A Structural View of Biology
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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.
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- 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
In situ structure of capping enzyme lambda2, penetration protein mu1 of mammalian reovirus capsid asymmetric unit.
XG005-bound SARS-CoV-2 S
SARS-CoV-2 nucleocapsid protein C-terminal domain (dodecamer)
Pectobacterium phage ZF40 apo-aca2 complexed with 26bp DNA substrate
Cryo-EM structure of VEEV VLP
DNA gyrase complexed with uncleaved DNA and Compound 7 to 2.6A resolution
444 in complex with tubulin
Cryo-EM structure of VEEV VLP at the 2-fold axes
Cyanophage Pam1 portal-adaptor complex
Crystal structure of the human METTL3-METTL14 complex with compound UOZ091
Features & Highlights
New PDB Citation MeSH Network Explorer
Find connections between articles describing PDB structures with this new browser
PDBx/mmCIF data files to include PI information
PI name, email, and ORCiD ID will be publicly available in PDBx/mmCIF data files starting September 24, 2021
Pairwise Structure Alignment
Comparisons can be made for any protein in the PDB archive and/or uploaded data files.
Improved Access to Chemical Component Definitions and Archive Inventories
Individual Chemical Component Dictionary entries and new archive inventory lists are now available
Explore Ligand Quality
New graphics summarize quality assessments
Small Molecule Search Results Options
For any search, retrieve small molecule information about associated chemical components and peptide-like antibiotic and inhibitor molecules
PDB adopts a standard Creative Commons open source license
PDB data can be copied, modified, and distributed, even for commercial purposes, all without asking permission
Search by Funding
Use Advanced Search to find structures by Funding Agency or Country
See new feature archive
Many thanks to the data depositors and users who have made the past 50 years possible » 10/21/2021
Protein Data Bank Marks 50 Years Helping to Unlock Mysteries of Human Disease » 10/20/2021
Today marks the 50th anniversary of the 1971 announcement of the PDB. Consider supporting 50 years of PDB's spirit of openness, cooperation, and education with a donation to the wwPDB Foundation. » 10/19/2021
These cards celebrate PDB50 and the structural biologists who have determined and deposited their many biomolecular structures » 10/19/2021
Celebrate Geis' birthday (October 18, 1908) with a tour of the Geis Digital Archive at PDB-101 » 10/18/2021
Biocurator Gregg Crichlow went inside Nanome to explore groundbreaking PDB structures for structure-based drug design » 10/15/2021
Access milestone PDB structures published in the Journal of Biological Chemistry » 10/14/2021
Helen Berman, Director Emerita of the RCSB PDB and PDB co-founder gives an overview of 50 years of community in a special feature in Nature Structural & Molecular Biology » 10/13/2021
Congratulations to wwPDB's Dr. Sutapa Ghosh and Dr. Monica Sekharan on processing more than 10,000 PDB structures » 10/12/2021
A new video looks at the history and the milestones that shaped the PDB » 10/11/2021
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Quarterly News (see archive)
PDB50; Opioids and Pain Signaling Video; Explore Ligand Quality; User Survey; and more; Education Corner on The SARS-CoV-2 Virion: Magnifying the Miniscule with Models of Digital, Plastic, and Paper. Fall 2021 Issue