PMC:7199903 / 10566-11210 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T57","span":{"begin":93,"end":105},"obj":"Body_part"}],"attributes":[{"id":"A57","pred":"fma_id","subj":"T57","obj":"http://purl.org/sig/ont/fma/fma62925"}],"text":"Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation. The glycans are colored according to oligomannose content as defined by the key. ACE2 receptor binding sites are highlighted in light blue. The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively. The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T43","span":{"begin":80,"end":88},"obj":"Disease"}],"attributes":[{"id":"A43","pred":"mondo_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation. The glycans are colored according to oligomannose content as defined by the key. ACE2 receptor binding sites are highlighted in light blue. The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively. The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T65","span":{"begin":358,"end":360},"obj":"http://purl.obolibrary.org/obo/CLO_0050050"},{"id":"T66","span":{"begin":365,"end":367},"obj":"http://purl.obolibrary.org/obo/CLO_0008922"},{"id":"T67","span":{"begin":365,"end":367},"obj":"http://purl.obolibrary.org/obo/CLO_0050052"}],"text":"Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation. The glycans are colored according to oligomannose content as defined by the key. ACE2 receptor binding sites are highlighted in light blue. The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively. The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T108","span":{"begin":15,"end":22},"obj":"Chemical"},{"id":"T109","span":{"begin":93,"end":105},"obj":"Chemical"},{"id":"T110","span":{"begin":111,"end":113},"obj":"Chemical"},{"id":"T111","span":{"begin":218,"end":225},"obj":"Chemical"},{"id":"T112","span":{"begin":365,"end":367},"obj":"Chemical"}],"attributes":[{"id":"A108","pred":"chebi_id","subj":"T108","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A109","pred":"chebi_id","subj":"T109","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A110","pred":"chebi_id","subj":"T110","obj":"http://purl.obolibrary.org/obo/CHEBI_141439"},{"id":"A111","pred":"chebi_id","subj":"T111","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A112","pred":"chebi_id","subj":"T112","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"}],"text":"Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation. The glycans are colored according to oligomannose content as defined by the key. ACE2 receptor binding sites are highlighted in light blue. The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively. The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions."}

{"project":"LitCovid-sample-PD-IDO","denotations":[{"id":"T53","span":{"begin":317,"end":322},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T54","span":{"begin":526,"end":531},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T55","span":{"begin":589,"end":594},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"}],"text":"Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation. The glycans are colored according to oligomannose content as defined by the key. ACE2 receptor binding sites are highlighted in light blue. The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively. The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions."}

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The glycans are colored according to oligomannose content as defined by the key. ACE2 receptor binding sites are highlighted in light blue. The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively. The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions."}

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T56","span":{"begin":93,"end":105},"obj":"Body_part"}],"attributes":[{"id":"A56","pred":"fma_id","subj":"T56","obj":"http://purl.org/sig/ont/fma/fma62925"}],"text":"Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation. The glycans are colored according to oligomannose content as defined by the key. ACE2 receptor binding sites are highlighted in light blue. The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively. The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions."}

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T82","span":{"begin":15,"end":22},"obj":"Chemical"},{"id":"T83","span":{"begin":93,"end":105},"obj":"Chemical"},{"id":"T84","span":{"begin":218,"end":225},"obj":"Chemical"}],"attributes":[{"id":"A84","pred":"chebi_id","subj":"T84","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A83","pred":"chebi_id","subj":"T83","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A82","pred":"chebi_id","subj":"T82","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"}],"text":"Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation. The glycans are colored according to oligomannose content as defined by the key. ACE2 receptor binding sites are highlighted in light blue. The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively. The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions."}

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T42","span":{"begin":80,"end":90},"obj":"Species"}],"attributes":[{"id":"A42","pred":"ncbi_taxonomy_id","subj":"T42","obj":"NCBItxid:2697049"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation. The glycans are colored according to oligomannose content as defined by the key. ACE2 receptor binding sites are highlighted in light blue. The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively. The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions."}

