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 | 61,837 |
Mus musculus | 8,543 |
synthetic construct | 7,762 |
Escherichia coli | 7,088 |
Escherichia coli K-12 | 4,131 |
Rattus norvegicus | 3,748 |
Bos taurus | 3,570 |
Saccharomyces cerevisiae | 3,238 |
Severe acute respiratory syndrome coronavirus 2 | 3,001 |
Saccharomyces cerevisiae S288C | 2,506 |
Gallus gallus | 2,344 |
Human immunodeficiency virus 1 | 2,036 |
Arabidopsis thaliana | 1,950 |
Mycobacterium tuberculosis H37Rv | 1,560 |
Staphylococcus aureus | 1,479 |
Mycobacterium tuberculosis | 1,397 |
Thermus thermophilus HB8 | 1,321 |
Sus scrofa | 1,259 |
Bacillus subtilis | 1,232 |
Drosophila melanogaster | 1,220 |
Pseudomonas aeruginosa | 1,220 |
Pseudomonas aeruginosa PAO1 | 1,218 |
Oryctolagus cuniculus | 1,129 |
Tequatrovirus T4 | 1,081 |
Cryphonectria parasitica | 801 |
Thermotoga maritima | 725 |
Thermus thermophilus | 671 |
Geobacillus stearothermophilus | 655 |
Lama glama | 646 |
Bacillus subtilis subsp. subtilis str. 168 | 634 |
Klebsiella pneumoniae | 602 |
Salmonella enterica subsp. enterica serovar Typhimurium | 590 |
Pseudomonas putida | 572 |
Danio rerio | 563 |
Aequorea victoria | 524 |
Plasmodium falciparum | 510 |
Plasmodium falciparum 3D7 | 509 |
Mycolicibacterium smegmatis MC2 155 | 486 |
Xenopus laevis | 475 |
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | 454 |
Pyrococcus horikoshii OT3 | 452 |
Caenorhabditis elegans | 451 |
Thermotoga maritima MSB8 | 446 |
Equus caballus | 443 |
Vibrio cholerae | 346 |
Saccharolobus solfataricus | 338 |
Physeter catodon | 336 |
Pyrococcus furiosus | 335 |
Thermochaetoides thermophila DSM 1495 | 325 |
Acinetobacter baumannii | 319 |
Bacteroides thetaiotaomicron VPI-5482 | 311 |
Archaeoglobus fulgidus | 309 |
Hirudo medicinalis | 308 |
Aquifex aeolicus | 305 |
Influenza A virus | 302 |
Trypanosoma brucei | 302 |
Saccharolobus solfataricus P2 | 301 |
Streptococcus pneumoniae | 299 |
Escherichia coli O157:H7 | 297 |
Methanocaldococcus jannaschii | 296 |
unidentified | 291 |
Aquifex aeolicus VF5 | 282 |
Trypanosoma cruzi | 277 |
Chlamydomonas reinhardtii | 274 |
Haemophilus influenzae | 269 |
Bacillus anthracis | 263 |
Streptomyces avidinii | 263 |
Helicobacter pylori | 262 |
Streptococcus pneumoniae TIGR4 | 257 |
Escherichia coli BL21(DE3) | 247 |
Schizosaccharomyces pombe | 245 |
Schizosaccharomyces pombe 972h- | 243 |
Helicobacter pylori 26695 | 242 |
Parengyodontium album | 240 |
Severe acute respiratory syndrome-related coronavirus | 240 |
Thermus thermophilus HB27 | 240 |
Bacillus cereus | 236 |
Zea mays | 235 |
Trypanosoma brucei brucei | 234 |
Hepacivirus C | 232 |
Agrobacterium fabrum str. C58 | 231 |
Pyrococcus horikoshii | 228 |
Vicugna pacos | 228 |
Vibrio cholerae O1 biovar El Tor str. N16961 | 226 |
Clostridium botulinum | 222 |
Cereibacter sphaeroides | 220 |
Leishmania major | 219 |
Enterococcus faecalis | 218 |
Ovis aries | 215 |
Schistosoma mansoni | 215 |
Legionella pneumophila subsp. pneumophila str. Philadelphia 1 | 211 |
Priestia megaterium | 209 |
Streptomyces coelicolor A3(2) | 208 |
Toxoplasma gondii | 207 |
Bacillus thermoproteolyticus | 204 |
Listeria monocytogenes EGD-e | 203 |
Yersinia pestis | 203 |
Methanocaldococcus jannaschii DSM 2661 | 200 |
Streptococcus pyogenes | 200 |
Campylobacter jejuni | 198 |
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 | 111,768 |
Bacteria | 68,905 |
Riboviria | 12,598 |
other sequences | 7,828 |
Archaea | 5,804 |
Duplodnaviria | 2,934 |
Varidnaviria | 658 |
Monodnaviria | 572 |
unclassified sequences | 451 |
unclassified bacterial viruses | 61 |
Naldaviricetes | 56 |
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) (33,538)
- All beta proteins (29,541)
- Alpha and beta proteins (a+b) (30,481)
- All alpha proteins (19,120)
- Artifacts (19,300)
- 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) | 33,538 |
All beta proteins | 29,541 |
Alpha and beta proteins (a+b) | 30,481 |
All alpha proteins | 19,120 |
Artifacts | 19,300 |
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 |