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.
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.
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
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- Membrane Protein
- MeSH (Medical Subject Headings)
- Molecular Function
- Protein Symmetry
- 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.
Drug-Target Complex: Atorvastatin bound to its target HMG-CoA reductase
Drug: Atorvastatin (Lipitor)
3D Structure Viewers
View PDB structures in 3D using Mol* from any entry's Structure Summary page.A 3D View (Mol*) User Guide is available.
Explore metabolic pathways maps that identify pathway components with PDB structures and homology models.
RCSB 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 RCSB Protein Feature View.
This feature is available in Structure Summary pages and Instance Sequence pages.
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.
Pairwise Structure Alignment
The standalone Mol* viewer application allows for calculating pairwise structure alignments.
Comparisons can be made for any protein in the PDB archive and for customized or local files not in the PDB.
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 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.Access the Mapping Tool
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 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
Searches and reports performed on this RCSB PDB website utilize data from the PDB archive. The PDB archive is maintained by the wwPDB at at FTP archive, ftp.wwpdb.org (data download details) and Versioned FTP, ftp-versioned.wwpdb.org (Versioning details).
- 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. Read More on FTP 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.
- PDB Structure Files
- Ligand Files
- Secondary Structure Files
- SIFTS Files
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
Cryo-EM strucutre of human acid-sensing ion channel 1a in complex with snake toxin Mambalgin1 at pH 8.0
Ligand binding domain of the P. putida receptor PcaY_PP in complex with quinate
Asymmetric model of CD4-bound B41 HIV-1 Env SOSIP in complex with small molecule GO52
PIKfyve/Fig4/Vac14 complex centered on Vac14 - map1
Isavuconazole bound complex of Acanthamoeba castellanii CYP51
Crystal structure of RXR alpha LBD in complexes with palmitic acid and GRIP-1 peptide
X-ray crystal structure of Vibrio alkaline phosphatase with the non-competitive inhibitor cyclohexylamine
Structure of OR51B2 bound FEM1C
NAD+-bound Sarm1 E642A in the self-inhibited state
NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)
Features & Highlights
Sequence Alignments in Search Results
For Sequence Similarity searches, display search results as "Polymer Entities" to view amino acid mismatches.
Build Customize Tabular Reports of PDB Data
After searching for a set of structures, create a table of information by selecting the columns of your choice. Tables can be saved in CSV or JSON formats.
Documentation for New and Improved APIs
Learn the concepts and syntax behind these new services. Legacy APIs will be discontinued November 2020
Search by Chemical Formula or Descriptor
Use Advanced Search>Chemical Search for small-molecule searching by formulae or descriptors (SMILES, InChI)
Updated Validation Reports for Released PDB Structures
Reports now include recalculated percentiles, 2D diagrams highlighting ligand quality, map and model fit for EM entries, and calculated map coefficients used for X-ray data validation.
Announcement: Legacy MyPDB Will Be Discontinued October 2020
Users should migrate to the new and improved version that uses third-party authentication
Explore Sequence-Structure Relationships
Protein Feature View maps PDB structures and corresponding UniProtKB sequences and other annotations in an updated interface
Real Time Structural Search of the PDB
A new paper describes a novel method that detects similarity between protein shapes and that works equally fast for any size of proteins or assemblies
Integrating PDB Data with NIH Common Fund Data Resources
Access information from PHAROS (important drug target protein families: GPCRs, ion channels and kinases), GTEx (tissue-specific gene expression and regulation) and IMPC (data related to mouse phenotypes).
See new feature archive
Today is the anniversary of the 1971 announcement of the PDB. wwPDB is celebrating by looking ahead to golden anniversary symposia and events planned for 2021 » 10/20/2020
Celebrate Geis' birthday (October 18, 1908) with a tour of the Tour the Geis Digital Archive developed in collaboration with HHMI. » 10/18/2020
RCSB PDB will be part of Strengthening virtual Chemistry and Biology Instruction Through 3D Modeling on Saturday October 24 » 10/16/2020
New publications; updated validation reports; exploring sequence-structure relationships; from Boot Camp to Poster Prize; and more. The Education Corner describes Using PDB Structures to Visualize Science by medical illustrator Veronica Falconieri. » 10/13/2020
New in Resources to Fight the COVID-19 Pandemic: Preventing too much of a good thing during SARS-CoV-2 infection » 10/12/2020
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This image of RNA Polymerase was selected as a national finalist in the 2019 Wiki Science Competition in the United States. The jury selected 36 finalists across six categories from 1,144 submissions. » 10/06/2020
Next week, Nobel Prizes will be announced that highlight achievements in physics, chemistry, physiology or medicine, literature, and for peace. » 09/29/2020
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Congratulations to Aya Narunsky for How proteins evolved to recognize an ancient nucleotide » 09/20/2020
Molecule of the Month
Quarterly News (see archive)
New publications; updated validation reports; exploring sequence-structure relationships; from Boot Camp to Poster Prize; and more. Fall 2020 Issue