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 | 62,561 |
Mus musculus | 8,665 |
synthetic construct | 7,918 |
Escherichia coli | 7,186 |
Escherichia coli K-12 | 4,187 |
Rattus norvegicus | 3,773 |
Bos taurus | 3,588 |
Saccharomyces cerevisiae | 3,256 |
Severe acute respiratory syndrome coronavirus 2 | 3,098 |
Saccharomyces cerevisiae S288C | 2,516 |
Gallus gallus | 2,385 |
Human immunodeficiency virus 1 | 2,069 |
Arabidopsis thaliana | 1,960 |
Mycobacterium tuberculosis H37Rv | 1,575 |
Staphylococcus aureus | 1,485 |
Mycobacterium tuberculosis | 1,405 |
Thermus thermophilus HB8 | 1,333 |
Sus scrofa | 1,275 |
Pseudomonas aeruginosa PAO1 | 1,235 |
Bacillus subtilis | 1,234 |
Pseudomonas aeruginosa | 1,228 |
Drosophila melanogaster | 1,226 |
Oryctolagus cuniculus | 1,159 |
Tequatrovirus T4 | 1,085 |
Cryphonectria parasitica | 809 |
Thermotoga maritima | 724 |
Thermus thermophilus | 672 |
Geobacillus stearothermophilus | 657 |
Lama glama | 657 |
Bacillus subtilis subsp. subtilis str. 168 | 647 |
Klebsiella pneumoniae | 611 |
Salmonella enterica subsp. enterica serovar Typhimurium | 595 |
Danio rerio | 573 |
Pseudomonas putida | 572 |
Aequorea victoria | 529 |
Plasmodium falciparum | 515 |
Plasmodium falciparum 3D7 | 514 |
Xenopus laevis | 496 |
Mycolicibacterium smegmatis MC2 155 | 489 |
Caenorhabditis elegans | 455 |
Thermotoga maritima MSB8 | 455 |
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | 454 |
Equus caballus | 453 |
Pyrococcus horikoshii OT3 | 452 |
Vibrio cholerae | 348 |
Saccharolobus solfataricus | 341 |
Physeter catodon | 338 |
Thermochaetoides thermophila DSM 1495 | 336 |
Pyrococcus furiosus | 335 |
Acinetobacter baumannii | 329 |
Bacteroides thetaiotaomicron VPI-5482 | 316 |
Aquifex aeolicus | 309 |
Archaeoglobus fulgidus | 309 |
Hirudo medicinalis | 308 |
Influenza A virus | 306 |
Trypanosoma brucei | 302 |
Saccharolobus solfataricus P2 | 301 |
Streptococcus pneumoniae | 299 |
Escherichia coli O157:H7 | 298 |
Methanocaldococcus jannaschii | 296 |
unidentified | 291 |
Aquifex aeolicus VF5 | 282 |
Trypanosoma cruzi | 277 |
Chlamydomonas reinhardtii | 276 |
Haemophilus influenzae | 271 |
Bacillus anthracis | 266 |
Helicobacter pylori | 266 |
Streptomyces avidinii | 263 |
Streptococcus pneumoniae TIGR4 | 257 |
Escherichia coli BL21(DE3) | 250 |
Helicobacter pylori 26695 | 247 |
Schizosaccharomyces pombe | 247 |
Schizosaccharomyces pombe 972h- | 244 |
Parengyodontium album | 241 |
Severe acute respiratory syndrome-related coronavirus | 240 |
Thermus thermophilus HB27 | 240 |
Zea mays | 239 |
Bacillus cereus | 237 |
Trypanosoma brucei brucei | 234 |
Vicugna pacos | 233 |
Hepacivirus C | 232 |
Agrobacterium fabrum str. C58 | 231 |
Pyrococcus horikoshii | 228 |
Vibrio cholerae O1 biovar El Tor str. N16961 | 228 |
Clostridium botulinum | 225 |
Cereibacter sphaeroides | 220 |
Leishmania major | 219 |
Enterococcus faecalis | 218 |
Campylobacter jejuni | 215 |
Ovis aries | 215 |
Schistosoma mansoni | 215 |
Toxoplasma gondii | 214 |
Legionella pneumophila subsp. pneumophila str. Philadelphia 1 | 212 |
Streptomyces coelicolor A3(2) | 210 |
Priestia megaterium | 209 |
Macaca mulatta | 206 |
Bacillus thermoproteolyticus | 204 |
Listeria monocytogenes EGD-e | 203 |
Staphylococcus aureus subsp. aureus Mu50 | 203 |
Yersinia pestis | 203 |
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 | 112,929 |
Bacteria | 69,593 |
Riboviria | 12,824 |
other sequences | 7,984 |
Archaea | 5,829 |
Duplodnaviria | 2,953 |
Varidnaviria | 675 |
Monodnaviria | 578 |
unclassified sequences | 472 |
unclassified bacterial viruses | 62 |
Naldaviricetes | 57 |
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) (33,537)
- 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) | 33,537 |
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 |