data_9A47 # _entry.id 9A47 # loop_ _atom_type.symbol C N O S # loop_ _audit_author.name _audit_author.pdbx_ordinal "Tsai, Y.-X." 1 "Chang, H.-T." 2 "Wang, Y.-S." 3 "Hsu, M.-F." 4 "Hanus, C." 5 "Sikora, M." 6 "Hsu, S.-T.D." 7 # loop_ _audit_conform.dict_location _audit_conform.dict_name _audit_conform.dict_version https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_ihm_ext.dic mmcif_ihm_ext.dic 1.26 http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic mmcif_pdbx.dic 5.395 # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB-Dev PDBDEV_00000228 PDBDEV_00000228 ? PDB 9A47 pdb_00009a47 10.2210/pdb9a47/pdb # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 9A47 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2023-12-16 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2024-05-24 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.type "C3 H7 N O2" 89.094 ALA . ALANINE . "L-peptide linking" "C6 H15 N4 O2 1" 175.212 ARG . ARGININE . "L-peptide linking" "C4 H8 N2 O3" 132.119 ASN . ASPARAGINE . "L-peptide linking" "C4 H7 N O4" 133.103 ASP . "ASPARTIC ACID" . "L-peptide linking" "C6 H12 O6" 180.156 BMA . beta-D-mannopyranose . "D-saccharide, beta linking" "C3 H7 N O2 S" 121.154 CYS . CYSTEINE . "L-peptide linking" "C5 H10 N2 O3" 146.146 GLN . GLUTAMINE . "L-peptide linking" "C5 H9 N O4" 147.13 GLU . "GLUTAMIC ACID" . "L-peptide linking" "C2 H5 N O2" 75.067 GLY . GLYCINE . "peptide linking" "C6 H10 N3 O2 1" 156.165 HIS . HISTIDINE . "L-peptide linking" "C6 H13 N O2" 131.175 ILE . ISOLEUCINE . "L-peptide linking" "C6 H13 N O2" 131.175 LEU . LEUCINE . "L-peptide linking" "C6 H15 N2 O2 1" 147.198 LYS . LYSINE . "L-peptide linking" "C6 H12 O6" 180.156 MAN . alpha-D-mannopyranose . "D-saccharide, alpha linking" "C5 H11 N O2 S" 149.208 MET . METHIONINE . "L-peptide linking" "C8 H15 N O6" 221.209 NAG . 2-acetamido-2-deoxy-beta-D-glucopyranose . "D-saccharide, beta linking" "C9 H11 N O2" 165.192 PHE . PHENYLALANINE . "L-peptide linking" "C5 H9 N O2" 115.132 PRO . PROLINE . "L-peptide linking" "C3 H7 N O3" 105.093 SER . SERINE . "L-peptide linking" "C4 H9 N O3" 119.12 THR . THREONINE . "L-peptide linking" "C11 H12 N2 O2" 204.229 TRP . TRYPTOPHAN . "L-peptide linking" "C9 H11 N O3" 181.191 TYR . TYROSINE . "L-peptide linking" "C5 H11 N O2" 117.148 VAL . VALINE . "L-peptide linking" # loop_ _citation.country _citation.id _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_issue _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year . 1 Cell . . . 5 187 1296 . 10.1016/j.cell.2024.01.034 38428397 "Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries" 2024 . 2 Structure . . . 2 19 244 256 10.1016/j.str.2010.11.016 21300292 "The Extracellular Architecture of Adherens Junctions Revealed by Crystal Structures of Type I Cadherins" 2011 . 3 "Biophys J." . . . 6 80 2946 2953 10.1016/S0006-3495(01)76260-1 11371467 "Determination of domain structure of proteins from X-ray solution scattering." 2001 . 4 " Biophys J." . . . 4 105 962 974 10.1016/j.bpj.2013.07.020 23972848 "Accurate SAXS profile computation and its assessment by contrast variation experiments" 2013 . 