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Section F, Structural biology communications", "date": "2022", "authors": "Kim M, Ryu SE", "reference": { "type": "PubMed", "id": "35787553", "url": "https://pubmed.ncbi.nlm.nih.gov/35787553" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "Q9HD43-1", "protein_name": "Receptor-type tyrosine-protein phosphatase H", "gene_name": "PTPRH", "tax_name": "Human" } ], "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HD43", "url": "https://www.uniprot.org/uniprotkb/Q9HD43" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "record_id": "pubmed.35787553", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { 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"authors": "Chen Li, Dong Jun, Liao Siyang, Wang Siyou, Wu Zhida, Zuo Meiling, Liu Bing, Yan Chaojun, Chen Yong, He He, Meng Qingtao, Song Zhiyin", "reference": { "type": "PubMed", "id": "35313046", "url": "https://pubmed.ncbi.nlm.nih.gov/35313046" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "Q9Y512-1", "protein_name": "Sorting and assembly machinery component 50 homolog", "gene_name": "SAMM50", "tax_name": "Human" } ], "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y512", "url": "https://www.uniprot.org/uniprotkb/Q9Y512" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "record_id": "pubmed.35313046", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ 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"count": 0 } ], "sort_fields": [] } ] }, { "title": "Discoidin domain receptor 1 regulates bronchial epithelial repair and matrix metalloproteinase production.", "journal": "The European respiratory journal", "date": "2011-06", "authors": "Roberts M E, Magowan L, Hall I P, Johnson S R", "reference": { "type": "PubMed", "id": "20884741", "url": "https://pubmed.ncbi.nlm.nih.gov/20884741" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "Q08345-1", "protein_name": "Epithelial discoidin domain-containing receptor 1", "gene_name": "DDR1", "tax_name": "Human" } ], "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "record_id": "pubmed.20884741", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], 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{ "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "PubMed", "id": "23899692", "url": "https://pubmed.ncbi.nlm.nih.gov/23899692" } ], "uniprot_canonical_ac": "Q08345-1" } ], "record_id": "pubmed.23899692", "abstract": "", "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { "table_id": "referenced_glycans", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": 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"Glycosylation at Asn211 regulates the activation state of the discoidin domain receptor 1 (DDR1).", "journal": "The Journal of biological chemistry", "date": "2014", "authors": "Fu HL, Valiathan RR, Payne L, Kumarasiri M, Mahasenan KV, Mobashery S, Huang P, Fridman R", "reference": { "type": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "Q08345-1", "protein_name": "Epithelial discoidin domain-containing receptor 1", "gene_name": "DDR1", "tax_name": "Human" } ], "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "other", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": 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"other", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true, "automatic_literature_mining": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_pos": 394, "start_aa": "Asn", "end_pos": 394, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn394", "evidence": [ { "id": "Q08345", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q08345#ptm_processing" }, { "id": "24509848", "database": "PubMed", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" }, { "id": "GLY_000481", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000481" } ], "mining_tool": "RLIMS-G_1.0", "mining_tool_list": [ { "label": "RLIMS-G_1.0" } ], "filter_code": "001000000000000000000.00010000000000.00.01101", "uniprot_canonical_ac": "Q08345-1" } ], "mutagenesis": [ { "start_pos": 105, "end_pos": 105, "sequence_org": "R", "sequence_mut": "A", "comment": "Inhibits collagen-induced phosphorylation.", "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "uniprot_canonical_ac": "Q08345-1" }, { "start_pos": 211, "end_pos": 211, "sequence_org": "N", "sequence_mut": "A", "comment": "Phosphorylates regardless of collagen presence, collagen addition does not alter significantly the levels of constitutive phosphorylation.", "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "uniprot_canonical_ac": "Q08345-1" }, { "start_pos": 211, "end_pos": 211, "sequence_org": "N", "sequence_mut": "Q", "comment": "Sustained phosphorylation regardless of collagen presence, collagen addition does not alter significantly the levels of constitutive phosphorylation. Located intracellularly and at the cell surface. Displays a reduced rate of receptor internalization, which is not altered in the presence of collagen. Able to bind collagen as wild-type. Exhibits enhanced collagen-independent receptor dimerization. Complete loss of the collagen-independent constitutive activation; when associated with A-655.", "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "uniprot_canonical_ac": "Q08345-1" }, { "start_pos": 213, "end_pos": 213, "sequence_org": "S", "sequence_mut": "A", "comment": "Phosphorylates regardless of collagen presence, collagen addition does not alter significantly the levels of constitutive phosphorylation.", "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "uniprot_canonical_ac": "Q08345-1" }, { "start_pos": 260, "end_pos": 