By Scientific Name of Source Organism
The scientific name associated with this taxonomy code aggregated by the NCBI Taxonomy Database. This name corresponds to the taxonomy identifier assigned by the PDB depositor, and includes natural, engineered, and synthetic source organisms.
Scientific Name of Source Organism | Number of Entries |
---|---|
Homo sapiens | 64,698 |
Mus musculus | 8,861 |
synthetic construct | 8,351 |
Escherichia coli | 7,377 |
Escherichia coli K-12 | 4,301 |
Rattus norvegicus | 3,842 |
Bos taurus | 3,635 |
Saccharomyces cerevisiae | 3,338 |
Severe acute respiratory syndrome coronavirus 2 | 3,294 |
Saccharomyces cerevisiae S288C | 2,555 |
Gallus gallus | 2,424 |
Human immunodeficiency virus 1 | 2,139 |
Arabidopsis thaliana | 2,018 |
Mycobacterium tuberculosis H37Rv | 1,622 |
Staphylococcus aureus | 1,518 |
Mycobacterium tuberculosis | 1,447 |
Thermus thermophilus HB8 | 1,346 |
Sus scrofa | 1,305 |
Pseudomonas aeruginosa | 1,277 |
Pseudomonas aeruginosa PAO1 | 1,265 |
Drosophila melanogaster | 1,240 |
Bacillus subtilis | 1,239 |
Oryctolagus cuniculus | 1,182 |
Tequatrovirus T4 | 1,097 |
Cryphonectria parasitica | 809 |
Thermotoga maritima | 728 |
Lama glama | 712 |
Thermus thermophilus | 676 |
Geobacillus stearothermophilus | 665 |
Bacillus subtilis subsp. subtilis str. 168 | 659 |
Klebsiella pneumoniae | 628 |
Salmonella enterica subsp. enterica serovar Typhimurium | 605 |
Danio rerio | 581 |
Pseudomonas putida | 573 |
Aequorea victoria | 548 |
Plasmodium falciparum | 531 |
Xenopus laevis | 529 |
Plasmodium falciparum 3D7 | 526 |
Mycolicibacterium smegmatis MC2 155 | 513 |
Caenorhabditis elegans | 463 |
Equus caballus | 462 |
Thermotoga maritima MSB8 | 459 |
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | 454 |
Pyrococcus horikoshii OT3 | 452 |
Vibrio cholerae | 369 |
Acinetobacter baumannii | 346 |
Saccharolobus solfataricus | 343 |
Physeter catodon | 340 |
Thermochaetoides thermophila DSM 1495 | 338 |
Pyrococcus furiosus | 335 |
Bacteroides thetaiotaomicron VPI-5482 | 332 |
Influenza A virus | 319 |
Aquifex aeolicus | 311 |
Archaeoglobus fulgidus | 309 |
Hirudo medicinalis | 308 |
Trypanosoma brucei | 308 |
Streptococcus pneumoniae | 302 |
Saccharolobus solfataricus P2 | 301 |
Escherichia coli O157:H7 | 300 |
Methanocaldococcus jannaschii | 298 |
unidentified | 295 |
Trypanosoma cruzi | 287 |
Aquifex aeolicus VF5 | 286 |
Chlamydomonas reinhardtii | 280 |
Haemophilus influenzae | 275 |
Streptomyces avidinii | 268 |
Bacillus anthracis | 267 |
Helicobacter pylori | 264 |
Streptococcus pneumoniae TIGR4 | 257 |
Thermus thermophilus HB27 | 256 |
Escherichia coli BL21(DE3) | 254 |
Schizosaccharomyces pombe | 248 |
Helicobacter pylori 26695 | 247 |
Parengyodontium album | 247 |
Vicugna pacos | 247 |
Bacillus cereus | 244 |
Schizosaccharomyces pombe 972h- | 243 |
Trypanosoma brucei brucei | 242 |
Severe acute respiratory syndrome-related coronavirus | 241 |
Zea mays | 240 |
Hepacivirus hominis | 232 |
Agrobacterium fabrum str. C58 | 231 |
Pyrococcus horikoshii | 228 |
Vibrio cholerae O1 biovar El Tor str. N16961 | 227 |
