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.
October Molecule of the Month
Crystal Structure Analysis of cp2 bound BCLxl
Structure of mouse Myomaker bound to Fab18G7 in detergent
rat TRPV2 in nanodiscs in the presence of weak acid at pH 5
XptA2 wild type
Cryo-EM structure of Mycobacterium tuberculosis LpqY-SugABC in complex with trehalose
Stacks of nucleocapsid rings of the N1-370 mutant of the human Respiratory Syncytial Virus
Structure of CC-Tri with Aib@b,c: CC-Tri-(UbUc)4
SARS-CoV-2 Main Protease (Mpro) H163A Mutant in Complex with GC376
The crystal structure of SARS-CoV-2 main protease in complex with 14a
Features & Highlights
ASBMB Members: Register Now for Virtual Event
Learn about Teaching enzymology with the Protein Data Bank: from pandemic to Paxlovid on October 19.
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
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Move the slider to use RCSB PDB tools with >1 million CSMs from AlphaFold and ModelArchive
See new feature archive
- Visit PDB-101 to explore connections between Nobel Prizes and more than 50 years of open access to the PDB archive.» 10/01/2023
- Limited spaces available for the Science Communication in Biology and Medicine Virtual Boot Camp: January 8-12, 2024. Applications due October 31, 2023.» 09/25/2023
- 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
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