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 | 75,326 |
synthetic construct | 10,619 |
Mus musculus | 10,176 |
Escherichia coli | 8,286 |
Severe acute respiratory syndrome coronavirus 2 | 5,156 |
Escherichia coli K-12 | 4,617 |
Rattus norvegicus | 4,475 |
Bos taurus | 3,998 |
Saccharomyces cerevisiae | 3,752 |
Gallus gallus | 2,686 |
Saccharomyces cerevisiae S288C | 2,686 |
Arabidopsis thaliana | 2,418 |
Human immunodeficiency virus 1 | 2,379 |
Mycobacterium tuberculosis H37Rv | 1,755 |
Staphylococcus aureus | 1,648 |
Mycobacterium tuberculosis | 1,565 |
Pseudomonas aeruginosa | 1,547 |
Sus scrofa | 1,508 |
Thermus thermophilus HB8 | 1,418 |
Bacillus subtilis | 1,373 |
Drosophila melanogaster | 1,366 |
Oryctolagus cuniculus | 1,364 |
Pseudomonas aeruginosa PAO1 | 1,361 |
Tequatrovirus T4 | 1,167 |
Lama glama | 1,019 |
Cryphonectria parasitica | 855 |
Thermotoga maritima | 775 |
Klebsiella pneumoniae | 762 |
Bacillus subtilis subsp. subtilis str. 168 | 731 |
Geobacillus stearothermophilus | 707 |
Xenopus laevis | 682 |
Thermus thermophilus | 681 |
Aequorea victoria | 655 |
Salmonella enterica subsp. enterica serovar Typhimurium | 646 |
Danio rerio | 645 |
Mycolicibacterium smegmatis MC2 155 | 622 |
Plasmodium falciparum 3D7 | 592 |
Pseudomonas putida | 584 |
Plasmodium falciparum | 583 |
Equus caballus | 527 |
Caenorhabditis elegans | 515 |
Coxsackievirus A16 | 498 |
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | 489 |
Thermotoga maritima MSB8 | 478 |
Pyrococcus horikoshii OT3 | 474 |
Influenza A virus | 449 |
Vibrio cholerae | 406 |
Acinetobacter baumannii | 402 |
Vicugna pacos | 392 |
Thermochaetoides thermophila DSM 1495 | 376 |
Zika virus | 360 |
Bacteroides thetaiotaomicron VPI-5482 | 357 |
Physeter macrocephalus | 356 |
Chlamydomonas reinhardtii | 353 |
Saccharolobus solfataricus | 348 |
Pyrococcus furiosus | 347 |
Aquifex aeolicus VF5 | 338 |
Streptococcus pneumoniae | 337 |
Hirudo medicinalis | 333 |
Aquifex aeolicus | 324 |
Saccharolobus solfataricus P2 | 322 |
Trypanosoma brucei | 322 |
Methanocaldococcus jannaschii | 316 |
unidentified | 316 |
Archaeoglobus fulgidus | 314 |
Escherichia coli O157:H7 | 314 |
Streptomyces avidinii | 302 |
Macaca mulatta | 297 |
Trypanosoma cruzi | 297 |
Escherichia coli BL21(DE3) | 294 |
Helicobacter pylori | 292 |
Schizosaccharomyces pombe 972h- | 286 |
Haemophilus influenzae | 281 |
Bacillus anthracis | 275 |
Zea mays | 273 |
Thermus thermophilus HB27 | 271 |
Helicobacter pylori 26695 | 270 |
Schizosaccharomyces pombe | 269 |
Streptococcus pneumoniae TIGR4 | 269 |
Trypanosoma brucei brucei | 266 |
Schistosoma mansoni | 258 |
Parengyodontium album | 256 |
Streptococcus pyogenes | 256 |
Bacillus cereus | 255 |
Synechocystis sp. PCC 6803 | 254 |
Clostridium botulinum | 251 |
Severe acute respiratory syndrome-related coronavirus | 251 |
Agrobacterium fabrum str. C58 | 250 |
Campylobacter jejuni | 243 |
Ovis aries | 240 |
Hepacivirus hominis | 238 |
Oryza sativa Japonica Group | 238 |
Legionella pneumophila | 237 |
Pyrococcus horikoshii | 235 |
Vibrio cholerae O1 biovar El Tor str. N16961 | 234 |
uncultured bacterium | 234 |
Listeria monocytogenes EGD-e | 232 |
Priestia megaterium | 232 |
Cereibacter sphaeroides | 231 |
Toxoplasma gondii | 231 |
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 | 132,128 |
Bacteria | 79,032 |
Riboviria | 17,625 |
other sequences | 10,709 |
Archaea | 6,333 |
Duplodnaviria | 3,697 |
Eukaryota (eukaryotes) | 1,631 |
Varidnaviria | 960 |
Monodnaviria | 731 |
unclassified sequences | 625 |
Riboviria (RNA viruses and viroids) | 275 |
Viruses incertae sedis | 116 |
unclassified bacterial viruses | 82 |
Adnaviria | 34 |
unclassified viruses | 16 |
environmental samples | 10 |
Ribozyviria | 8 |
Singelaviria | 7 |
unclassified archaeal viruses | 1 |
unclassified satellites | 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) (33,521)
- All beta proteins (29,538)
- Alpha and beta proteins (a+b) (30,475)
- All alpha proteins (19,116)
- 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) | 33,521 |
All beta proteins | 29,538 |
Alpha and beta proteins (a+b) | 30,475 |
All alpha proteins | 19,116 |
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 |