A Structural View of Biology
This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease.
The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond.
Deposition Preparation Tools
- pdb_extract: Extract and harvest data in PDBx/mmCIF format from structure determination programs
- SF-Tool: Convert structure factor files among various formats
- Ligand Expo: Search the Chemical Component Dictionary for the IDs of released ligands
Data Format Conversion
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).
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?
From any page on the site, a Basic Search can be run by entering a search term in the top Search Bar.
As you enter a term, you will see suggestions appearing in the dropdown menu that appears below the search bar. The suggestions are grouped by attribute name, indicating in the specific field or fields in which the search term was found.You can click on an item in the dropdown menu to see results matching only that particular attribute, or click the
The Advanced Search Query Builder tool allows you to construct complex boolean queries by specifying values for a wide range of structure attributes.
Text-based queries can be combined with sequence and structure similarity searches.
Search results can be returned at the structure, entity, or assembly level, and viewed in a variety of formats, for example, as a summary view, an images only gallery view, or in a Tabular Report format.
Any query and its results can be further refined by selecting additional criteria from the 'Refinements' panel.
Search by Sequences
Search protein and nucleic acid sequences using the mmseqs2 method to find similar protein or nucleic acid chains in the PDB.
The new Advanced Search Query Builder tool can be used to run sequence searches, and to combine the results with the other search criteria that are available.
Chemical Sketch Tool
You can search the PDB archive for a specific ligand or similar ligands based on the 2D chemical drawing of a molecule. In doing so you don’t have to know the specific chemical descriptors (e.g., SMILES and/or InChI) because they will be automatically generated. You can also edit a molecule that is drawn or loaded into the tool to add or remove atoms or groups of atoms and then use the new molecule to query the PDB archive.
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.
Browse by Annotation
PDB entries have been annotated by various ontologies and hierarchical classification schemes.
- Anatomical Therapeutic Chemical Classification System
- Biological Process
- CATH (Structure Classification)
- Cellular Component
- Enzyme Classification
- Genome Location
- MeSH (Medical Subject Headings)
- Molecular Function
- mpstruc (Membrane Proteins)
- OPM (Membrane Proteins)
- Protein Symmetry
- SCOP (Structure Classification)
- Source Organism
Explore the PDB Archive
Search ligands bound to macromolecules in the PDB by:
- SMILES String, InChI
- Chemical Formula
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)
Mol* 3D Viewer
Launch Mol* from the Structure Summary page for any entry.
A standalone version of Mol* is available. Users can upload their custom files into this tool.
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.
This feature is available in Structure Summary pages and Instance Sequence pages.
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.
This feature is available from the Structure Summary page Genome tab.
Pairwise Structure Alignment
The protein structure alignment tool allows for calculating pairwise structure alignments using different alignment methods. See the detailed documentation at this help page. Comparisons can be made for any protein in the PDB archive and for customized or local files not in the PDB.
Also, the standalone Mol* viewer application allows for calculating pairwise structure alignments based on sequence alignment. See detailed instructions on how to superpose structures at the Mol* help page.
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.
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.
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.1D-coordinates API tutorial
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.
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 Coordinate & Experimental Data Files
By entering PDB IDs, multiple files can be downloaded in batches containg one or more file formats.
Coordinate Data Files can be downloaded in the following formats:
- PDBML/XML (Header only)
- Biological Assemblies in PDB
- Biological Assemblies in PDBx/mmCIF
Experimental Data Files can be downloaded in the following formats:
- Structure Factors
- NMR Restraints
- Chemical Shifts
- NMR Restraints v2
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
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
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).
- 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. Read More on File Download 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.More
Crystal structure of VIM-2 MBL in complex with 1-(but-3-en-1-yl)-1H-imidazole-2-carboxylic acid
Crystal structure of VIM-2 MBL in complex with (R)-1-(sec-butyl)-1H-imidazole-2-carboxylic acid
CspA-27 cotranslational folding intermediate 3
Crystal structure of TFAM (mitochondrial transcription factor A) bridging two non-sequence specific DNA substrates
Substrate-engaged mycobacterial Proteasome-associated ATPase - focused 3D refinement (state B)
structure of adenylyl cyclase 9 in complex with DARPin C4 and ATP-aS
Cfr-modified Escherichia coli stalled ribosome with antibiotic radezolid
structure of adenylyl cyclase 9 in complex with DARPin C4 and ATP-aS
Crystal structure of human Biliverdin IX-beta reductase B with Olsalazine Sodium (OSS)
Crystal Structure of human RIPK1 kinase domain in complex with a novel inhibitor
Features & Highlights
Improved support for extended PDBx/mmCIF structure factor files
Extensions to the PDBx/mmCIF dictionary for reflection data with anisotropic diffraction limits, for unmerged reflection data, and for quality metrics of anomalous diffraction data are now supported in OneDep.
Time-stamped Copies of PDB and EMDB Archives
A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org) as of January 3, 2022 has been added to ftp://snapshots.wwpdb.org and ftp://snapshots.pdbj.org.
Paper Published in Glycobiology
Read about the Modernized uniform representation of carbohydrate molecules in the Protein Data Bank
Remove Redundancy in Search Results
Use the new Group option to simplify results based on sequence identity, UniProt ID, and group depositions.
Deposition of Half-maps for Certain EM Entries to Become Mandatory
Deposition of half-maps for single-particle, single-particle-based helical, and sub-tomogram averaging reconstructions to EMDB will become mandatory starting February 25, 2022.
Watch Workshops on Open-Source Tools for Chemistry
The Royal Society of Chemistry hosted two webinars on Protein Data Bank at 50: Accessing, Understanding, and Assessing PDB Data
Watch Presentations from the May PDB50 Celebration
The inaugural PDB50 symposium hosted by ASBMB hosted speakers from around the world who have made tremendous advances in structural biology and bioinformatics
New Chemical Sketch Tool
Build chemical drawings to search for small molecules in the PDB
Obituary for John Westbrook
John D. Westbrook Jr. (1957-2021) passed away on October 18, 2021. He was incredibly beloved and respected by his colleagues at Rutgers and throughout the world, known for his dry wit and endless enthusiasm for thinking about all aspects of data and data management.
See new feature archive
Resources for structure-facilitated design of mRNA vaccines for existing and emerging viral pathogens » 01/18/2022
PDB50 recap; 2021 Statistics; PDB Citation MeSH Network Explorer, and more; Education Corner on Inktober SciArt Celebrating PDB50 » 01/12/2022
Download our new calendar that highlights the method of choice for determining structures of large macromolecular complexes » 01/01/2022
Best wishes for a happy new year » 12/24/2021
New preprint available: Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces » 12/20/2021
Congratulations to wwPDB's Dr. Brian P. Hudson on processing more than 10,000 PDB structures » 12/17/2021
Molecule of the Month
Quarterly News (see archive)
PDB50 recap; 2021 Statistics; PDB Citation MeSH Network Explorer and more; Education Corner on Inktober SciArt Celebrating PDB50. Winter 2022 Issue