{ "bcoid": "GLY_000043", "title": "Mouse Glycosylation Sites (RCSB PDB)", "description": "The Mouse Glycosylation Sites (RCSB PDB) dataset contains mouse [taxid:10090] proteins glycosites mapped ...", "filename": "mouse_proteoform_glycosylation_sites_pdb.csv", "filetype": "csv", "categories": { "species": "Mus musculus", "molecule": "Proteoform", "tags": "Glycosylation Sites", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q01705-1...", "O-linked..." ], [ "Q01705-1...", "O-linked..." ] ], "headers": [ "uniprotkb_ca...", "glycosylatio..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "glycosylation_type" }, { "type": "string", "label": "saccharide" }, { "type": "string", "label": "amino_acid" }, { "type": "string", "label": "glycosylation_site_uniprotkb" }, { "type": "string", "label": "evidence" }, { "type": "string", "label": "pdb_id" }, { "type": "string", "label": "amino_acid_chain" }, { "type": "string", "label": "glycosylation_site_pdb" } ], [ "Q01705-1", "O-linked", "FUC", "Thr", "466", "", "2RQZ", "A", "15" ], [ "Q01705-1", "O-linked", "FUC", "Thr", "466", "", "2RR2", "A", "15" ], [ "Q62011-1", "O-linked", "A2G", "Thr", "77", "", "3IET", "X", "2" ], [ "P09803-1", "O-linked", "MAN", "Thr", "580", "", "3Q2V", "B", "424" ], [ "P09803-1", "O-linked", "MAN", "Thr", "360", "", "3Q2V", "B", "204" ], [ "P09803-1", "O-linked", "MAN", "Thr", "578", "", "3Q2V", "A", "422" ], [ "P09803-1", "O-linked", "MAN", "Thr", "580", "", "3Q2V", "A", "424" ], [ "P09803-1", "O-linked", "MAN", "Thr", "582", "", "3Q2V", "B", "426" ], [ "P09803-1", "O-linked", "MAN", "Thr", "360", "", "3Q2V", "A", "204" ], [ "P09803-1", "O-linked", "MAN", "Thr", "472", "", "3Q2V", "B", "316" ], [ "P09803-1", "O-linked", "MAN", "Thr", "474", "", "3Q2V", "B", "318" ], [ "P09803-1", "O-linked", "MAN", "Thr", "578", "", "3Q2V", "B", "422" ], [ "P09803-1", "O-linked", "MAN", "Thr", "474", "", "3Q2V", "A", "318" ], [ "P09803-1", "O-linked", "MAN", "Thr", "511", "", "3Q2V", "A", "355" ], [ "P09803-1", "O-linked", "MAN", "Thr", "582", "", "3Q2V", "A", "426" ], [ "P09803-1", "O-linked", "MAN", "Thr", "472", "", "3Q2V", "A", "316" ], [ "P09803-1", "O-linked", "MAN", "Thr", "511", "", "3Q2V", "B", "355" ], [ "P15116-1", "O-linked", "MAN", "Thr", "483", "", "3Q2W", "A", "324" ], [ "P15116-1", "O-linked", "MAN", "Thr", "588", "", "3Q2W", "A", "429" ], [ "P15116-1", "O-linked", "MAN", "Thr", "481", "", "3Q2W", "A", "322" ], [ "P15116-1", "O-linked", "MAN", "Thr", "590", "", "3Q2W", "A", "431" ], [ "P15116-1", "O-linked", "MAN", "Thr", "367", "", "3Q2W", "A", "208" ], [ "P15116-1", "O-linked", "MAN", "Thr", "290", "", "3Q2W", "A", "131" ], [ "P15116-1", "O-linked", "MAN", "Thr", "365", "", "3Q2W", "A", "206" ], [ "Q91Y09-1", "O-linked", "MAN", "Thr", "239", "", "4ZPM", "A", "198" ], [ "Q91Y09-1", "O-linked", "MAN", "Thr", "239", "", "4ZPM", "B", "198" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "4ZPN", "A", "201" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "4ZPN", "B", "201" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "4ZPO", "A", "196" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "4ZPP", "A", "196" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "4ZPP", "B", "196" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "4ZPQ", "A", "196" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "4ZPQ", "B", "196" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "4ZPQ", "C", "196" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "4ZPS", "A", "196" ], [ "Q91Y13-1", "O-linked", "MAN", "Thr", "223", "", "5DZV", "A", "194" ], [ "Q91Y13-1", "O-linked", "MAN", "Thr", "225", "", "5DZV", "A", "196" ], [ "Q91Y13-1", "O-linked", "MAN", "Thr", "223", "", "5DZV", "B", "194" ], [ "Q91Y13-1", "O-linked", "MAN", "Thr", "225", "", "5DZV", "B", "196" ], [ "Q91Y13-1", "O-linked", "MAN", "Thr", "438", "", "5DZV", "B", "409" ], [ "O88689-1", "O-linked", "MAN", "Thr", "438", "", "5DZW", "A", "409" ], [ "Q91XZ4-1", "O-linked", "MAN", "Thr", "225", "", "5DZX", "B", "197" ], [ "Q91XZ2-1", "O-linked", "MAN", "Thr", "225", "", "5DZY", "C", "197" ], [ "Q91XZ2-1", "O-linked", "MAN", "Thr", "227", "", "5DZY", "C", "199" ], [ "Q91XZ2-1", "O-linked", "MAN", "Thr", "225", "", "5DZY", "D", "197" ], [ "Q91XZ2-1", "O-linked", "MAN", "Thr", "227", "", "5DZY", "D", "199" ], [ "Q91XZ2-1", "O-linked", "MAN", "Thr", "225", "", "5DZY", "E", "197" ], [ "Q91XZ2-1", "O-linked", "MAN", "Thr", "227", "", "5DZY", "E", "199" ], [ "Q91XZ2-1", "O-linked", "MAN", "Thr", "225", "", "5DZY", "F", "197" ], [ "Q91XZ2-1", "O-linked", "MAN", "Thr", "227", "", "5DZY", "F", "199" ], [ "Q91XZ2-1", "O-linked", "MAN", "Thr", "225", "", "5DZY", "A", "197" ], [ "Q91XZ2-1", "O-linked", "MAN", "Thr", "227", "", "5DZY", "A", "199" ], [ "Q91XZ2-1", "O-linked", "MAN", "Thr", "225", "", "5DZY", "B", "197" ], [ "Q91XZ2-1", "O-linked", "MAN", "Thr", "227", "", "5DZY", "B", "199" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "5SZL", "C", "197" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "5SZL", "D", "197" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "5SZL", "A", "197" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "5SZL", "B", "197" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "5SZM", "A", "196" ], [ "Q91XX9-1", "O-linked", "MAN", "Thr", "226", "", "5SZN", "A", "197" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "5SZO", "A", "195" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "5SZO", "B", "195" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "5SZP", "A", "195" ], [ "Q91XW9-1", "O-linked", "MAN", "Thr", "225", "", "5SZP", "B", "195" ], [ "Q99PJ1-1", "O-linked", "MAN", "Thr", "170", "", "6CV7", "A", "144" ], [ "Q99PJ1-1", "O-linked", "MAN", "Thr", "251", "", "6CV7", "A", "225" ], [ "Q99PJ1-1", "O-linked", "MAN", "Thr", "253", "", "6CV7", "A", "227" ], [ "Q99PJ1-1", "O-linked", "MAN", "Thr", "255", "", "6CV7", "A", "229" ], [ "Q99PJ1-1", "O-linked", "MAN", "Thr", "257", "", "6CV7", "A", "231" ], [ "O35744-1", "O-linked", "GCS", "Tyr", "233", "", "1E9L", "A", "212" ], [ "P01901-1", "N-linked", "NAG", "Arg", "178", "", "1BQH", "D", "157" ], [ "Q8BGN3-1", "N-linked", "FUL", "Arg", "351", "", "5EGE", "C", "351" ], [ "P36368-1", "N-linked", "NAG", "Asn", "119", "", "1AO5", "A", "95" ], [ "P36368-1", "N-linked", "NAG", "Asn", "119", "", "1AO5", "B", "95" ], [ "P01731-1", "N-linked", "NAG", "Asn", "69", "", "1BQH", "H", "42" ], [ "P01731-1", "N-linked", "NAG", "Asn", "69", "", "1BQH", "I", "42" ], [ "P01731-1", "N-linked", "NAG", "Asn", "69", "", "1BQH", "K", "42" ], [ "P01731-1", "N-linked", "NDG", "Asn", "69", "", "1BQH", "G", "42" ], [ "P40223-1", "N-linked", "NAG", "Asn", "129", "", "1CD9", "B", "10" ], [ "P40223-1", "N-linked", "NAG", "Asn", "129", "", "1CD9", "D", "10" ], [ "P01901-1", "N-linked", "NAG", "Asn", "107", "", "1FZJ", "A", "86" ], [ "P01901-1", "N-linked", "NAG", "Asn", "197", "", "1FZJ", "A", "176" ], [ "P01901-1", "N-linked", "NAG", "Asn", "197", "", "1FZK", "A", "176" ], [ "P01901-1", "N-linked", "NAG", "Asn", "107", "", "1FZK", "A", "86" ] ] }, "readme": "Name\n - Mouse Glycosylation Sites (RCSB