5 bioRxiv . . . . . . . 10.1101/2021.08.04.455134 . "GlycoSHIELD: a versatile pipeline to assess glycan impact on protein structures" 2022 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal 1 "Tsai, Y.-X." 1 1 "Chang, N.E." 2 1 "Reuter, K." 3 1 "Chang, H.T." 4 1 "Yang, T.J." 5 1 "von Bulow, S." 6 1 "Sehrawat, V." 7 1 "Zerrouki, N." 8 1 "Tuffery, M." 9 1 "Gecht, M." 10 1 "Grothaus, I.L." 11 1 "Colombi Ciacchi, L." 12 1 "Wang, Y.S." 13 1 "Hsu, M.F." 14 1 "Khoo, K.H." 15 1 "Hummer, G." 16 1 "Hsu, S.D." 17 1 "Hanus, C." 18 1 "Sikora, M." 19 2 "Harrison, O.J." 1 2 "Jin, X." 2 2 "Hong, S." 3 2 "Bahna, F." 4 2 "Ahlsen, G." 5 2 "Brasch, J." 6 2 "Wu, Y." 7 2 "Vendome, J." 8 2 "Felsovalyi, K." 9 2 "Hampton, C.M." 10 2 "Troyanovsky, R.B." 11 2 "Ben-Shaul, A." 12 2 "Frank, J." 13 2 "Troyanovsky, S.M." 14 2 "Shapiro, L." 15 2 "Honig, B." 16 3 "Svergun, D.I." 1 3 "Petoukhov, M.V." 2 3 "Koch, M.H." 3 4 "Schneidman-Duhovny, D." 1 4 "Hammel, M." 2 4 "Tainer, J.A." 3 4 "Sali, A." 4 5 "Gecht, M." 1 5 "von Bulow, S." 2 5 "Penet, C." 3 5 "Hummer, G." 4 5 "Hanus, C." 5 5 "Sikora, M." 6 # loop_ _entity.details _entity.formula_weight _entity.id _entity.pdbx_description _entity.pdbx_number_of_molecules _entity.src_method _entity.type . 27208.803 1 Cadherin-2 1 MAN polymer . 2063.822 2 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose 4 MAN BRANCHED # _entity_poly.entity_id 1 _entity_poly.nstd_chirality . _entity_poly.nstd_linkage NO _entity_poly.nstd_monomer NO _entity_poly.pdbx_seq_one_letter_code DVNENPYFAPNPKIIRQEEGLHAGTMLTTLTAQDPDRYMQQNIRYTKLSDPANWLKIDPVNGQITTIAVLDRESPNVKNNIYNATFLASDNGIPPMSGTGTLQIYLLDINDNAPQVLPQEAETCETPEPNSINITALDYDIDPNAGPFAFDLPLSPVTIKRNWTINRLNGDFAQLNLKIKFEAGIYEVPIIITDSGNPPKSNISILRVKVC _entity_poly.pdbx_seq_one_letter_code_can DVNENPYFAPNPKIIRQEEGLHAGTMLTTLTAQDPDRYMQQNIRYTKLSDPANWLKIDPVNGQITTIAVLDRESPNVKNNIYNATFLASDNGIPPMSGTGTLQIYLLDINDNAPQVLPQEAETCETPEPNSINITALDYDIDPNAGPFAFDLPLSPVTIKRNWTINRLNGDFAQLNLKIKFEAGIYEVPIIITDSGNPPKSNISILRVKVC _entity_poly.pdbx_sequence_evidence_code . _entity_poly.pdbx_strand_id A _entity_poly.type polypeptide(L) # loop_ _entity_poly_seq.entity_id _entity_poly_seq.hetero _entity_poly_seq.mon_id _entity_poly_seq.num 1 . ASP 1 1 . VAL 2 1 . ASN 3 1 . GLU 4 1 . ASN 5 1 . PRO 6 1 . TYR 7 1 . PHE 8 1 . ALA 9 1 . PRO 10 1 . ASN 11 1 . PRO 12 1 . LYS 13 1 . ILE 14 1 . ILE 15 1 . ARG 16 1 . GLN 17 1 . GLU 18 1 . GLU 19 1 . GLY 20 1 . LEU 21 1 . HIS 22 1 . ALA 23 1 . GLY 24 1 . THR 25 1 . MET 26 1 . LEU 27 1 . THR 28 1 . THR 29 1 . LEU 30 1 . THR 31 1 . ALA 32 1 . GLN 33 1 . ASP 34 1 . PRO 35 1 . ASP 36 1 . ARG 37 1 . TYR 38 1 . MET 39 1 . GLN 40 1 . GLN 41 1 . ASN 42 1 . ILE 43 1 . ARG 44 1 . TYR 45 1 . THR 46 1 . LYS 47 1 . LEU 48 1 . SER 49 1 . ASP 50 1 . PRO 51 1 . ALA 52 1 . ASN 53 1 . TRP 54 1 . LEU 55 1 . LYS 56 1 . ILE 57 1 . ASP 58 1 . PRO 59 1 . VAL 60 1 . ASN 61 1 . GLY 62 1 . GLN 63 1 . ILE 64 1 . THR 65 1 . THR 66 1 . ILE 67 1 . ALA 68 1 . VAL 69 1 . LEU 70 1 . ASP 71 1 . ARG 72 1 . GLU 73 1 . SER 74 1 . PRO 75 1 . ASN 76 1 . VAL 77 1 . LYS 78 1 . ASN 79 1 . ASN 80 1 . ILE 