{"display":true,"structure":{"allele":{"alpha":{"identifier":"uniprot:P01899","locus":"h2-d","match_type":"histo:exact","name":"H2-Db","slug":"h2_db","species_stem":"H2"},"beta":{}},"assemblies":{"1":{"assembly_name":"1hoc_1","chains":["A","B","C"],"downloaded_at":"2022-11-09T14:33:00.556517"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B"],"match_type":"histo:assign_chains","score":1.0,"sequence":"IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM"},"class_i_alpha":{"chains":["A"],"match_type":"histo:assign_chains","score":0.99,"sequence":"GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYWERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEGRDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLLRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTL"},"peptide":{"chains":["C"],"match_type":"histo:classify_peptide","sequence":"ASNENMETM"}},"chronology":{"deposition_date":"1994-01-02","deposition_year":1994,"release_date":"1994-04-30","release_year":1994,"revision_date":"2019-08-14","revision_year":2019},"class":"class_i","classical":true,"complex_type":"class_i_with_peptide","components":["class_i_alpha","beta2m","peptide"],"experimental_method":"X-ray diffraction","facets":{},"ligands":[],"locus":"h2-d","manually_edited":{},"missing_residues":[],"page_title":"1HOC | H2-Db binding \"ASNENMETM\"","pdb_code":"1hoc","pdb_title":"The three-dimensional structure of H-2Db at 2.4 A resolution: implications for antigen-determinant selection.","peptide":{"C":{"actual_length":9,"actual_sequence":"ASNENMETM","chain_id":"C","features":["correct_sequence_and_length"],"full_length":9,"full_sequence":"ASNENMETM"}},"peptide_length":9,"peptide_length_name":"nonamer","peptide_neighbours":{"1":{"neighbours":[{"position":33,"residue":"PHE"},{"position":5,"residue":"MET"},{"position":171,"residue":"TYR"},{"position":159,"residue":"TYR"},{"position":59,"residue":"TYR"},{"position":167,"residue":"TRP"},{"position":66,"residue":"LYS"},{"position":163,"residue":"GLU"},{"position":63,"residue":"GLU"},{"position":7,"residue":"TYR"}],"position":1,"residue":"ALA"},"2":{"neighbours":[{"position":24,"residue":"SER"},{"position":63,"residue":"GLU"},{"position":7,"residue":"TYR"},{"position":159,"residue":"TYR"},{"position":66,"residue":"LYS"},{"position":45,"residue":"TYR"}],"position":2,"residue":"SER"},"3":{"neighbours":[{"position":114,"residue":"LEU"},{"position":70,"residue":"GLN"},{"position":159,"residue":"TYR"},{"position":9,"residue":"GLU"},{"position":155,"residue":"HIS"},{"position":66,"residue":"LYS"},{"position":99,"residue":"SER"},{"position":156,"residue":"TYR"}],"position":3,"residue":"ASN"},"4":{"neighbours":[{"position":156,"residue":"TYR"},{"position":70,"residue":"GLN"},{"position":155,"residue":"HIS"},{"position":66,"residue":"LYS"}],"position":4,"residue":"GLU"},"5":{"neighbours":[{"position":9,"residue":"GLU"},{"position":155,"residue":"HIS"},{"position":97,"residue":"GLN"},{"position":70,"residue":"GLN"},{"position":74,"residue":"PHE"},{"position":156,"residue":"TYR"},{"position":116,"residue":"PHE"},{"position":73,"residue":"TRP"}],"position":5,"residue":"ASN"},"6":{"neighbours":[{"position":156,"residue":"TYR"},{"position":73,"residue":"TRP"},{"position":152,"residue":"ALA"},{"position":155,"residue":"HIS"}],"position":6,"residue":"MET"},"7":{"neighbours":[{"position":150,"residue":"SER"},{"position":146,"residue":"LYS"},{"position":147,"residue":"TRP"},{"position":156,"residue":"TYR"},{"position":73,"residue":"TRP"},{"position":152,"residue":"ALA"}],"position":7,"residue":"GLU"},"8":{"neighbours":[{"position":80,"residue":"ASN"},{"position":146,"residue":"LYS"},{"position":143,"residue":"THR"},{"position":76,"residue":"VAL"},{"position":77,"residue":"SER"},{"position":147,"residue":"TRP"},{"position":73,"residue":"TRP"}],"position":8,"residue":"THR"},"9":{"neighbours":[{"position":142,"residue":"ILE"},{"position":143,"residue":"THR"},{"position":81,"residue":"LEU"},{"position":123,"residue":"TYR"},{"position":146,"residue":"LYS"},{"position":116,"residue":"PHE"},{"position":73,"residue":"TRP"},{"position":95,"residue":"LEU"},{"position":84,"residue":"TYR"},{"position":77,"residue":"SER"},{"position":124,"residue":"ILE"},{"position":147,"residue":"TRP"},{"position":80,"residue":"ASN"}],"position":9,"residue":"MET"}},"peptide_sequence":"ASNENMETM","pockets":{"a":{"a159":{"number":159,"one_letter":"Y","three_letter":"TYR"},"a163