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

Advanced Search

The Advanced Search interface enables queries by specific categories. Queries can be combined with AND or OR to construct complex searches.

Search categories:

• IDs and keywords
• Structure annotation
• Deposition
• Structure features
• Sequence features
• Chemical components
• Biology
• Methods
• Publication

Search by Sequences

Choose Option A or B to search for protein and nucleic acid sequences.  Read Tutorial | Advanced Sequence Searching

NOTE Parameters: BLAST method, E-value cutoff: 10.0, Mask Low Complexity: On.

Search by Ligands

Search ligands bound to macromolecules in the PDB by:

• Identifier or Name
• SMILES String, InChI or InChI Key
• Chemical Formula or Molecular Weight
• Chemical Substructure or Similarity

Right image: MarvinJS by ChemAxon for Ligand Search of Lipitor

Search by Drugs & Drug Targets

Drugs & Drug Targets in the PDB have been mapped to DrugBank.

• 

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

• 

  Drug: Atorvastatin (Lipitor)

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 Tuesday Dec 04 2018 there are 146861 structures.

• Access new data entries this week
• Access new structure publications this week
• Search unreleased entries

Next data entry update in:

Browse by Annotation

PDB entries have been annotated by various ontologies and hierarchical classification schemes.

• Anatomical Therapeutic Chemical Classification System
• Membrane Proteins
• Protein Modification
• Protein Symmetry
• Biological Process, Cell Component, Molecular Function
• Enzyme Classification
• Transporter Classification
• Source Organism
• Genome Location
• MeSH (Medical Subject Headings)
• SCOP and CATH

Search PDB Statistics

The PDB Statistics page lists the current holdings in the PDB and various growth statistics and histograms.

• Summary Table of Released Entries
• Growth of Released Structures Per Year
• Growth of X-ray Structures Per Year

Pathway View

Explore metabolic pathways maps that identify pathway components with PDB structures and homology models.

Maps can be accessed from the Protein View (see example P29401), and the main Pathway View page.

PoseView

Biotin bound to Streptavidin

PDB ID:1STP

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.

Protein Feature View

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.

Examples: Breast Cancer Type 1 Protein, Gag-Pol Polyprotein, and Hemoglobin Alpha (shown image).

This feature is available from the Molecular Description widget on Structure Summary pages and by entering a UniProt ID below.

Human Gene View

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.

Examples: Breast Cancer 1 (early onset) and Hemoglobin, Alpha 1 (shown image).

This feature is available from the Molecular Description widget on Structure Summary pages and by entering an HGNC Human Gene Symbol below (examples).

Protein Symmetry

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.

• 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 Position to Protein

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).

Example of SNP in Breast Cancer 1 Gene

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.

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.

Download: Sequences

Enter PDB IDs separated by comma or white space. Download Help 

Download a FASTA file containing all PDB sequences: uncompressed | gzipped

Download: Ligands

Enter ligand IDs separated by comma or white space. Download Help 

FTP 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 ftp.wwpdb.org (data download details).

Major Directories

• The directory pub/pdb is the entry directory for the ftp site.
• 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 FTP Archive is available at ftp://ftp-versioned.wwpdb.org (See announcement). 

HTTP/HTTPS Services

PDB structure files, chemical component files, and several other files are available for download via http/https. These URLs are useful in scripted downloads using utilities such as wget.

Downloadable Files

• PDB Structure Files
• Ligand Files
• Secondary Structure Files
• SIFTS Files

RESTful Web Services

The RCSB PDB supports RESTful (REpresentational State Transfer) Web Services to make accessing data easier.

Generally we are trying to implement two types of services for our RESTful interface:

• Search services: to return a list of IDs (e.g., PDB IDs, chain IDs, ligand IDs)
• Fetch services: to return data given a ID (e.g. reports, descriptions, data items)