81 1 . TYR 82 1 . ASN 83 1 . ALA 84 1 . THR 85 1 . PHE 86 1 . LEU 87 1 . ALA 88 1 . SER 89 1 . ASP 90 1 . ASN 91 1 . GLY 92 1 . ILE 93 1 . PRO 94 1 . PRO 95 1 . MET 96 1 . SER 97 1 . GLY 98 1 . THR 99 1 . GLY 100 1 . THR 101 1 . LEU 102 1 . GLN 103 1 . ILE 104 1 . TYR 105 1 . LEU 106 1 . LEU 107 1 . ASP 108 1 . ILE 109 1 . ASN 110 1 . ASP 111 1 . ASN 112 1 . ALA 113 1 . PRO 114 1 . GLN 115 1 . VAL 116 1 . LEU 117 1 . PRO 118 1 . GLN 119 1 . GLU 120 1 . ALA 121 1 . GLU 122 1 . THR 123 1 . CYS 124 1 . GLU 125 1 . THR 126 1 . PRO 127 1 . GLU 128 1 . PRO 129 1 . ASN 130 1 . SER 131 1 . ILE 132 1 . ASN 133 1 . ILE 134 1 . THR 135 1 . ALA 136 1 . LEU 137 1 . ASP 138 1 . TYR 139 1 . ASP 140 1 . ILE 141 1 . ASP 142 1 . PRO 143 1 . ASN 144 1 . ALA 145 1 . GLY 146 1 . PRO 147 1 . PHE 148 1 . ALA 149 1 . PHE 150 1 . ASP 151 1 . LEU 152 1 . PRO 153 1 . LEU 154 1 . SER 155 1 . PRO 156 1 . VAL 157 1 . THR 158 1 . ILE 159 1 . LYS 160 1 . ARG 161 1 . ASN 162 1 . TRP 163 1 . THR 164 1 . ILE 165 1 . ASN 166 1 . ARG 167 1 . LEU 168 1 . ASN 169 1 . GLY 170 1 . ASP 171 1 . PHE 172 1 . ALA 173 1 . GLN 174 1 . LEU 175 1 . ASN 176 1 . LEU 177 1 . LYS 178 1 . ILE 179 1 . LYS 180 1 . PHE 181 1 . GLU 182 1 . ALA 183 1 . GLY 184 1 . ILE 185 1 . TYR 186 1 . GLU 187 1 . VAL 188 1 . PRO 189 1 . ILE 190 1 . ILE 191 1 . ILE 192 1 . THR 193 1 . ASP 194 1 . SER 195 1 . GLY 196 1 . ASN 197 1 . PRO 198 1 . PRO 199 1 . LYS 200 1 . SER 201 1 . ASN 202 1 . ILE 203 1 . SER 204 1 . ILE 205 1 . LEU 206 1 . ARG 207 1 . VAL 208 1 . LYS 209 1 . VAL 210 1 . CYS 211 # _ihm_dataset_group.application . _ihm_dataset_group.details . _ihm_dataset_group.id 1 _ihm_dataset_group.name . # loop_ _ihm_dataset_group_link.dataset_list_id _ihm_dataset_group_link.group_id 1 1 2 1 # loop_ _ihm_dataset_list.data_type _ihm_dataset_list.database_hosted _ihm_dataset_list.details _ihm_dataset_list.id "SAS data" YES SASDT45 1 "Experimental model" YES 3Q2W 2 # loop_ _ihm_dataset_related_db_reference.accession_code _ihm_dataset_related_db_reference.dataset_list_id _ihm_dataset_related_db_reference.db_name _ihm_dataset_related_db_reference.details _ihm_dataset_related_db_reference.id _ihm_dataset_related_db_reference.version SASDT45 1 SASBDB . 1 . 3Q2W 2 PDB . 2 . # _ihm_ensemble_info.details . _ihm_ensemble_info.ensemble_clustering_feature . _ihm_ensemble_info.ensemble_clustering_method . _ihm_ensemble_info.ensemble_file_id . _ihm_ensemble_info.ensemble_id 1 _ihm_ensemble_info.ensemble_name . _ihm_ensemble_info.ensemble_precision_value . _ihm_ensemble_info.model_group_id 1 _ihm_ensemble_info.num_ensemble_models 20 _ihm_ensemble_info.num_ensemble_models_deposited 20 _ihm_ensemble_info.post_process_id . _ihm_ensemble_info.sub_sample_flag . _ihm_ensemble_info.sub_sampling_type . # _ihm_entity_poly_segment.comp_id_begin ASP _ihm_entity_poly_segment.comp_id_end CYS _ihm_entity_poly_segment.entity_id 1 _ihm_entity_poly_segment.id 1 _ihm_entity_poly_segment.seq_id_begin 1 _ihm_entity_poly_segment.seq_id_end 211 # _ihm_model_group.details . _ihm_model_group.id 1 _ihm_model_group.name . # loop_ _ihm_model_group_link.group_id _ihm_model_group_link.model_id 1 1 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 1 10 1 11 1 12 1 13 1 14 1 15 1 16 1 17 1 18 1 19 1 20 # loop_ _ihm_model_list.assembly_id _ihm_model_list.model_id _ihm_model_list.model_name _ihm_model_list.protocol_id _ihm_model_list.representation_id 1 1 . 