":{"number":163,"one_letter":"E","three_letter":"GLU"},"a167":{"number":167,"one_letter":"W","three_letter":"TRP"},"a171":{"number":171,"one_letter":"Y","three_letter":"TYR"},"a5":{"number":5,"one_letter":"M","three_letter":"MET"},"a59":{"number":59,"one_letter":"Y","three_letter":"TYR"},"a63":{"number":63,"one_letter":"E","three_letter":"GLU"},"a66":{"number":66,"one_letter":"K","three_letter":"LYS"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"}},"b":{"a24":{"number":24,"one_letter":"S","three_letter":"SER"},"a34":{"number":34,"one_letter":"V","three_letter":"VAL"},"a45":{"number":45,"one_letter":"Y","three_letter":"TYR"},"a63":{"number":63,"one_letter":"E","three_letter":"GLU"},"a66":{"number":66,"one_letter":"K","three_letter":"LYS"},"a67":{"number":67,"one_letter":"A","three_letter":"ALA"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"},"a70":{"number":70,"one_letter":"Q","three_letter":"GLN"},"a9":{"number":9,"one_letter":"E","three_letter":"GLU"},"a99":{"number":99,"one_letter":"S","three_letter":"SER"}},"c":{"a70":{"number":70,"one_letter":"Q","three_letter":"GLN"},"a73":{"number":73,"one_letter":"W","three_letter":"TRP"},"a74":{"number":74,"one_letter":"F","three_letter":"PHE"},"a9":{"number":9,"one_letter":"E","three_letter":"GLU"},"a97":{"number":97,"one_letter":"Q","three_letter":"GLN"}},"d":{"a114":{"number":114,"one_letter":"L","three_letter":"LEU"},"a155":{"number":155,"one_letter":"H","three_letter":"HIS"},"a156":{"number":156,"one_letter":"Y","three_letter":"TYR"},"a159":{"number":159,"one_letter":"Y","three_letter":"TYR"},"a160":{"number":160,"one_letter":"L","three_letter":"LEU"},"a99":{"number":99,"one_letter":"S","three_letter":"SER"}},"e":{"a114":{"number":114,"one_letter":"L","three_letter":"LEU"},"a147":{"number":147,"one_letter":"W","three_letter":"TRP"},"a152":{"number":152,"one_letter":"A","three_letter":"ALA"},"a156":{"number":156,"one_letter":"Y","three_letter":"TYR"},"a97":{"number":97,"one_letter":"Q","three_letter":"GLN"}},"f":{"a116":{"number":116,"one_letter":"F","three_letter":"PHE"},"a123":{"number":123,"one_letter":"Y","three_letter":"TYR"},"a143":{"number":143,"one_letter":"T","three_letter":"THR"},"a146":{"number":146,"one_letter":"K","three_letter":"LYS"},"a147":{"number":147,"one_letter":"W","three_letter":"TRP"},"a77":{"number":77,"one_letter":"S","three_letter":"SER"},"a80":{"number":80,"one_letter":"N","three_letter":"ASN"},"a81":{"number":81,"one_letter":"L","three_letter":"LEU"},"a84":{"number":84,"one_letter":"Y","three_letter":"TYR"},"a95":{"number":95,"one_letter":"L","three_letter":"LEU"}}},"publication":{"abstract":"Solution at 2.4 A resolution of the structure of H-2Db with the influenza virus peptide NP366-374 (ASNEN-METM) and comparison with the H-2Kb-VSV (RGY-VYQGL) structure allow description of the molecular details of MHC class I peptide binding interactions for mice of the H-2b haplotype, revealing a strategy that maximizes the repertoire of peptides than can be presented. The H-2Db cleft has a mouse-specific hydrophobic ridge that causes a compensatory arch in the backbone of the peptide, exposing the arch residues to TCR contact and requiring the peptide to be at least 9 residues. This ridge occurs in about 40% of the known murine D and L allelic molecules, classifying them as a structural subgroup.","bibjson":{"author":[{"initials":"AC","lastname":"Young","name":"Young AC"},{"initials":"W","lastname":"Zhang","name":"Zhang W"},{"initials":"JC","lastname":"Sacchettini","name":"Sacchettini JC"},{"initials":"SG","lastname":"Nathenson","name":"Nathenson SG"}],"identifier":[{"id":"10.1016/0092-8674(94)90171-6","type":"doi"},{"id":"7506996","type":"pubmed"}],"issue":["1"],"journal":{"iso_abbreviation":"Cell","name":""},"pages":["39-50"],"title":"The three-dimensional structure of H-2Db at 2.4 A resolution: implications for antigen-determinant selection.","type":"article","url":"https://www.sciencedirect.com/science/article/abs/pii/0092867494901716","volume":["76"],"year":[1994]},"in_pmc":"N","in_pmce":"N","open_access":"N"},"resolution":"2.40","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/1hoc"},"rcsb":{"url":"https://www.rcsb.org/structure/1hoc"}},"species":{"common_name":"Mouse","match_type":"histo:assign_species","scientific_name":"Mus musculus","slug":"mus_musculus"},"tcr":null,"title":"H2-Db binding \"ASNENMETM\" at 2.40&#8491; resolution","unique_chain_count":3}}
