PMC:5118421 / 9830-11419 JSONTXT

{"project":"TEST0","denotations":[{"id":"27920779-136-142-3100218","span":{"begin":568,"end":570},"obj":"[\"21460441\"]"}],"text":"Structures of Ab–Ag complexes were acquired from the database at http://www.rcsb.org/pdb/home/home.do. The search criterion used was “antibody–antigen,” and the inclusion criterion was that the Ag had to be proteinaceous. Only Ab sequences from human or mouse were analyzed. Sequences were downloaded based on their order of appearance in the RCSB protein data bank (pdb) database. Duplicate structures were excluded from analysis. Contact residues between Ab and Ag were calculated using ncont from the CCP4 program suite with an atom to atom cutoff distance of 4 Å (25). When calculating, Ag contacts, the complete Ab heavy and light chain sequences (as written in the individual pdb files) along with the complete Ag sequence were used in the search parameter. The heavy and light chain search sequences were restricted to amino acid side-chain atoms only while contact residues in the Ag were not restricted. If more than one Ab–Ag complex was present in the asymmetric unit, only one complex was included in the analysis. A total of 46 M. musculus and 26 H. sapiens immune complexes crystal structures were analyzed and the pdb files for these are 4ot1, 4rrp, 4tsc, 4v1d, 4xak, 4xvu, 4zs6, 5c0s, 2dd8, 3gbn, 3lzf, 3sdy, 4fqi, 4hkx, 4m5z, 4o58, 4py8, 4r8w, 4xnm, 4yjz, 5a3i, 5dum, 4dgv, 4mwf, 4n0y, 4uta, 1eo8, 1nca, 1nma, 1qfu, 2aep, 2b2x, 2xqy, 2nr6, 2ypv, 3gi9, 3hb3, 3i50, 3mj9, 3o0r, 3rv, 3v7a, 3wfb, 3wfc, 4aei, 4cad, 4etg, 4ffv, 4gag, 4gms, 4hlz_2, 4k2u, 4lqf, 4u0r, 4m1g, 4m48, 4mhh, 4n8c, 4oii, 4okv, 4plj, 4qnp, 4qww, 4rgn, 4rgo, 4tuk, 4u6h, 4xpa, 5c0n, 5dj8, 5dlm, and 5en2."}

{"project":"2_test","denotations":[{"id":"27920779-21460441-34707941","span":{"begin":568,"end":570},"obj":"21460441"}],"text":"Structures of Ab–Ag complexes were acquired from the database at http://www.rcsb.org/pdb/home/home.do. The search criterion used was “antibody–antigen,” and the inclusion criterion was that the Ag had to be proteinaceous. Only Ab sequences from human or mouse were analyzed. Sequences were downloaded based on their order of appearance in the RCSB protein data bank (pdb) database. Duplicate structures were excluded from analysis. Contact residues between Ab and Ag were calculated using ncont from the CCP4 program suite with an atom to atom cutoff distance of 4 Å (25). When calculating, Ag contacts, the complete Ab heavy and light chain sequences (as written in the individual pdb files) along with the complete Ag sequence were used in the search parameter. The heavy and light chain search sequences were restricted to amino acid side-chain atoms only while contact residues in the Ag were not restricted. If more than one Ab–Ag complex was present in the asymmetric unit, only one complex was included in the analysis. A total of 46 M. musculus and 26 H. sapiens immune complexes crystal structures were analyzed and the pdb files for these are 4ot1, 4rrp, 4tsc, 4v1d, 4xak, 4xvu, 4zs6, 5c0s, 2dd8, 3gbn, 3lzf, 3sdy, 4fqi, 4hkx, 4m5z, 4o58, 4py8, 4r8w, 4xnm, 4yjz, 5a3i, 5dum, 4dgv, 4mwf, 4n0y, 4uta, 1eo8, 1nca, 1nma, 1qfu, 2aep, 2b2x, 2xqy, 2nr6, 2ypv, 3gi9, 3hb3, 3i50, 3mj9, 3o0r, 3rv, 3v7a, 3wfb, 3wfc, 4aei, 4cad, 4etg, 4ffv, 4gag, 4gms, 4hlz_2, 4k2u, 4lqf, 4u0r, 4m1g, 4m48, 4mhh, 4n8c, 4oii, 4okv, 4plj, 4qnp, 4qww, 4rgn, 4rgo, 4tuk, 4u6h, 4xpa, 5c0n, 5dj8, 5dlm, and 5en2."}

{"project":"MyTest","denotations":[{"id":"27920779-21460441-34707941","span":{"begin":568,"end":570},"obj":"21460441"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"Structures of Ab–Ag complexes were acquired from the database at http://www.rcsb.org/pdb/home/home.do. The search criterion used was “antibody–antigen,” and the inclusion criterion was that the Ag had to be proteinaceous. Only Ab sequences from human or mouse were analyzed. Sequences were downloaded based on their order of appearance in the RCSB protein data bank (pdb) database. Duplicate structures were excluded from analysis. Contact residues between Ab and Ag were calculated using ncont from the CCP4 program suite with an atom to atom cutoff distance of 4 Å (25). When calculating, Ag contacts, the complete Ab heavy and light chain sequences (as written in the individual pdb files) along with the complete Ag sequence were used in the search parameter. The heavy and light chain search sequences were restricted to amino acid side-chain atoms only while contact residues in the Ag were not restricted. If more than one Ab–Ag complex was present in the asymmetric unit, only one complex was included in the analysis. A total of 46 M. musculus and 26 H. sapiens immune complexes crystal structures were analyzed and the pdb files for these are 4ot1, 4rrp, 4tsc, 4v1d, 4xak, 4xvu, 4zs6, 5c0s, 2dd8, 3gbn, 3lzf, 3sdy, 4fqi, 4hkx, 4m5z, 4o58, 4py8, 4r8w, 4xnm, 4yjz, 5a3i, 5dum, 4dgv, 4mwf, 4n0y, 4uta, 1eo8, 1nca, 1nma, 1qfu, 2aep, 2b2x, 2xqy, 2nr6, 2ypv, 3gi9, 3hb3, 3i50, 3mj9, 3o0r, 3rv, 3v7a, 3wfb, 3wfc, 4aei, 4cad, 4etg, 4ffv, 4gag, 4gms, 4hlz_2, 4k2u, 4lqf, 4u0r, 4m1g, 4m48, 4mhh, 4n8c, 4oii, 4okv, 4plj, 4qnp, 4qww, 4rgn, 4rgo, 4tuk, 4u6h, 4xpa, 5c0n, 5dj8, 5dlm, and 5en2."}