RCSB Protein Data Bank (RCSB PDB) enables breakthroughs in science and education by providing access and tools for exploration, visualization, and analysis of:
Experimentally-determined 3D structures from the Protein Data Bank (PDB) archive
Computed Structure Models (CSM) from AlphaFold DB and ModelArchive
These data can be explored in context of external annotations providing a structural view of biology.
September Molecule of the Month
T95R mutant IRF4 DNA-binding domain bound to an DNA containing GACA motif
Cryo-EM structure of IOC3-N2 nucleosome
Tau - CTE-MIA10 (tau intermediate amyloid)
Crystal structure of the human dihydroorotase domain in complex with malic acid
Structure of RutB
Cryo-EM structure of NADH bound SLA dehydrogenase RlGabD from Rhizobium leguminosarum bv. trifolii SRD1565
Crystal structure of Danio reroof histone deacetylase 6 catalytic domain 2 complexed with (R)-Lipoic Acid
Crystal structure of HORMA domain-containing protein 1 (HORMAD1) from Homo sapiens
Cryo-EM structure of hZnT7-Fab complex in zinc-unbound state, determined in outward-facing conformation
Structure of R2 with 3'UTR and DNA in unwinding state
Features & Highlights
Register Now for October Virtual Crash Courses on RCSB PDB APIs
Learn about Leveraging RCSB PDB APIs for Bioinformatics Analyses and Machine Learning. Part 1 will introduce the Data and Search APIs. Part 2 will offer hands-on exercises.
Coming Soon: PDB Entries with Novel Ligands Distributed Only in PDBx/mmCIF and PDBML File Formats
PDB will run out of 3-character CCD IDs before the end of 2023. Afterwards, PDB entries with novel ligands will not be distributed in the legacy PDB file format.
Turning Global Data into Global Knowledge
RCSB PDB is highlighted in EdgeDiscovery, a publication that highlights research and research computing initiatives in New Jersey and beyond
Updated Annotation and Standardization of Peptide Residues
In October 2023, wwPDB will roll out updated CCD data files with additional annotation and standardized atom naming of peptide residues.
PDB NextGen Archive Now Provides Intra-molecular Connectivity
With this release, intra-molecular connectivity for each residue present in an entry has been provided to help users transitioning from legacy PDB format to PDBx/mmCIF
DNS name changes for PDB archive downloads from RCSB PDB starting September 2023
Programmatic users (ftp, rsync or https) should update scripts as soon as possible.
Explore PDB Data Distributions
Many statistics are available, including PDB holdings by experimental method and molecular type, along with numbers for structures with experimental and small molecule data
Toggle to "Opt-in" to Access Computed Structure Models Alongside PDB Data
Move the slider to use RCSB PDB tools with >1 million CSMs from AlphaFold and ModelArchive
Guide to Understanding PDB Data: Intro to APIs
PDB-101's Guide helps non-experts navigate through the PDB. A new chapter introduces the APIs that query and deliver PDB data at RCSB.org.
See new feature archive
- Congratulations to Alexander Paredes for Biophysical characterization of the Pseudomonas aeruginosa BqsR/BqsS two-component system» 09/19/2023
- Programmatic users (ftp, rsync or https) should update scripts» 09/15/2023
- Congratulations to Nele Quast for A Structure-Focused Analysis of Antigens Presented by the Class 1 Major Histocompatibility Complex» 09/12/2023
- Use PDB-101 resources, training materials, and curricula to explore biology from AAA+ Proteases to Zika Virus» 09/05/2023
- Learn how the Schrödinger Education team describes Empowering Educators with Research-Grade Computational Tools.» 08/29/2023
- All members of the American Crystallographic Association are invited to submit videos to be eligible for a $500 (USD). Deadline is October 31.» 08/23/2023
- Join us for presentations and more at the 26th Congress of the International Union of Crystallography (August 22-29).» 08/16/2023
- Bragg Your Pattern has something for everyone: school-aged children and their teachers/parents; IUCr attendees; and all structural biology enthusiasts» 08/08/2023
- Shiga Toxin 2 in Complex with Ribosomal P-stalk» 08/01/2023
- In this issue: Explore Bioenergy; Upload Structure Files to Search; Preparing PDB Depositions; more. In the Education Corner, learn about Empowering Educators with Research-Grade Computational Tools» 07/18/2023
Molecule of the Month
Quarterly News (see archive)
In this issue: Explore Bioenergy; Upload Structure Files to Search; Preparing PDB Depositions; and more. In the Education Corner, learn about Empowering Educators with Research-Grade Computational Tools