1 1 1 2 . 1 1 1 3 . 1 1 1 4 . 1 1 1 5 . 1 1 1 6 . 1 1 1 7 . 1 1 1 8 . 1 1 1 9 . 1 1 1 10 . 1 1 1 11 . 1 1 1 12 . 1 1 1 13 . 1 1 1 14 . 1 1 1 15 . 1 1 1 16 . 1 1 1 17 . 1 1 1 18 . 1 1 1 19 . 1 1 1 20 . 1 1 # _ihm_model_representation.details . _ihm_model_representation.id 1 _ihm_model_representation.name . # loop_ _ihm_model_representation_details.description _ihm_model_representation_details.entity_asym_id _ihm_model_representation_details.entity_description _ihm_model_representation_details.entity_id _ihm_model_representation_details.entity_poly_segment_id _ihm_model_representation_details.id _ihm_model_representation_details.model_granularity _ihm_model_representation_details.model_mode _ihm_model_representation_details.model_object_count _ihm_model_representation_details.model_object_primitive _ihm_model_representation_details.representation_id _ihm_model_representation_details.starting_model_id . A . 1 1 1 by-atom flexible . atomistic 1 1 . B alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose 2 . 2 by-atom flexible . atomistic 1 . . C alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose 2 . 3 by-atom flexible . atomistic 1 . . D alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose 2 . 4 by-atom flexible . atomistic 1 . . E alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose 2 . 5 by-atom flexible . atomistic 1 . # _ihm_model_representative.id 1 _ihm_model_representative.model_group_id 1 _ihm_model_representative.model_id 1 _ihm_model_representative.selection_criteria . # _ihm_modeling_protocol.details . _ihm_modeling_protocol.id 1 _ihm_modeling_protocol.num_steps 1 _ihm_modeling_protocol.protocol_name modeling # _ihm_modeling_protocol_details.dataset_group_id 1 _ihm_modeling_protocol_details.description . _ihm_modeling_protocol_details.ensemble_flag YES _ihm_modeling_protocol_details.id 1 _ihm_modeling_protocol_details.multi_scale_flag NO _ihm_modeling_protocol_details.multi_state_flag NO _ihm_modeling_protocol_details.num_models_begin 1 _ihm_modeling_protocol_details.num_models_end 20 _ihm_modeling_protocol_details.ordered_flag NO _ihm_modeling_protocol_details.protocol_id 1 _ihm_modeling_protocol_details.script_file_id . _ihm_modeling_protocol_details.software_id 1 _ihm_modeling_protocol_details.step_id 1 _ihm_modeling_protocol_details.step_method "Use GlycoSHIELD, the tool we have developed, to graft MD-simulated glycan ensemble onto the ectodomains 4 to 5 of x-ray protein structure (PDB ID: 3Q2W)." _ihm_modeling_protocol_details.step_name . _ihm_modeling_protocol_details.struct_assembly_description . _ihm_modeling_protocol_details.struct_assembly_id 1 # _ihm_sas_restraint.chi_value 20.66 _ihm_sas_restraint.dataset_list_id 1 _ihm_sas_restraint.details SASDT45 _ihm_sas_restraint.fitting_atom_type . _ihm_sas_restraint.fitting_method GASBOR _ihm_sas_restraint.fitting_state Multiple _ihm_sas_restraint.id 1 _ihm_sas_restraint.model_id 1 _ihm_sas_restraint.profile_segment_flag YES _ihm_sas_restraint.radius_of_gyration 33.9 _ihm_sas_restraint.struct_assembly_id 1 # _ihm_starting_model_details.asym_id A _ihm_starting_model_details.dataset_list_id 2 _ihm_starting_model_details.description "The starting model is the same x-ray diffraction data mentioned in the input datasets. PDB id: 3Q2W" _ihm_starting_model_details.entity_description . _ihm_starting_model_details.entity_id 1 _ihm_starting_model_details.entity_poly_segment_id 1 _ihm_starting_model_details.starting_model_auth_asym_id A _ihm_starting_model_details.starting_model_id 1 _ihm_starting_model_details.starting_model_sequence_offset -330 _ihm_starting_model_details.starting_model_source "experimental model" # _ihm_struct_assembly.description "Man9 fully-glycosylated model of mouse N-cadherin EC4-EC5 modeled using SAS and X-ray diffraction" _ihm_struct_assembly.id 1 _ihm_struct_assembly.name "Man9 fully-glycosylated model of mouse N-cadherin EC4-EC5" # loop_ _ihm_struct_assembly_details.assembly_id _ihm_struct_assembly_details.asym_id _ihm_struct_assembly_details.entity_description _ihm_struct_assembly_details.entity_id _ihm_struct_assembly_details.entity_poly_segment_id _ihm_struct_assembly_details.id _ihm_struct_assembly_details.parent_assembly_id 1 A . 1 1 1 1 1 B alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose 2 . 2 1 1 C alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose 2 . 3 1 1 D alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose 2 . 4 1 1 E alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose 2 . 5 1 # loop_ _software.citation_id _software.classification _software.description _software.location _software.name _software.pdbx_ordinal _software.type _software.version 5 "model building" . https://github.com/GlycoSHIELD-MD/GlycoSHIELD-MD GlycoSHIELD 1 . . 3 "model building" . https://www.embl-hamburg.de/biosaxs/gasbor.html GASBOR 2 . . 4 "data analysis" . https://modbase.compbio.ucsf.edu/foxsdock/ FoXSDock 3 . . # _struct.entry_id 9A47 _struct.pdbx_CASP_flag . _struct.pdbx_descriptor . _struct.pdbx_details . _struct.pdbx_model_details . _struct.pdbx_model_type_details . _struct.title "Man9 fully-glycosylated model of mouse N-cadherin EC4-EC5" _struct.pdbx_structure_determination_methodology integrative # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_PDB_id _struct_asym.pdbx_alt_id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.pdbx_order _struct_asym.pdbx_type . 1 A . . . . . . . 2 B . . . . . . . 2 C . . . . . . . 2 D . . . . . . . 2 E . . . . . . # _struct_ref.db_code CADH2_MOUSE _struct_ref.db_name UNP _struct_ref.details . _struct_ref.entity_id 1 _struct_ref.id 1 _struct_ref.pdbx_align_begin 490 _struct_ref.pdbx_db_accession P15116 _struct_ref.pdbx_seq_one_letter_code . # _struct_ref_seq.align_id 1 _struct_ref_seq.db_align_beg 490 _struct_ref_seq.db_align_end 701 _struct_ref_seq.ref_id 1 _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.seq_align_end 211 # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.hetero 2 1 NAG . 