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T72","span":{"begin":0,"end":213},"obj":"Sentence"},{"id":"T73","span":{"begin":214,"end":294},"obj":"Sentence"},{"id":"T74","span":{"begin":295,"end":353},"obj":"Sentence"},{"id":"T75","span":{"begin":354,"end":473},"obj":"Sentence"},{"id":"T76","span":{"begin":474,"end":644},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation. The glycans are colored according to oligomannose content as defined by the key. ACE2 receptor binding sites are highlighted in light blue. The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively. The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions."}

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T37","span":{"begin":80,"end":90},"obj":"Disease"}],"attributes":[{"id":"A37","pred":"mondo_id","subj":"T37","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation. The glycans are colored according to oligomannose content as defined by the key. ACE2 receptor binding sites are highlighted in light blue. The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively. The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions."}

{"project":"LitCovid-sample-Pubtator","denotations":[{"id":"356","span":{"begin":295,"end":299},"obj":"Gene"},{"id":"357","span":{"begin":91,"end":92},"obj":"Gene"},{"id":"358","span":{"begin":80,"end":90},"obj":"Species"},{"id":"359","span":{"begin":15,"end":22},"obj":"Chemical"},{"id":"360","span":{"begin":218,"end":225},"obj":"Chemical"},{"id":"361","span":{"begin":251,"end":263},"obj":"Chemical"},{"id":"362","span":{"begin":519,"end":525},"obj":"Chemical"},{"id":"363","span":{"begin":582,"end":588},"obj":"Chemical"}],"attributes":[{"id":"A363","pred":"pubann:denotes","subj":"363","obj":"MESH:D011134"},{"id":"A356","pred":"pubann:denotes","subj":"356","obj":"Gene:59272"},{"id":"A357","pred":"pubann:denotes","subj":"357","obj":"Gene:43740568"},{"id":"A360","pred":"pubann:denotes","subj":"360","obj":"MESH:D011134"},{"id":"A362","pred":"pubann:denotes","subj":"362","obj":"MESH:D011134"},{"id":"A359","pred":"pubann:denotes","subj":"359","obj":"MESH:D011134"},{"id":"A358","pred":"pubann:denotes","subj":"358","obj":"Tax:2697049"}],"text":"Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation. The glycans are colored according to oligomannose content as defined by the key. ACE2 receptor binding sites are highlighted in light blue. The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively. The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions."}

