{ "bcoid": "GLY_001412", "title": "Human Glycosylation Sites and Glycans (RCSB PDB)", "description": "The Human Glycosylation Sites and Glycans (RCSB PDB) dataset contains Homo sapiens [taxid:9606] glycosylation ...", "filename_list": "human_proteoform_glycosylation_sites_rcsb_pdb.csv", "filename": "human_proteoform_glycosylation_sites_rcsb_pdb.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Proteoform" ], "tag": [ "Glycosylation Sites" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P13671-1...", "38..." ], [ "Q76LX8-1...", "399..." ] ], "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": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" }, { "type": "string", "label": "pdb_id" }, { "type": "string", "label": "pdb_extended_id" }, { "type": "string", "label": "amino_acid_chain" }, { "type": "string", "label": "glycosylation_site_pdb" }, { "type": "string", "label": "pdb_glycan_entity_id" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "start_aa" }, { "type": "string", "label": "end_aa" }, { "type": "string", "label": "site_seq" }, { "type": "string", "label": "n_sequon" }, { "type": "string", "label": "n_sequon_type" } ], [ "P13671-1", "38", "Thr", "G36855WW", "O-linked", "protein_xref_pubmed", "22267737", "protein_xref_pdb4glycans", "3T5O", "3T5O", "pdb_00003t5o", "A", "17", "3T5O_3", "38", "38", "THR", "THR", "T", "", "" ], [ "Q76LX8-1", "399", "Ser", "G36855WW", "O-linked", "protein_xref_pubmed", "23621748", "protein_xref_pdb4glycans", "3VN4", "3VN4", "pdb_00003vn4", "A", "115", "3VN4_3", "399", "399", "SER", "SER", "S", "", "" ] ] }, "readme": "Name\n - Human Glycosylation Sites and Glycans (RCSB PDB)\n\nVersion\n - v-2.9.1\n\nCreated on\n - 2025-07-18T14:47:24\n\nModified on\n - 2025-07-18T15:36:56.744Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Kate Warner [k.warner1@gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The Human Glycosylation Sites and Glycans (RCSB PDB) dataset contains Homo sapiens [taxid:9606] glycosylation sites and associated glycans provided by the RCSB PDB database. Data is retrieved using the RCSB PDB Search API (https://search.rcsb.org/#search-api), Data API (https://data.rcsb.org/index.html#data-api) and Sequence Coordinates Server API (https://sequence-coordinates.rcsb.org/#sequence-coordinates-api). If you use this dataset please provide proper attribution to RCSB PDB and GlyGen.\n\nDescription Domain\n Keywords\n - glycosylation\n - reported glycosylation\n - UniProtKB\n - PubMed\n - DOI\n - GlyTouCan\n - RCSB PDB\n - PDB\n\n Pipeline Steps\n - Step-1: The script retrieves data from RCSB PDB in three steps: (1) their RCSB PDB Search API (https://search.rcsb.org/#search-api) is used to retrieve any PDB structures with glycosylation data for this species, followed by (2) their RCSB PDB Data API (https://data.rcsb.org/index.html#data-api) to retrieve data on the glycosylated structures identified in step one, including data on the PDB glycosite position, GlyTouCan IDs and publications, and then (3) the RCSB PDB Sequence Coordinates Server API (https://sequence-coordinates.rcsb.org/#sequence-coordinates-api) to map the chain glycosites to the full UniProtKB protein sequence. The script then extracts the data from the API responses to create the dataset.\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/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_sequon_info.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/misc/n_sequon_info.csv\n Name: glycosites_rcsb_pdb.csv\n URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/glycosites_rcsb_pdb.csv\n Output Subdomain\n Name: human_proteoform_glycosylation_sites_rcsb_pdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/human_proteoform_glycosylation_sites_rcsb_pdb.csv\n Name: human_proteoform_glycosylation_sites_rcsb_pdb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/human_proteoform_glycosylation_sites_rcsb_pdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"212\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"268\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"3\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"131\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"2\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"3\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"602\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"899\"\n Name: \"pdb_id\"\n Description: \"PDB ID associated with the UniProtKB accession.\"\n Unique Values: \"899\"\n Name: \"pdb_extended_id\"\n Description: \"\"\n Unique Values: \"899\"\n Name: \"amino_acid_chain\"\n Description: \"Amino acid chain in pdb\"\n Unique Values: \"21\"\n Name: \"glycosylation_site_pdb\"\n Description: \"Site on the protein sequence of the PDB entry where glycosylation is observed\"\n Unique Values: \"291\"\n Name: \"pdb_glycan_entity_id\"\n Description: \"\"\n Unique Values: \"1288\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"268\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"268\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"3\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"3\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"3\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"39\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"4\"", "downloadurl": "/ln2data/releases/data/v-2.9.1/reviewed/human_proteoform_glycosylation_sites_rcsb_pdb.csv" }