Clostridium botulinum | 225 |
Campylobacter jejuni | 223 |
Enterococcus faecalis | 221 |
Cereibacter sphaeroides | 220 |
Macaca mulatta | 220 |
Leishmania major | 219 |
Schistosoma mansoni | 219 |
Toxoplasma gondii | 217 |
Ovis aries | 216 |
Priestia megaterium | 216 |
Streptomyces coelicolor A3(2) | 216 |
Legionella pneumophila subsp. pneumophila str. Philadelphia 1 | 215 |
Methanocaldococcus jannaschii DSM 2661 | 208 |
Synechocystis sp. PCC 6803 | 207 |
uncultured bacterium | 207 |
Listeria monocytogenes EGD-e | 206 |
By Taxonomy
A parent scientific name in the NCBI taxonomy hierarchy of the source organism assigned by the PDB depositor. For cellular organism this corresponds to a superkingdom (e.g., Archaea, Bacteria, Eukaryota). For viruses this corresponds to a clade (e.g. Adnaviria, Bicaudaviridae, Clavaviridae). For other and unclassified entries this corresponds to the first level of any taxonomic rank below the root level.
Taxonomy | Number of Entries |
---|---|
Eukaryota | 116,072 |
Bacteria | 71,212 |
Riboviria | 13,347 |
other sequences | 8,423 |
Archaea | 5,887 |
Duplodnaviria | 3,038 |
Varidnaviria | 714 |
Monodnaviria | 600 |
unclassified sequences | 492 |
unclassified bacterial viruses | 64 |
Naldaviricetes | 60 |
Adnaviria | 34 |
Bicaudaviridae | 17 |
unclassified viruses | 13 |
Fuselloviridae | 12 |
environmental samples | 10 |
Ribozyviria | 7 |
Globuloviridae | 5 |
Polydnaviriformidae | 2 |
Clavaviridae | 1 |
Finnlakeviridae | 1 |
Portogloboviridae | 1 |
By Polymer Entity Type
PDB structures may contain multiple entities of different macromolecular types.
By Refinement Resolution (Å)
Distribution by structure resolution (Å). Data shown include structures solved by X-ray crystallography or electron microscopy.
By Release Date
The year a structure entry was released in the PDB archive.
By Enzyme Classification Name
Enzyme Classification is based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB). EC (Enzyme Commission) numbers are assigned to PDB structures using UniProtKB/GenBank/KEGG/author-specified mapping.
By Symmetry Type
Protein symmetry is calculated for all protein complexes in the PDB, and updated weekly.
By SCOP Classification
The SCOP database aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.
- Alpha and beta proteins (a/b) (33,535)
- All beta proteins (29,541)
- Alpha and beta proteins (a+b) (30,480)
- All alpha proteins (19,119)
- Artifacts (19,299)
- Multi-domain proteins (alpha and beta) (3,462)
- Membrane and cell surface proteins and peptides (2,050)
- Small proteins (3,765)
- Coiled coil proteins (981)
- Others (1,124)
SCOP Classification | Number of Entries |
---|---|
Alpha and beta proteins (a/b) | 33,535 |
All beta proteins | 29,541 |
Alpha and beta proteins (a+b) | 30,480 |
All alpha proteins | 19,119 |
Artifacts | 19,299 |
Multi-domain proteins (alpha and beta) | 3,462 |
Membrane and cell surface proteins and peptides | 2,050 |
Small proteins | 3,765 |
Coiled coil proteins | 981 |
Low resolution protein structures | 202 |
Peptides | 754 |
Designed proteins | 168 |