  

  PDB ID:1IFD

Structure Quality

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 X-ray structures).

Map Genomic Locations to/from PDB

The 1D-coordinates API provides means to map between genomic coordinates and PDB positions. Find more information about this and other APIs in the webservices page.

EPPIC Biological Assemblies

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.

PDB Citation MeSH Network Explorer

The National Library of Medicine assigns MeSH (Medical Subject Headings) from a controlled vocabulary to index articles for PubMed. MeSH terms typically appear in a hierarchical tree structure that starts with 16 main branches. The PDB Citation MeSH Network Explorer flattens these trees into co-occurence networks of MeSH terms associated with PDB entries. Each node on the graph is a publication, and nodes are linked when they share MeSH terms. 

Download: Sequences

By entering PDB IDs, sequences can be downloaded in FASTA format.

Sequences can be provided for any of these identifiers:

• Entry IDs
• Entity IDs
• Asym IDs

Go to the Sequences Downloads Page

Download: Ligands

By entering chemical component IDs, SDF files with ligand coordinates can be downloaded.

Downloads are provided for:

• Coordinates of first chemical component instance from each PDB entry
• Coordinates of all chemical component instances from each PDB entry
• Ideal coordinates from Chemical Component Dictionary

Go to the Ligands Downloads Page

File Download Services

Searches and reports performed on this RCSB PDB website utilize data from the PDB archive. The PDB archive is maintained by the wwPDB at the main archive, ftp.wwpdb.org (data download details) and the versioned archive, ftp-versioned.wwpdb.org (Versioning details).

Major Directories

• The directory pub/pdb is the entry directory for the PDB archive.
• The directory pub/pdb/data/structures/divided contains the current PDB contents including PDB, mmCIF, and PDBML/XML formatted coordinate files, structure factors and NMR restraints

Annual snapshots of PDB Archive are available. 

The Versioned Archive is available at https://ftp-versioned.wwpdb.org (See announcement). 

Web Services

Programmatic access to individual structures and/or specific data items is provided through Web Service Application Program Interfaces (APIs).

New Web Service APIs are being developed; users should register with the RCSB PDB API electronic list for announcements.

Contact RCSB PDB with questions suggestions for specific services.