2 2 NAG . 2 3 BMA . 2 4 MAN . 2 5 MAN . 2 6 MAN . 2 7 MAN . 2 8 MAN . 2 9 MAN . 2 10 MAN . 2 11 MAN . # # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide # # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code A 1 1 ASP 331 331 ASP ASP A ? A 1 2 VAL 332 332 VAL VAL A ? A 1 3 ASN 333 333 ASN ASN A ? A 1 4 GLU 334 334 GLU GLU A ? A 1 5 ASN 335 335 ASN ASN A ? A 1 6 PRO 336 336 PRO PRO A ? A 1 7 TYR 337 337 TYR TYR A ? A 1 8 PHE 338 338 PHE PHE A ? A 1 9 ALA 339 339 ALA ALA A ? A 1 10 PRO 340 340 PRO PRO A ? A 1 11 ASN 341 341 ASN ASN A ? A 1 12 PRO 342 342 PRO PRO A ? A 1 13 LYS 343 343 LYS LYS A ? A 1 14 ILE 344 344 ILE ILE A ? A 1 15 ILE 345 345 ILE ILE A ? A 1 16 ARG 346 346 ARG ARG A ? A 1 17 GLN 347 347 GLN GLN A ? A 1 18 GLU 348 348 GLU GLU A ? A 1 19 GLU 349 349 GLU GLU A ? A 1 20 GLY 350 350 GLY GLY A ? A 1 21 LEU 351 351 LEU LEU A ? A 1 22 HIS 352 352 HIS HIS A ? A 1 23 ALA 353 353 ALA ALA A ? A 1 24 GLY 354 354 GLY GLY A ? A 1 25 THR 355 355 THR THR A ? A 1 26 MET 356 356 MET MET A ? A 1 27 LEU 357 357 LEU LEU A ? A 1 28 THR 358 358 THR THR A ? A 1 29 THR 359 359 THR THR A ? A 1 30 LEU 360 360 LEU LEU A ? A 1 31 THR 361 361 THR THR A ? A 1 32 ALA 362 362 ALA ALA A ? A 1 33 GLN 363 363 GLN GLN A ? A 1 34 ASP 364 364 ASP ASP A ? A 1 35 PRO 365 365 PRO PRO A ? A 1 36 ASP 366 366 ASP ASP A ? A 1 37 ARG 367 367 ARG ARG A ? A 1 38 TYR 368 368 TYR TYR A ? A 1 39 MET 369 369 MET MET A ? A 1 40 GLN 370 370 GLN GLN A ? A 1 41 GLN 371 371 GLN GLN A ? A 1 42 ASN 372 372 ASN ASN A ? A 1 43 ILE 373 373 ILE ILE A ? A 1 44 ARG 374 374 ARG ARG A ? A 1 45 TYR 375 375 TYR TYR A ? A 1 46 THR 376 376 THR THR A ? A 1 47 LYS 377 377 LYS LYS A ? A 1 48 LEU 378 378 LEU LEU A ? A 1 49 SER 379 379 SER SER A ? A 1 50 ASP 380 380 ASP ASP A ? A 1 51 PRO 381 381 PRO PRO A ? A 1 52 ALA 382 382 ALA ALA A ? A 1 53 ASN 383 383 ASN ASN A ? A 1 54 TRP 384 384 TRP TRP A ? A 1 55 LEU 385 385 LEU LEU A ? A 1 56 LYS 386 386 LYS LYS A ? A 1 57 ILE 387 387 ILE ILE A ? A 1 58 ASP 388 388 ASP ASP A ? A 1 59 PRO 389 389 PRO PRO A ? A 1 60 VAL 390 390 VAL VAL A ? A 1 61 ASN 391 391 ASN ASN A ? A 1 62 GLY 392 392 GLY GLY A ? A 1 63 GLN 393 393 GLN GLN A ? A 1 64 ILE 394 394 ILE ILE A ? A 1 65 THR 395 395 THR THR A ? A 1 66 THR 396 396 THR THR A ? A 1 67 ILE 397 397 ILE ILE A ? A 1 68 ALA 398 398 ALA ALA A ? A 1 69 VAL 399 399 VAL VAL A ? A 1 70 LEU 400 400 LEU LEU A ? A 1 71 ASP 401 401 ASP ASP A ? A 1 72 ARG 402 402 ARG ARG A ? A 1 73 GLU 403 403 GLU GLU A ? A 1 74 SER 404 404 SER SER A ? A 1 75 PRO 405 405 PRO PRO A ? A 1 76 ASN 406 406 ASN ASN A ? A 1 77 VAL 407 407 VAL VAL A ? A 1 78 LYS 408 408 LYS LYS A ? A 1 79 ASN 409 409 ASN ASN A ? A 1 80 ASN 410 410 ASN ASN A ? A 1 81 ILE 411 411 ILE ILE A ? A 1 82 TYR 412 412 TYR TYR A ? A 1 83 ASN 413 413 ASN ASN A ? A 1 84 ALA 414 414 ALA ALA A ? A 1 85 THR 415 415 THR THR A ? A 1 86 PHE 416 416 PHE PHE A ? A 1 87 LEU 417 417 LEU LEU A ? A 1 88 ALA 418 418 ALA ALA A ? A 1 89 SER 419 419 SER SER A ? A 1 90 ASP 420 420 ASP ASP A ? A 1 91 ASN 