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Modeling and structural analysis of PA clan serine proteases.
(2012) BMC Res Notes 5
PubMed: 22624962 | PubMedCentral: PMC3434108 | DOI: 10.1186/1756-0500-5-256
Table 6 Structural parameters of experimentally determined and predicted 3D structures of PA serine proteases ID Taxa Species Superposed of AA % RMSD Å Distances between the catalytic triad ... 000c5; 1ARC-A Bacteria A.lyticus 10.6 0.932 6.4 8.2 9.7 1QY6-A Bacteria S. aureus 16.2 0.753 7.1 8.4 9.9 1SGC-A Bacteria S. griseus 19.3 0.744 6.2 8.5 9.8 1TRY-A Fungi F. oxysporum 41.6 0.493 6.2 8.4 10.1 1EKB-B Animalia B. taurus 41.3 0.744 6.4 8.0 9.3 1JRS-A Animalia B. taurus 45.3 0.642 6.5 8.4 10.3 1M9U-A Animalia E. fetida 41.9 0.768 6.5 8.5 10.2 1SGI-B Animalia H. sapiens 100 0.000 6.4 8.4 10.3 1A0L-A Animalia H. sapiens 42.3 0.552 6.4 8.3 10.3 1ABJ-H Animalia H. sapiens 100 0.424 6.6 8.1 9.3 2ANY-A Animalia H. sapiens 42.4 0.541 6.3 8.3 9.8 1AO5-A Animalia M. musculus 44.1 0.552 6.6 8.2 9.7 1DPO-A Animalia R. rattus 45.5 0.652 6.3 7.6 9.8 1BIT-A Animalia S. salar 46.4 0.610 6.3 9.9 9.9 1EQ9-A Animalia S. invicta 44.6 0.593 6.3 8.1 10.1 1BQY-A Animalia T. stejnejer 41.5 0.645 6.4 8.3 9.7 Mean ± SD of the Cα distances between the triad residues 6.4±0.01 8.4±0.03 9.8±0.02 PM0075793 Protozoa P. falciparum 15.0 1.003 6.2 8.4 9.9 PM0075794 Archaea P. furiosus 22.5 0.756 6.5 8.3 9.7 PM0075795 Fungi N. crassa 13.0 1.311 6.4 9.4 10.8 PM0075796 Plantae A. thaliana 16.4 1.761 6.7 9.6 10.1 Mean ± SD of the Cα distances between the triad residues 6.5±0.06 8.9±0.19 10.1±0.14 Figure 1 Superposed structures of X-ray and modeled structures of the selected proteases of the PA clan.
Table 1 Experimental structures and predicted structures of PA serine proteases across different taxa Species Structure MEROPS ID Bacteria Achromobacter lyticus PBD: 1ARC-A MER000277 Staphylococcus aureus PBD: 1QY6-A MER000264 Streptomyces griseus PBD: 1SGC-A MER000251 Protozoa Plasmodium falciparum PMDB: PM0075793 MER024901 Archaea Pyrococcus furiosus PMDB: PM0075794 MER017398 Fungi Fusarium oxysporum PBD: 1TRY-A MER000073 Neurospora crassa PMDB: PM0075795 MER028331 Plantae Arabidopsis thaliana PMDB: PM0075796 MER016541 Animalia Bos taurus PBD: 1EKB-B MER000207 PBD: 1JRS-A MER000024 Eisenia fetida PBD: 1M9U-A MER011050 Homo sapiens PBD: 1SGI-B MER000188 PBD: 1A0L-A MER000136 PBD: 1ABJ-H MER000188 PBD: 2ANY-A MER000203 Mus musculus PBD: 1AO5-A MER000103 Rattus rattus PBD: 1DPO-A MER000030 Salmo salar PBD: 1BIT-A MER000035 Solenopsis invicta PBD: 1EQ9-A MER027244 Trimeresurus stejnejer PBD: 1BQY-A MER002805 Results and Discussion Modeling of protease structures The protozoan protease from P. falciparum was the only sequence that had significant homology with proteases of known experimental structure for successful structure prediction using SWISS-MODEL.
Publication Year: 2012
Association of putative members to family of mosquito odorant binding proteins: scoring scheme using fuzzy functional templates and cys residue positions.
(2013) Bioinform Biol Insights 7
PubMed: 23908587 | PubMedCentral: PMC3728099 | DOI: 10.4137/BBI.S11096
29 For the serine protease family, 11 structural entries from the thrombin subfamily (1ai8, 1avg, 1hao, 1mkx, 1ucy, 2hpp, 3hk3, 3k65, 3nxp, 3pma, 3qlp), 15 structural entries from the trypsin family (... aoj, 1aks, 1an1, 1fxy, 1hj8, 1jrs, 1pq7, 2a31, 2eek, 2f91, 2ra3, 3beu, 3fp7, 3mi4, 3p95) and 4 structural entries from the plasminogen activator (1a5h, 1a5i, 1bqy, 1rtf) subfamily were used for the construction of the structural alignment.
Publication Year: 2013
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