{ "bcoid": "GLY_000042", "title": "Human Glycosylation Sites (RCSB PDB)", "description": "The Human Glycosylation Sites (RCSB PDB) dataset contains human [taxid:9606] proteins glycosites mapped ...", "filename": "human_proteoform_glycosylation_sites_pdb.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Proteoform", "tags": "Glycosylation Sites", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P05451-1...", "27..." ], [ "Q14118-1...", "422..." ] ], "headers": [ "uniprotkb_ca...", "glycosylatio..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "glycosylation_site_uniprotkb" }, { "type": "string", "label": "amino_acid" }, { "type": "string", "label": "saccharide" }, { "type": "string", "label": "glycosylation_type" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": 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"2MK7", "2MK7", "A", "6", "A2G", "", "" ], [ "Q14118-1", "421", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "2MK7", "protein_xref_pdb4glycosylation", "2MK7", "2MK7", "A", "4", "A2G", "", "" ], [ "P04062-1", "60", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "2NT0", "protein_xref_pdb4glycosylation", "2NT0", "2NT0", "D", "21", "NAG", "", "" ], [ "P13671-1", "38", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "3T5O", "protein_xref_pdb4glycosylation", "3T5O", "3T5O", "A", "17", "FUC", "", "" ], [ "P13671-1", "392", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "3T5O", "protein_xref_pdb4glycosylation", "3T5O", "3T5O", "A", "371", "FUL", "", "" ], [ "Q86YL7-1", "89", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "3WSR", "protein_xref_pdb4glycosylation", "3WSR", "3WSR", "C", "52", "A2G", "", "" ], [ "Q86YL7-1", "89", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "3WSR", "protein_xref_pdb4glycosylation", "3WSR", "3WSR", "D", 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"O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "I", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "A", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "J", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "K", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "L", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "M", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "N", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "O", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "P", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "Q", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "R", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "S", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "B", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "T", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "U", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "V", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "C", "497", "NAG", "", "" ], [ "P02748-1", "518", "Thr", "", "O-linked", "protein_xref_pdb4glycosylation", "6DLW", "protein_xref_pdb4glycosylation", "6DLW", "6DLW", "D", "497", "NAG", "", "" ], [ "P61586-1", "34", "Tyr", "", "O-linked", "protein_xref_pdb4glycosylation", "5A0F", "protein_xref_pdb4glycosylation", "5A0F", "5A0F", "A", "34", "NDG", "", "" ], [ "O15118-1", "475", "Tyr", "", "O-linked", "protein_xref_pdb4glycosylation", "5U74", "protein_xref_pdb4glycosylation", "5U74", "5U74", "A", "475", "NAG", "", "" ], [ "P14384-1", "240", "Asp", "", "O-linked", "protein_xref_pdb4glycosylation", "1UWY", "protein_xref_pdb4glycosylation", "1UWY", "1UWY", "A", "223", "NAG", "", "" ], [ "P04746-1", "212", "Asp", "", "O-linked", "protein_xref_pdb4glycosylation", "3IJ7", "protein_xref_pdb4glycosylation", "3IJ7", "3IJ7", "A", "197", "B9D", "", "" ], [ "P04746-1", "212", "Asp", "", "O-linked", "protein_xref_pdb4glycosylation", "3IJ8", "protein_xref_pdb4glycosylation", "3IJ8", "3IJ8", "A", "197", "B9D", "", "" ], [ "P04746-1", "212", "Asp", "", "O-linked", "protein_xref_pdb4glycosylation", "3IJ9", "protein_xref_pdb4glycosylation", "3IJ9", "3IJ9", "A", "197", "B9D", "", "" ], [ "P08637-1", "82", "Asp", "", "O-linked", "protein_xref_pdb4glycosylation", "3SGK", "protein_xref_pdb4glycosylation", "3SGK", "3SGK", "C", "64", "NAG", "", "" ], [ "P12821-1", "625", "Glu", "", "O-linked", "protein_xref_pdb4glycosylation", "2C6F", "protein_xref_pdb4glycosylation", "2C6F", "2C6F", "A", "596", "NAG", "", "" ], [ "Q9H227-1", "373", "Glu", "", "O-linked", "protein_xref_pdb4glycosylation", "2ZOX", "protein_xref_pdb4glycosylation", "2ZOX", "2ZOX", "A", "373", "GLC", "", "" ], [ "Q9H227-1", "373", "Glu", "", "O-linked", "protein_xref_pdb4glycosylation", "3VKK", "protein_xref_pdb4glycosylation", "3VKK", "3VKK", "A", "373", "MAN", "", "" ], [ "O15118-1", "1067", "Glu", "", "O-linked", "protein_xref_pdb4glycosylation", "5U73", "protein_xref_pdb4glycosylation", "5U73", "5U73", "A", "1067", "NAG", "", "" ], [ "P05121-1", "288", "Asn", "", "N-linked", "protein_xref_pdb4glycosylation", "1A7C", "protein_xref_pdb4glycosylation", "1A7C", "1A7C", "A", "265", "NAG", "NMT", "NXT" ], [ "P05121-1", "232", "Asn", "", "N-linked", "protein_xref_pdb4glycosylation", "1A7C", "protein_xref_pdb4glycosylation", "1A7C", "1A7C", "A", "209", "NAG", "NYT", "NXT" ], [ "P20160-1", "140", "Asn", "", "N-linked", "protein_xref_pdb4glycosylation", "1A7S", "protein_xref_pdb4glycosylation", "1A7S", "1A7S", "A", "114", "NAG", "NAT", "NXT" ], [ "P20160-1", "171", "Asn", "", "N-linked", "protein_xref_pdb4glycosylation", "1A7S", "protein_xref_pdb4glycosylation", "1A7S", "1A7S", "A", "145", "NAG", "NVT", "NXT" ], [ "P20160-1", "140", "Asn", "", "N-linked", "protein_xref_pdb4glycosylation", "1AE5", "protein_xref_pdb4glycosylation", "1AE5", "1AE5", "A", "114", "NAG", "NAT", "NXT" ], [ "P20160-1", "171", "Asn", "", "N-linked", "protein_xref_pdb4glycosylation", "1AE5", "protein_xref_pdb4glycosylation", "1AE5", "1AE5", "A", "145", "NAG", "NVT", "NXT" ], [ "P20933-1", "38", "Asn", "", "N-linked", "protein_xref_pdb4glycosylation", "1APY", "protein_xref_pdb4glycosylation", "1APY", "1APY", "A", "15", "NAG", "NAT", "NXT" ], [ "P20933-1", "38", "Asn", "", "N-linked", "protein_xref_pdb4glycosylation", "1APY", "protein_xref_pdb4glycosylation", "1APY", "1APY", "C", "15", "NAG", "NAT", "NXT" ], [ "P20933-1", "38", "Asn", "", "N-linked", "protein_xref_pdb4glycosylation", "1APZ", "protein_xref_pdb4glycosylation", "1APZ", "1APZ", "A", "15", "NAG", "NAT", "NXT" ], [ "P20933-1", "38", "Asn", "", "N-linked", "protein_xref_pdb4glycosylation", "1APZ", "protein_xref_pdb4glycosylation", "1APZ", "1APZ", "C", "15", "NAG", "NAT", "NXT" ], [ "P01574-1", "101", "Asn", "", "N-linked", "protein_xref_pdb4glycosylation", "1AU1", "protein_xref_pdb4glycosylation", "1AU1", "1AU1", "A", "80", "BGC", "NET", "NXT" ], [ "P01574-1", "101", "Asn", "", "N-linked", "protein_xref_pdb4glycosylation", "1AU1", "protein_xref_pdb4glycosylation", "1AU1", "1AU1", "B", "80", "BGC", "NET", "NXT" ], [ "P01008-1", "187", "Asn", "", "N-linked", "protein_xref_pdb4glycosylation", "1AZX", "protein_xref_pdb4glycosylation", "1AZX", "1AZX", "I", "155", "NAG", "NET", "NXT" ], [ "P01008-1", "187", "Asn", "", "N-linked", "protein_xref_pdb4glycosylation", "1AZX", "protein_xref_pdb4glycosylation", "1AZX", "1AZX", "L", "155", "NAG", "NET", "NXT" ], [ "P01008-1", "224", "Asn", "", "N-linked", "protein_xref_pdb4glycosylation", "1AZX", "protein_xref_pdb4glycosylation", "1AZX", "1AZX", "L", "192", "NAG", "NKT", "NXT" ] ] }, "readme": "Name\n - Human Glycosylation Sites (RCSB PDB)\n\nVersion\n - 1.8.25\n\nCreated on\n - 2019-01-23T17:21:05.909814\n\nModified on\n - 2020-04-10T11:28:20.560562\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@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 Human Glycosylation Sites (RCSB PDB) dataset contains human [taxid:9606] 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 - Step-0: \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/ln2data/releases/data/v-1.8.25/source/N-linked-ARG-details\n Name: O-linked-ASP-details\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/source/O-linked-ASP-details\n Name: O-linked-GLU-details\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/source/O-linked-GLU-details\n Name: O-linked-SER-details\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/source/O-linked-SER-details\n Name: O-linked-THR-details\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/source/O-linked-THR-details\n Name: O-linked-TYR-details\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/source/O-linked-TYR-details\n Name: human_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_protein_masterlist.csv\n Name: human_protein_canonicalsequences.fasta\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_protein_canonicalsequences.fasta\n Name: pdb_chain_uniprot_2018_11_8_11_44_50.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/source/pdb_chain_uniprot_2018_11_8_11_44_50.csv\n Output Subdomain\n Name: human_proteoform_glycosylation_sites_pdb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_proteoform_glycosylation_sites_pdb.csv\n Name: human_proteoform_glycosylation_sites_pdb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_proteoform_glycosylation_sites_pdb.stat.csv\n\nFields\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"119\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"119\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"120\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"49\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"118\"\n Name: \"publication_date\"\n Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n Unique Values: \"117\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"115\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.8.25/reviewed/human_proteoform_glycosylation_sites_pdb.csv" }