{"project":"LitCovid-sample-UniProt","denotations":[{"id":"T1234","span":{"begin":91,"end":105},"obj":"Protein"},{"id":"T1333","span":{"begin":134,"end":137},"obj":"Protein"},{"id":"T1342","span":{"begin":295,"end":299},"obj":"Protein"}],"attributes":[{"id":"A1234","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q9QAS2"},{"id":"A1235","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q9QAR5"},{"id":"A1236","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q9QAQ8"},{"id":"A1237","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q9IW04"},{"id":"A1238","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q9IKD1"},{"id":"A1239","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q990M4"},{"id":"A1240","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q990M3"},{"id":"A1241","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q990M2"},{"id":"A1242","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q990M1"},{"id":"A1243","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q91AV1"},{"id":"A1244","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q91A26"},{"id":"A1245","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q8V436"},{"id":"A1246","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q8JSP8"},{"id":"A1247","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q8BB25"},{"id":"A1248","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q86623"},{"id":"A1249","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q85088"},{"id":"A1250","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q85087"},{"id":"A1251","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q80BV6"},{"id":"A1252","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q7TFB1"},{"id":"A1253","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q7TFA2"},{"id":"A1254","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q7TA19"},{"id":"A1255","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q7T6T3"},{"id":"A1256","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q7T696"},{"id":"A1257","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q77NC4"},{"id":"A1258","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q6TNF9"},{"id":"A1259","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q6R1L7"},{"id":"A1260","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q6QU82"},{"id":"A1261","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q6Q1S2"},{"id":"A1262","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q696Q6"},{"id":"A1263","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q66291"},{"id":"A1264","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q66290"},{"id":"A1265","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q66199"},{"id":"A1266","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q66177"},{"id":"A1267","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q66176"},{"id":"A1268","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q66174"},{"id":"A1269","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q65984"},{"id":"A1270","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q5MQD0"},{"id":"A1271","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q5I5X9"},{"id":"A1272","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q5DIY0"},{"id":"A1273","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q5DIX9"},{"id":"A1274","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q5DIX8"},{"id":"A1275","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q5DIX7"},{"id":"A1276","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q52PA3"},{"id":"A1277","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q4ZJS1"},{"id":"A1278","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q4U5G0"},{"id":"A1279","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q3T8J0"},{"id":"A1280","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q3LZX1"},{"id":"A1281","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q3I5J5"},{"id":"A1282","pred":"uniprot_id","subj":"T1234","obj":"https://www.uniprot.org/uniprot/Q14E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,"obj":"https://www.uniprot.org/uniprot/Q63491"},{"id":"A1335","pred":"uniprot_id","subj":"T1333","obj":"https://www.uniprot.org/uniprot/Q62815"},{"id":"A1336","pred":"uniprot_id","subj":"T1333","obj":"https://www.uniprot.org/uniprot/Q62691"},{"id":"A1337","pred":"uniprot_id","subj":"T1333","obj":"https://www.uniprot.org/uniprot/Q01542"},{"id":"A1338","pred":"uniprot_id","subj":"T1333","obj":"https://www.uniprot.org/uniprot/P27732"},{"id":"A1339","pred":"uniprot_id","subj":"T1333","obj":"https://www.uniprot.org/uniprot/O09024"},{"id":"A1340","pred":"uniprot_id","subj":"T1333","obj":"https://www.uniprot.org/uniprot/O09023"},{"id":"A1341","pred":"uniprot_id","subj":"T1333","obj":"https://www.uniprot.org/uniprot/O09022"},{"id":"A1342","pred":"uniprot_id","subj":"T1342","obj":"https://www.uniprot.org/uniprot/Q9UFZ6"}],"text":"Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation. The glycans are colored according to oligomannose content as defined by the key. ACE2 receptor binding sites are highlighted in light blue. The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively. The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions."}

{"project":"LitCovid-sentences","denotations":[{"id":"T72","span":{"begin":0,"end":213},"obj":"Sentence"},{"id":"T73","span":{"begin":214,"end":294},"obj":"Sentence"},{"id":"T74","span":{"begin":295,"end":353},"obj":"Sentence"},{"id":"T75","span":{"begin":354,"end":473},"obj":"Sentence"},{"id":"T76","span":{"begin":474,"end":644},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation. The glycans are colored according to oligomannose content as defined by the key. ACE2 receptor binding sites are highlighted in light blue. The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively. The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions."}

{"project":"LitCovid-PubTator","denotations":[{"id":"356","span":{"begin":295,"end":299},"obj":"Gene"},{"id":"357","span":{"begin":91,"end":92},"obj":"Gene"},{"id":"358","span":{"begin":80,"end":90},"obj":"Species"},{"id":"359","span":{"begin":15,"end":22},"obj":"Chemical"},{"id":"360","span":{"begin":218,"end":225},"obj":"Chemical"},{"id":"361","span":{"begin":251,"end":263},"obj":"Chemical"},{"id":"362","span":{"begin":519,"end":525},"obj":"Chemical"},{"id":"363","span":{"begin":582,"end":588},"obj":"Chemical"}],"attributes":[{"id":"A356","pred":"tao:has_database_id","subj":"356","obj":"Gene:59272"},{"id":"A357","pred":"tao:has_database_id","subj":"357","obj":"Gene:43740568"},{"id":"A358","pred":"tao:has_database_id","subj":"358","obj":"Tax:2697049"},{"id":"A359","pred":"tao:has_database_id","subj":"359","obj":"MESH:D011134"},{"id":"A360","pred":"tao:has_database_id","subj":"360","obj":"MESH:D011134"},{"id":"A362","pred":"tao:has_database_id","subj":"362","obj":"MESH:D011134"},{"id":"A363","pred":"tao:has_database_id","subj":"363","obj":"MESH:D011134"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation. The glycans are colored according to oligomannose content as defined by the key. ACE2 receptor binding sites are highlighted in light blue. The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively. The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions."}