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September Molecule of the Month
W-formate dehydrogenase C872A from Desulfovibrio vulgaris - with Formamide
Subsection of a helical nucleocapsid of the Respiratory Syncytial Virus
Outward-facing SLC15A4 dimer
MTH1 in complex with TH013071
Cryo-EM structure of the ABCG25
Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome
The nucleoprotein complex of Rep protein with iteron containing dsDNA and DUE ssDNA
Carbonic Anhydrase II in complex with the diaryl urea molecule J2
ATM(Q2971A) dimeric C-terminal region in complex with Mg AMP-PNP
Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (AMP-PNP bound)
Features & Highlights
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Learn about Teaching enzymology with the Protein Data Bank: from pandemic to Paxlovid on October 19.
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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
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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.
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See new feature archive
- 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
- Shiga Toxin 2 in Complex with Ribosomal P-stalk» 08/01/2023
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