Protein Data Bank 3D Structural Biology Data

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/pdb-3d-structural-biology-data-dataset")

fs.listdir("s3://pdbsnapshots")

Description:

The "Protein Data Bank (PDB) archive" was established in 1971 as the first open-access digital data archive in biology. It is a collection of three-dimensional (3D) atomic-level structures of biological macromolecules (i.e., proteins, DNA, and RNA) and their complexes with one another and various small-molecule ligands (e.g., US FDA approved drugs, enzyme co-factors). For each PDB entry (unique identifier: 1abc or PDB_0000001abc) multiple data files contain information about the 3D atomic coordinates, sequences of biological macromolecules, information about any small molecules/ligands present in the entry, details about the structure-determination experiment, authors and publication information, experimental data, and the wwPDB validation report. Additional content stored in the archive includes documentation, summary reports, and software (among others). The PDB is a jointly-managed core archive of the Worldwide Protein Data Bank partnership [RCSB Protein Data Bank (RCSB PDB, rcsb.org); Protein Data Bank in Europe (PDBe, pdbe.org); Protein Data Bank Japan (PDBj, pdbj.org); Electron Microscopy Data Bank (EMDB, emdb-empiar.org); and Biological Magnetic Resonance Bank (BMRB, bmrb.io)]. RCSB PDB serves as the wwPDB-designated Archive Keeper for the Protein Data Bank. Additional wwPDB Core Archives are as follows: Electron Microscopy Data Bank (wwPDB-designated Archive Keeper: EMDB) Biological Magnetic Resonance Bank (wwPDB-designated Archive Keeper: BMRB)

Contact:

The "Protein Data Bank (PDB) archive" was established in 1971 as the first open-access digital data archive in biology. It is a collection of three-dimensional (3D) atomic-level structures of biological macromolecules (i.e., proteins, DNA, and RNA) and their complexes with one another and various small-molecule ligands (e.g., US FDA approved drugs, enzyme co-factors). For each PDB entry (unique identifier: 1abc or PDB_0000001abc) multiple data files contain information about the 3D atomic coordinates, sequences of biological macromolecules, information about any small molecules/ligands present in the entry, details about the structure-determination experiment, authors and publication information, experimental data, and the wwPDB validation report. Additional content stored in the archive includes documentation, summary reports, and software (among others). The PDB is a jointly-managed core archive of the Worldwide Protein Data Bank partnership [RCSB Protein Data Bank (RCSB PDB, rcsb.org); Protein Data Bank in Europe (PDBe, pdbe.org); Protein Data Bank Japan (PDBj, pdbj.org); Electron Microscopy Data Bank (EMDB, emdb-empiar.org); and Biological Magnetic Resonance Bank (BMRB, bmrb.io)]. RCSB PDB serves as the wwPDB-designated Archive Keeper for the Protein Data Bank. Additional wwPDB Core Archives are as follows: Electron Microscopy Data Bank (wwPDB-designated Archive Keeper: EMDB) Biological Magnetic Resonance Bank (wwPDB-designated Archive Keeper: BMRB)

Update Frequency:

New and updated data files are published weekly and released on Wednesdays 0:00 UTC.

Managed By:

wwpdb.org

Resources:

1. resource:

   • Description: Globally cached distribution of the dataset. Web frontend also available to browse the dataset and file directory.

   • Region: us-west-2

   • Type: CloudFront Distribution

   • Explore: Browse Dataset

2. resource:

   • Description: Historical snapshots of archival datasets from 2005 onwards. Snapshots are generated annually and at major milestone.

   • ARN: arn:aws:s3:::pdbsnapshots

   • Region: us-west-2

   • Type: S3 Bucket

   • Explore: Browse Bucket

Tags:

aws-pds, amino acid, archives, bioinformatics, biomolecular modeling, cell biology, chemical biology, COVID-19, electron microscopy, electron tomography, enzyme, life sciences, molecule, nuclear magnetic resonance, pharmaceutical, protein, protein template, SARS-CoV-2, structural biology, x-ray crystallography

Publication:

1. publication:

   • Title: Announcing the worldwide Protein Data Bank
   • URL: https://doi.org/10.1038/nsb1203-980
   • AuthorName: Berman, H., Henrick, K. & Nakamura, H.

2. publication:

   • Title: Protein Data Bank: the single global archive for 3D macromolecular structure data
   • URL: https://doi.org/10.1093/nar/gky949
   • AuthorName: wwPDB consortium