260, "sequence_org": "N", "sequence_mut": "Q", "comment": "Phosphorylates in response to collagen, but at lower levels compared to wild-type. No activation in the absence of collagen.", "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "uniprot_canonical_ac": "Q08345-1" }, { "start_pos": 371, "end_pos": 371, "sequence_org": "N", "sequence_mut": "Q", "comment": "Phosphorylates in response to collagen, but at lower levels compared to wild-type. No activation in the absence of collagen.", "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "uniprot_canonical_ac": "Q08345-1" }, { "start_pos": 379, "end_pos": 379, "sequence_org": "T", "sequence_mut": "A", "comment": "Phosphorylates in response to collagen, but at lower levels compared to wild-type. Phosphorylates in response to collagen, but at lower levels compared to wild-type; when associated with A-393.", "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "uniprot_canonical_ac": "Q08345-1" }, { "start_pos": 393, "end_pos": 393, "sequence_org": "T", "sequence_mut": "A", "comment": "Phosphorylates in response to collagen, but at lower levels compared to wild-type. Phosphorylates in response to collagen, but at lower levels compared to wild-type; when associated with A-379.", "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "uniprot_canonical_ac": "Q08345-1" }, { "start_pos": 394, "end_pos": 394, "sequence_org": "N", "sequence_mut": "Q", "comment": "Phosphorylates in response to collagen, but at lower levels compared to wild-type. No activation in the absence of collagen.", "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "uniprot_canonical_ac": "Q08345-1" }, { "start_pos": 655, "end_pos": 655, "sequence_org": "K", "sequence_mut": "A", "comment": "Loss of kinase activity. Complete loss of the collagen-independent constitutive activation; when associated with Q-211.", "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "uniprot_canonical_ac": "Q08345-1" } ], "phosphorylation": [ { "start_pos": 213, "end_pos": 213, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q08345", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "site_lbl": "Ser213", "uniprot_canonical_ac": "Q08345-1" }, { "start_pos": 484, "end_pos": 484, "kinase_uniprot_canonical_ac": "Q08345-1", "kinase_gene_name": "DDR1", "residue": "Tyr", "comment": "", "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "iPTMnet", "id": "Q08345", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "site_lbl": "Tyr484", "uniprot_canonical_ac": "Q08345-1" }, { "start_pos": 513, "end_pos": 513, "kinase_uniprot_canonical_ac": "Q08345-1", "kinase_gene_name": "DDR1", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q08345", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q08345" }, { "database": "PubMed", "id": "9659899", "url": "https://pubmed.ncbi.nlm.nih.gov/9659899" }, { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "site_lbl": "Tyr513", "uniprot_canonical_ac": "Q08345-1" }, { "start_pos": 520, "end_pos": 520, "kinase_uniprot_canonical_ac": "Q08345-1", "kinase_gene_name": "DDR1", "residue": "Tyr", "comment": "", "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "iPTMnet", "id": "Q08345", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "site_lbl": "Tyr520", "uniprot_canonical_ac": "Q08345-1" }, { "start_pos": 792, "end_pos": 792, "kinase_uniprot_canonical_ac": "Q08345-1", "kinase_gene_name": "DDR1", "residue": "Tyr", "comment": "", "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "iPTMnet", "id": "Q08345", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "site_lbl": "Tyr792", "uniprot_canonical_ac": "Q08345-1" }, { "start_pos": 796, "end_pos": 796, "kinase_uniprot_canonical_ac": "Q08345-1", "kinase_gene_name": "DDR1", "residue": "Tyr", "comment": "", "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "iPTMnet", "id": "Q08345", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "site_lbl": "Tyr796", "uniprot_canonical_ac": "Q08345-1" }, { "start_pos": 797, "end_pos": 797, "kinase_uniprot_canonical_ac": "Q08345-1", "kinase_gene_name": "DDR1", "residue": "Tyr", "comment": "", "evidence": [ { "database": "UniProtKB", "id": "Q08345", "url": "https://www.uniprot.org/uniprotkb/Q08345" }, { "database": "iPTMnet", "id": "Q08345", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q08345" }, { "database": "PubMed", "id": "24509848", "url": "https://pubmed.ncbi.nlm.nih.gov/24509848" } ], "site_lbl": "Tyr797", "uniprot_canonical_ac": "Q08345-1" } ], "record_id": "pubmed.24509848", "abstract": "", "snv": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { "table_id": "referenced_glycans", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 4 }, { "field": "total_sites", "count": 4 }, { "field": "n_linked_sites", "count": 4 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 4 }, { "field": "exact_n_linked_sites", "count": 4 }, { "field": "fuzzy_sites", "count": 0 } ], "sort_fields": [ "glytoucan_ac", "type", 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U.S.A.", "date": "1992", "authors": "Flejter WL, McDaniel LD, Johns D, Friedberg EC, Schultz RA", "reference": { "type": "PubMed", "id": "1729695", "url": "https://pubmed.ncbi.nlm.nih.gov/1729695" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P18074-1", "protein_name": "General transcription and DNA repair factor IIH helicase subunit XPD", "gene_name": "ERCC2", "tax_name": "Human" } ], "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P18074", "url": "https://www.uniprot.org/uniprotkb/P18074" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "record_id": "pubmed.1729695", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", 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