421 421 ASN ASN A ? A 1 92 GLY 422 422 GLY GLY A ? A 1 93 ILE 423 423 ILE ILE A ? A 1 94 PRO 424 424 PRO PRO A ? A 1 95 PRO 425 425 PRO PRO A ? A 1 96 MET 426 426 MET MET A ? A 1 97 SER 427 427 SER SER A ? A 1 98 GLY 428 428 GLY GLY A ? A 1 99 THR 429 429 THR THR A ? A 1 100 GLY 430 430 GLY GLY A ? A 1 101 THR 431 431 THR THR A ? A 1 102 LEU 432 432 LEU LEU A ? A 1 103 GLN 433 433 GLN GLN A ? A 1 104 ILE 434 434 ILE ILE A ? A 1 105 TYR 435 435 TYR TYR A ? A 1 106 LEU 436 436 LEU LEU A ? A 1 107 LEU 437 437 LEU LEU A ? A 1 108 ASP 438 438 ASP ASP A ? A 1 109 ILE 439 439 ILE ILE A ? A 1 110 ASN 440 440 ASN ASN A ? A 1 111 ASP 441 441 ASP ASP A ? A 1 112 ASN 442 442 ASN ASN A ? A 1 113 ALA 443 443 ALA ALA A ? A 1 114 PRO 444 444 PRO PRO A ? A 1 115 GLN 445 445 GLN GLN A ? A 1 116 VAL 446 446 VAL VAL A ? A 1 117 LEU 447 447 LEU LEU A ? A 1 118 PRO 448 448 PRO PRO A ? A 1 119 GLN 449 449 GLN GLN A ? A 1 120 GLU 450 450 GLU GLU A ? A 1 121 ALA 451 451 ALA ALA A ? A 1 122 GLU 452 452 GLU GLU A ? A 1 123 THR 453 453 THR THR A ? A 1 124 CYS 454 454 CYS CYS A ? A 1 125 GLU 455 455 GLU GLU A ? A 1 126 THR 456 456 THR THR A ? A 1 127 PRO 457 457 PRO PRO A ? A 1 128 GLU 458 458 GLU GLU A ? A 1 129 PRO 459 459 PRO PRO A ? A 1 130 ASN 460 460 ASN ASN A ? A 1 131 SER 461 461 SER SER A ? A 1 132 ILE 462 462 ILE ILE A ? A 1 133 ASN 463 463 ASN ASN A ? A 1 134 ILE 464 464 ILE ILE A ? A 1 135 THR 465 465 THR THR A ? A 1 136 ALA 466 466 ALA ALA A ? A 1 137 LEU 467 467 LEU LEU A ? A 1 138 ASP 468 468 ASP ASP A ? A 1 139 TYR 469 469 TYR TYR A ? A 1 140 ASP 470 470 ASP ASP A ? A 1 141 ILE 471 471 ILE ILE A ? A 1 142 ASP 472 472 ASP ASP A ? A 1 143 PRO 473 473 PRO PRO A ? A 1 144 ASN 474 474 ASN ASN A ? A 1 145 ALA 475 475 ALA ALA A ? A 1 146 GLY 476 476 GLY GLY A ? A 1 147 PRO 477 477 PRO PRO A ? A 1 148 PHE 478 478 PHE PHE A ? A 1 149 ALA 479 479 ALA ALA A ? A 1 150 PHE 480 480 PHE PHE A ? A 1 151 ASP 481 481 ASP ASP A ? A 1 152 LEU 482 482 LEU LEU A ? A 1 153 PRO 483 483 PRO PRO A ? A 1 154 LEU 484 484 LEU LEU A ? A 1 155 SER 485 485 SER SER A ? A 1 156 PRO 486 486 PRO PRO A ? A 1 157 VAL 487 487 VAL VAL A ? A 1 158 THR 488 488 THR THR A ? A 1 159 ILE 489 489 ILE ILE A ? A 1 160 LYS 490 490 LYS LYS A ? A 1 161 ARG 491 491 ARG ARG A ? A 1 162 ASN 492 492 ASN ASN A ? A 1 163 TRP 493 493 TRP TRP A ? A 1 164 THR 494 494 THR THR A ? A 1 165 ILE 495 495 ILE ILE A ? A 1 166 ASN 496 496 ASN ASN A ? A 1 167 ARG 497 497 ARG ARG A ? A 1 168 LEU 498 498 LEU LEU A ? A 1 169 ASN 499 499 ASN ASN A ? A 1 170 GLY 500 500 GLY GLY A ? A 1 171 ASP 501 501 ASP ASP A ? A 1 172 PHE 502 502 PHE PHE A ? A 1 173 ALA 503 503 ALA ALA A ? A 1 174 GLN 504 504 GLN GLN A ? A 1 175 LEU 505 505 LEU LEU A ? A 1 176 ASN 506 506 ASN ASN A ? A 1 177 LEU 507 507 LEU LEU A ? A 1 178 LYS 508 508 LYS LYS A ? A 1 179 ILE 509 509 ILE ILE A ? A 1 180 LYS 510 510 LYS LYS A ? A 1 181 PHE 511 511 PHE PHE A ? A 1 182 GLU 513 513 GLU GLU A ? A 1 183 ALA 514 514 ALA ALA A ? A 1 184 GLY 515 515 GLY GLY A ? A 1 185 ILE 516 516 ILE ILE A ? A 1 186 TYR 517 517 TYR TYR A ? A 1 187 GLU 518 518 GLU GLU A ? A 1 188 VAL 