PDB)\n\nVersion\n - 1.5.18\n\nCreated on\n - 2019-01-23T17:21:05.910839\n\nModified on\n - 2020-04-10T12:35:07.324192\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu]\n\nAuthors\n - Jasmine Young [jasmine@rcsb.rutgers.edu], Chenghua Shao [chenghua@rcsb.rutgers.edu]\n\nChecksum\n - \n\nUsability Domain\n - The Mouse Glycosylation Sites (RCSB PDB) dataset contains mouse [taxid:10090] proteins glycosites mapped from the associated RCSB PDB Id's using SIFTS database (https://www.ebi.ac.uk/pdbe/docs/sifts/). The glycosylation data (PDB ID, GlycoSite, Chain ID, Sugar (first link)) was retrieved from RCSB group. [www.rcsb.org, Nucleic Acids Research, 28: 235-242.(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102472/)].\n\nDescription Domain\n Keywords\n - PDB\n - glycosylation sites\n - amino acid\n - amino acid chain\n\n Pipeline Steps\n - Step-1: The script extracts the PDB IDs and PDB glycosite from the input .tsv files and maps it to the corresponding UniProtKB accessions and position using the coordinate file downloaded from the SIFTS database using the formula:(SP_BEG-RES_BEG)+ PDB-Position)]. The script also validates the UniProtKB glycosite (amino acid + position) with the corresponding fasta sequences downloaded from UniProtKB.\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-proteoform-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: N-linked-ARG-details\n URI: https://data.glygen.org/ln2wwwdata/source/N-linked-ARG-details\n Name: O-linked-ASP-details\n URI: https://data.glygen.org/ln2wwwdata/source/O-linked-ASP-details\n Name: O-linked-GLU-details\n URI: https://data.glygen.org/ln2wwwdata/source/O-linked-GLU-details\n Name: O-linked-SER-details\n URI: https://data.glygen.org/ln2wwwdata/source/O-linked-SER-details\n Name: O-linked-THR-details\n URI: https://data.glygen.org/ln2wwwdata/source/O-linked-THR-details\n Name: O-linked-TYR-details\n URI: https://data.glygen.org/ln2wwwdata/source/O-linked-TYR-details\n Name: mouse_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_masterlist.csv\n Name: mouse_protein_canonicalsequences.fasta\n URI: https://data.glygen.org/ln2wwwdata/source/mouse_protein_canonicalsequences.fasta\n Name: pdb_chain_uniprot_2018_11_8_11_44_50.csv\n URI: https://data.glygen.org/ln2wwwdata/source/pdb_chain_uniprot_2018_11_8_11_44_50.csv\n Output Subdomain\n Name: mouse_proteoform_glycosylation_sites_pdb.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_proteoform_glycosylation_sites_pdb.csv\n Name: mouse_proteoform_glycosylation_sites_pdb.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_proteoform_glycosylation_sites_pdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"63\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"130\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"2\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"5\"\n Name: \"glycosylation_site_pdb\"\n Description: \"Site on the protein sequence of the PDB entry where glycosylation is observed\"\n Unique Values: \"127\"\n Name: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) as evidence for the entry/annotation\"\n Unique Values: \"1\"\n Name: \"pdb_id\"\n Description: \"4-character id assigned to each protein structure in Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)\"\n Unique Values: \"233\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"7\"\n Name: \"amino_acid_chain\"\n Description: \"Amino acid chain in pdb\"\n Unique Values: \"15\"", "downloadurl": "/ln2data/releases/data/v-1.5.18/reviewed/mouse_proteoform_glycosylation_sites_pdb.csv" }