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 | 69,258 |
Mus musculus | 9,395 |
synthetic construct | 9,282 |
Escherichia coli | 7,733 |
Escherichia coli K-12 | 4,424 |
Severe acute respiratory syndrome coronavirus 2 | 4,387 |
Rattus norvegicus | 4,038 |
Bos taurus | 3,786 |
Saccharomyces cerevisiae | 3,495 |
Saccharomyces cerevisiae S288C | 2,606 |
Gallus gallus | 2,545 |
Human immunodeficiency virus 1 | 2,258 |
Arabidopsis thaliana | 2,196 |
Mycobacterium tuberculosis H37Rv | 1,684 |
Staphylococcus aureus | 1,555 |
Mycobacterium tuberculosis | 1,489 |
Sus scrofa | 1,435 |
Pseudomonas aeruginosa | 1,423 |
Thermus thermophilus HB8 | 1,369 |
Pseudomonas aeruginosa PAO1 | 1,325 |
Drosophila melanogaster | 1,299 |
Bacillus subtilis | 1,294 |
Oryctolagus cuniculus | 1,252 |
Tequatrovirus T4 | 1,118 |
Lama glama | 827 |
Cryphonectria parasitica | 809 |
Thermotoga maritima | 740 |
Bacillus subtilis subsp. subtilis str. 168 | 709 |
Geobacillus stearothermophilus | 695 |
Klebsiella pneumoniae | 695 |
Thermus thermophilus | 678 |
Salmonella enterica subsp. enterica serovar Typhimurium | 630 |
Danio rerio | 602 |
Aequorea victoria | 584 |
Xenopus laevis | 582 |
Pseudomonas putida | 574 |
Plasmodium falciparum 3D7 | 544 |
Mycolicibacterium smegmatis MC2 155 | 543 |
Plasmodium falciparum | 541 |
Equus caballus | 512 |
Caenorhabditis elegans | 484 |
Thermotoga maritima MSB8 | 467 |
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | 461 |
Pyrococcus horikoshii OT3 | 458 |
Vibrio cholerae | 378 |
Influenza A virus | 365 |
Thermochaetoides thermophila DSM 1495 | 365 |
Acinetobacter baumannii | 358 |
Physeter catodon | 350 |
Saccharolobus solfataricus | 343 |
Pyrococcus furiosus | 340 |
Bacteroides thetaiotaomicron VPI-5482 | 339 |
Hirudo medicinalis | 332 |
Trypanosoma brucei | 319 |
Aquifex aeolicus | 318 |
Streptococcus pneumoniae | 314 |
Archaeoglobus fulgidus | 313 |
Saccharolobus solfataricus P2 | 309 |
Vicugna pacos | 309 |
Escherichia coli O157:H7 | 307 |
Methanocaldococcus jannaschii | 302 |
unidentified | 297 |
Aquifex aeolicus VF5 | 294 |
Chlamydomonas reinhardtii | 288 |
Trypanosoma cruzi | 287 |
Haemophilus influenzae | 281 |
Helicobacter pylori | 280 |
Schizosaccharomyces pombe 972h- | 280 |
Streptomyces avidinii | 278 |
Escherichia coli BL21(DE3) | 274 |
Bacillus anthracis | 270 |
Streptococcus pneumoniae TIGR4 | 266 |
Zika virus | 261 |
Schizosaccharomyces pombe | 259 |
Thermus thermophilus HB27 | 259 |
Schistosoma mansoni | 258 |
Helicobacter pylori 26695 | 257 |
Trypanosoma brucei brucei | 253 |
Zea mays | 253 |
Bacillus cereus | 251 |
Macaca mulatta | 249 |
Parengyodontium album | 247 |
Severe acute respiratory syndrome-related coronavirus | 247 |
Campylobacter jejuni | 238 |
Streptococcus pyogenes | 238 |
Agrobacterium fabrum str. C58 | 236 |
Clostridium botulinum | 235 |
Hepacivirus hominis | 233 |
Synechocystis sp. PCC 6803 | 232 |
Ovis aries | 230 |
Vibrio cholerae O1 biovar El Tor str. N16961 | 229 |
Pyrococcus horikoshii | 228 |
Oryza sativa Japonica Group | 227 |
Cereibacter sphaeroides | 226 |
Priestia megaterium | 226 |
Enterococcus faecalis | 223 |
Streptomyces coelicolor A3(2) | 221 |
Toxoplasma gondii | 221 |
Leishmania major | 220 |
Legionella pneumophila subsp. pneumophila str. Philadelphia 1 | 218 |
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 | 122,606 |
Bacteria | 74,428 |
Riboviria | 15,367 |
other sequences | 9,362 |
Archaea | 6,099 |
Duplodnaviria | 3,351 |
Eukaryota (eukaryotes) | 1,508 |
Varidnaviria | 826 |
Monodnaviria | 642 |
unclassified sequences | 527 |
Riboviria (RNA viruses and viroids) | 267 |
unclassified bacterial viruses | 70 |
Naldaviricetes | 64 |
Adnaviria | 34 |
Bicaudaviridae | 17 |
unclassified viruses | 16 |
Fuselloviridae | 12 |
environmental samples | 10 |
Ribozyviria | 8 |
Globuloviridae | 5 |
Polydnaviriformidae | 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-e 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) (33,523)
- All beta proteins (29,540)
- Alpha and beta proteins (a+b) (30,480)
- All alpha proteins (19,117)
- Artifacts (19,298)
- 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) | 33,523 |
All beta proteins | 29,540 |
Alpha and beta proteins (a+b) | 30,480 |
All alpha proteins | 19,117 |
Artifacts | 19,298 |
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 |