519 519 VAL VAL A ? A 1 189 PRO 520 520 PRO PRO A ? A 1 190 ILE 521 521 ILE ILE A ? A 1 191 ILE 522 522 ILE ILE A ? A 1 192 ILE 523 523 ILE ILE A ? A 1 193 THR 524 524 THR THR A ? A 1 194 ASP 525 525 ASP ASP A ? A 1 195 SER 526 526 SER SER A ? A 1 196 GLY 527 527 GLY GLY A ? A 1 197 ASN 528 528 ASN ASN A ? A 1 198 PRO 529 529 PRO PRO A ? A 1 199 PRO 530 530 PRO PRO A ? A 1 200 LYS 531 531 LYS LYS A ? A 1 201 SER 532 532 SER SER A ? A 1 202 ASN 533 533 ASN ASN A ? A 1 203 ILE 534 534 ILE ILE A ? A 1 204 SER 535 535 SER SER A ? A 1 205 ILE 536 536 ILE ILE A ? A 1 206 LEU 537 537 LEU LEU A ? A 1 207 ARG 538 538 ARG ARG A ? A 1 208 VAL 539 539 VAL VAL A ? A 1 209 LYS 540 540 LYS LYS A ? A 1 210 VAL 541 541 VAL VAL A ? A 1 211 CYS 542 542 CYS CYS A ? # # loop_ _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_ins_code _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.pdb_asym_id B 2 NAG 1 1 . 565 NAG NAG B B 2 NAG 2 2 . 566 NAG NAG B B 2 BMA 3 3 . 567 BMA BMA B B 2 MAN 4 4 . 568 MAN MAN B B 2 MAN 5 5 . 569 MAN MAN B B 2 MAN 6 6 . 570 MAN MAN B B 2 MAN 7 7 . 571 MAN MAN B B 2 MAN 8 8 . 572 MAN MAN B B 2 MAN 9 9 . 573 MAN MAN B B 2 MAN 10 10 . 574 MAN MAN B B 2 MAN 11 11 . 575 MAN MAN B C 2 NAG 1 1 . 543 NAG NAG C C 2 NAG 2 2 . 544 NAG NAG C C 2 BMA 3 3 . 545 BMA BMA C C 2 MAN 4 4 . 546 MAN MAN C C 2 MAN 5 5 . 547 MAN MAN C C 2 MAN 6 6 . 548 MAN MAN C C 2 MAN 7 7 . 549 MAN MAN C C 2 MAN 8 8 . 550 MAN MAN C C 2 MAN 9 9 . 551 MAN MAN C C 2 MAN 10 10 . 552 MAN MAN C C 2 MAN 11 11 . 553 MAN MAN C D 2 NAG 1 1 . 576 NAG NAG D D 2 NAG 2 2 . 577 NAG NAG D D 2 BMA 3 3 . 578 BMA BMA D D 2 MAN 4 4 . 579 MAN MAN D D 2 MAN 5 5 . 580 MAN MAN D D 2 MAN 6 6 . 581 MAN MAN D D 2 MAN 7 7 . 582 MAN MAN D D 2 MAN 8 8 . 583 MAN MAN D D 2 MAN 9 9 . 584 MAN MAN D D 2 MAN 10 10 . 585 MAN MAN D D 2 MAN 11 11 . 586 MAN MAN D E 2 NAG 1 1 . 554 NAG NAG E E 2 NAG 2 2 . 555 NAG NAG E E 2 BMA 3 3 . 556 BMA BMA E E 2 MAN 4 4 . 557 MAN MAN E E 2 MAN 5 5 . 558 MAN MAN E E 2 MAN 6 6 . 559 MAN MAN E E 2 MAN 7 7 . 560 MAN MAN E E 2 MAN 8 8 . 561 MAN MAN E E 2 MAN 9 9 . 562 MAN MAN E E 2 MAN 10 10 . 563 MAN MAN E E 2 MAN 11 11 . 564 MAN MAN E # # loop_ _pdbx_entity_branch_descriptor.ordinal _pdbx_entity_branch_descriptor.entity_id _pdbx_entity_branch_descriptor.descriptor _pdbx_entity_branch_descriptor.type _pdbx_entity_branch_descriptor.program _pdbx_entity_branch_descriptor.program_version 1 2 DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH 'Glycam Condensed Sequence' GMML 1.0 2 2 '[][D-1,2-deoxy-Glcp]{[(4+1)][b-D-2-deoxy-Glcp]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}' LINUCS PDB-CARE ? # # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.value_order _pdbx_entity_branch_link.details 1 2 2 NAG C1 O1 1 NAG O4 HO4 sing ? 2 2 3 BMA C1 O1 2 NAG O4 HO4 sing ? 3 2 4 MAN C1 O1 3 BMA O3 HO3 sing ? 4 2 5 MAN C1 O1 4 MAN O2 HO2 sing ? 5 2 6 MAN C1 O1 5 MAN O2 HO2 sing ? 6 2 7 MAN C1 O1 3 BMA O6 HO6 sing ? 7 2 8 MAN C1 O1 7 MAN O3 HO3 sing ? 8 2 9 MAN C1 O1 8 MAN O2 HO2 sing ? 9 2 10 MAN C1 O1 7 MAN O6 HO6 sing ? 10 2 11 MAN C1 O1 10 MAN O2 HO2 sing ? # # loop_ # #