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 | 57738 |
Mus musculus | 8032 |
synthetic construct | 6774 |
Escherichia coli | 6748 |
Escherichia coli K-12 | 3973 |
Rattus norvegicus | 3610 |
Bos taurus | 3430 |
Saccharomyces cerevisiae | 3098 |
Severe acute respiratory syndrome coronavirus 2 | 2251 |
Gallus gallus | 2223 |
Saccharomyces cerevisiae S288C | 2190 |
Human immunodeficiency virus 1 | 1946 |
Arabidopsis thaliana | 1819 |
Mycobacterium tuberculosis H37Rv | 1477 |
Staphylococcus aureus | 1433 |
Mycobacterium tuberculosis | 1355 |
Thermus thermophilus HB8 | 1277 |
Bacillus subtilis | 1214 |
Pseudomonas aeruginosa | 1186 |
Drosophila melanogaster | 1179 |
Sus scrofa | 1163 |
Pseudomonas aeruginosa PAO1 | 1137 |
Oryctolagus cuniculus | 1076 |
Escherichia virus T4 | 1044 |
Cryphonectria parasitica | 754 |
Thermotoga maritima | 713 |
Thermus thermophilus | 666 |
Geobacillus stearothermophilus | 640 |
Bacillus subtilis subsp. subtilis str. 168 | 612 |
Salmonella enterica subsp. enterica serovar Typhimurium | 568 |
Pseudomonas putida | 558 |
Klebsiella pneumoniae | 557 |
Lama glama | 556 |
Danio rerio | 515 |
Aequorea victoria | 500 |
Plasmodium falciparum 3D7 | 473 |
Mycolicibacterium smegmatis MC2 155 | 452 |
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | 452 |
Plasmodium falciparum | 445 |
Pyrococcus horikoshii OT3 | 445 |
Xenopus laevis | 440 |
Thermotoga maritima MSB8 | 432 |
Caenorhabditis elegans | 427 |
Equus caballus | 419 |
Saccharolobus solfataricus | 335 |
Pyrococcus furiosus | 329 |
Physeter catodon | 328 |
Vibrio cholerae | 323 |
Bacteroides thetaiotaomicron VPI-5482 | 308 |
Aquifex aeolicus | 304 |
Hirudo medicinalis | 303 |
Archaeoglobus fulgidus | 302 |
Trypanosoma brucei | 295 |
Streptococcus pneumoniae | 293 |
Escherichia coli O157:H7 | 292 |
Methanocaldococcus jannaschii | 291 |
Saccharolobus solfataricus P2 | 289 |
Acinetobacter baumannii | 287 |
Influenza A virus | 285 |
Chaetomium thermophilum var. thermophilum DSM 1495 | 274 |
Trypanosoma cruzi | 274 |
Aquifex aeolicus VF5 | 272 |
Haemophilus influenzae | 266 |
unidentified | 263 |
Bacillus anthracis | 261 |
Streptomyces avidinii | 260 |
Chlamydomonas reinhardtii | 257 |
Helicobacter pylori | 256 |
Streptococcus pneumoniae TIGR4 | 255 |
Helicobacter pylori 26695 | 240 |
Thermus thermophilus HB27 | 239 |
Bacillus cereus | 236 |
Schizosaccharomyces pombe 972h- | 235 |
Zea mays | 233 |
Agrobacterium fabrum str. C58 | 227 |
Hepacivirus C | 227 |
Severe acute respiratory syndrome-related coronavirus | 225 |
Vibrio cholerae O1 biovar El Tor str. N16961 | 224 |
Escherichia coli BL21(DE3) | 222 |
Schizosaccharomyces pombe | 222 |
Pyrococcus horikoshii | 220 |
Leishmania major | 216 |
Clostridium botulinum | 214 |
Trypanosoma brucei brucei | 211 |
Enterococcus faecalis | 209 |
Parengyodontium album | 209 |
Legionella pneumophila subsp. pneumophila str. Philadelphia 1 | 208 |
Ovis aries | 208 |
Schistosoma mansoni | 207 |
Bacillus thermoproteolyticus | 204 |
Cereibacter sphaeroides | 201 |
Methanocaldococcus jannaschii DSM 2661 | 200 |
Streptomyces coelicolor A3(2) | 197 |
Priestia megaterium | 195 |
Yersinia pestis | 195 |
Dictyostelium discoideum | 194 |
Campylobacter jejuni | 191 |
Staphylococcus aureus subsp. aureus Mu50 | 190 |
Pyrococcus furiosus DSM 3638 | 189 |
uncultured bacterium | 188 |
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 | 105015 |
Bacteria | 65967 |
Riboviria | 11261 |
other sequences | 6839 |
Archaea | 5664 |
Duplodnaviria | 2739 |
Varidnaviria | 632 |
Monodnaviria | 527 |
unclassified sequences | 389 |
Naldaviricetes | 49 |
unclassified bacterial viruses | 48 |
Adnaviria | 34 |
Bicaudaviridae | 17 |
Fuselloviridae | 11 |
unclassified viruses | 11 |
Ribozyviria | 7 |
environmental samples | 7 |
Globuloviridae | 5 |
Polydnaviridae | 2 |
Clavaviridae | 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) (33555)
- All beta proteins (29547)
- Alpha and beta proteins (a+b) (30492)
- All alpha proteins (19126)
- Artifacts (19311)
- Multi-domain proteins (alpha and beta) (3462)
- Membrane and cell surface proteins and peptides (2051)
- Small proteins (3765)
- Coiled coil proteins (981)
- Others (1124)
SCOP Classification | Number of Entries |
---|---|
Alpha and beta proteins (a/b) | 33555 |
All beta proteins | 29547 |
Alpha and beta proteins (a+b) | 30492 |
All alpha proteins | 19126 |
Artifacts | 19311 |
Multi-domain proteins (alpha and beta) | 3462 |
Membrane and cell surface proteins and peptides | 2051 |
Small proteins | 3765 |
Coiled coil proteins | 981 |
Low resolution protein structures | 202 |
Peptides | 754 |
Designed proteins | 168 |