data_7WP5 # _entry.id 7WP5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.397 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 7WP5 pdb_00007wp5 10.2210/pdb7wp5/pdb WWPDB D_1300027170 ? ? EMDB EMD-32669 ? ? # 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 2022-07-13 2 'Structure model' 1 1 2024-10-16 # _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 ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 2 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' em_admin 4 2 'Structure model' pdbx_entry_details 5 2 'Structure model' pdbx_modification_feature # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_em_admin.last_update' 2 2 'Structure model' '_pdbx_entry_details.has_protein_modification' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7WP5 _pdbx_database_status.recvd_initial_deposition_date 2022-01-22 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Cryo-EM structure of SARS-CoV-2 Omicron S6P trimer in complex with neutralizing antibody VacW-209 (local refinement)' _pdbx_database_related.db_id EMD-32669 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 2 _pdbx_contact_author.email shaowei@xmu.edu.cn _pdbx_contact_author.name_first Shaowei _pdbx_contact_author.name_last Li _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-3374-1038 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Zheng, Q.' 1 ? 'Sun, H.' 2 ? 'Ju, B.' 3 ? 'Zhang, Z.' 4 ? 'Li, S.' 5 ? 'Xia, N.' 6 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country CN _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Cell Res.' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1001-0602 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 32 _citation.language ? _citation.page_first 491 _citation.page_last 494 _citation.title ;Immune escape by SARS-CoV-2 Omicron variant and structural basis of its effective neutralization by a broad neutralizing human antibody VacW-209. ; _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41422-022-00638-6 _citation.pdbx_database_id_PubMed 35260792 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ju, B.' 1 ? primary 'Zheng, Q.' 2 0000-0002-7516-9965 primary 'Guo, H.' 3 ? primary 'Fan, Q.' 4 ? primary 'Li, T.' 5 0000-0002-9917-7804 primary 'Song, S.' 6 0000-0002-0289-2941 primary 'Sun, H.' 7 ? primary 'Shen, S.' 8 ? primary 'Zhou, X.' 9 ? primary 'Xue, W.' 10 ? primary 'Cui, L.' 11 ? primary 'Zhou, B.' 12 ? primary 'Li, S.' 13 0000-0002-3374-1038 primary 'Xia, N.' 14 0000-0003-0179-5266 primary 'Zhang, Z.' 15 0000-0002-3544-1389 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'VacW-209 light chain' 11514.575 1 ? ? ? ? 2 polymer man 'VacW-209 heavy chain' 14460.097 1 ? ? ? ? 3 polymer man 'Spikeprotein S1' 21638.412 1 ? ? ? ? 4 branched man '2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose' 424.401 1 ? ? ? ? # _entity_name_com.entity_id 3 _entity_name_com.name 'S glycoprotein,E2,Peplomer protein' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no ;QSVLTQPPSVSGAPGQRVTISCTGSSSNIGAGYDVHWYQQLPGTAPKLLIYGNSNRPSGVPDRFSGSKSGTSASLAITGL QAEDEADYYCQSYDSSLSGWVFGGGTKLTVL ; ;QSVLTQPPSVSGAPGQRVTISCTGSSSNIGAGYDVHWYQQLPGTAPKLLIYGNSNRPSGVPDRFSGSKSGTSASLAITGL QAEDEADYYCQSYDSSLSGWVFGGGTKLTVL ; L ? 2 'polypeptide(L)' no no ;QVQLVESGGGVVQPGRSLRLSCAASGFTFSSIAMHWVRQAPGKGLEWVAVMSFDGSIKYYGDSVKGRFTISRDNSKSTLY LQMNSLRAEDTAVYYCARGVQGYYDRSGYYNLDYNYGMDVWGQGTTVTVSS ; ;QVQLVESGGGVVQPGRSLRLSCAASGFTFSSIAMHWVRQAPGKGLEWVAVMSFDGSIKYYGDSVKGRFTISRDNSKSTLY LQMNSLRAEDTAVYYCARGVQGYYDRSGYYNLDYNYGMDVWGQGTTVTVSS ; H ? 3 'polypeptide(L)' no no ;TNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAP GQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPL RSYSFRPTYGVGHQPYRVVVLSFELLHAP ; ;TNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAP GQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPL RSYSFRPTYGVGHQPYRVVVLSFELLHAP ; F ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLN n 1 2 SER n 1 3 VAL n 1 4 LEU n 1 5 THR n 1 6 GLN n 1 7 PRO n 1 8 PRO n 1 9 SER n 1 10 VAL n 1 11 SER n 1 12 GLY n 1 13 ALA n 1 14 PRO n 1 15 GLY n 1 16 GLN n 1 17 ARG n 1 18 VAL n 1 19 THR n 1 20 ILE n 1 21 SER n 1 22 CYS n 1 23 THR n 1 24 GLY n 1 25 SER n 1 26 SER n 1 27 SER n 1 28 ASN n 1 29 ILE n 1 30 GLY n 1 31 ALA n 1 32 GLY n 1 33 TYR n 1 34 ASP n 1 35 VAL n 1 36 HIS n 1 37 TRP n 1 38 TYR n 1 39 GLN n 1 40 GLN n 1 41 LEU n 1 42 PRO n 1 43 GLY n 1 44 THR n 1 45 ALA n 1 46 PRO n 1 47 LYS n 1 48 LEU n 1 49 LEU n 1 50 ILE n 1 51 TYR n 1 52 GLY n 1 53 ASN n 1 54 SER n 1 55 ASN n 1 56 ARG n 1 57 PRO n 1 58 SER n 1 59 GLY n 1 60 VAL n 1 61 PRO n 1 62 ASP n 1 63 ARG n 1 64 PHE n 1 65 SER n 1 66 GLY n 1 67 SER n 1 68 LYS n 1 69 SER n 1 70 GLY n 1 71 THR n 1 72 SER n 1 73 ALA n 1 74 SER n 1 75 LEU n 1 76 ALA n 1 77 ILE n 1 78 THR n 1 79 GLY n 1 80 LEU n 1 81 GLN n 1 82 ALA n 1 83 GLU n 1 84 ASP n 1 85 GLU n 1 86 ALA n 1 87 ASP n 1 88 TYR n 1 89 TYR n 1 90 CYS n 1 91 GLN n 1 92 SER n 1 93 TYR n 1 94 ASP n 1 95 SER n 1 96 SER n 1 97 LEU n 1 98 SER n 1 99 GLY n 1 100 TRP n 1 101 VAL n 1 102 PHE n 1 103 GLY n 1 104 GLY n 1 105 GLY n 1 106 THR n 1 107 LYS n 1 108 LEU n 1 109 THR n 1 110 VAL n 1 111 LEU n 2 1 GLN n 2 2 VAL n 2 3 GLN n 2 4 LEU n 2 5 VAL n 2 6 GLU n 2 7 SER n 2 8 GLY n 2 9 GLY n 2 10 GLY n 2 11 VAL n 2 12 VAL n 2 13 GLN n 2 14 PRO n 2 15 GLY n 2 16 ARG n 2 17 SER n 2 18 LEU n 2 19 ARG n 2 20 LEU n 2 21 SER n 2 22 CYS n 2 23 ALA n 2 24 ALA n 2 25 SER n 2 26 GLY n 2 27 PHE n 2 28 THR n 2 29 PHE n 2 30 SER n 2 31 SER n 2 32 ILE n 2 33 ALA n 2 34 MET n 2 35 HIS n 2 36 TRP n 2 37 VAL n 2 38 ARG n 2 39 GLN n 2 40 ALA n 2 41 PRO n 2 42 GLY n 2 43 LYS n 2 44 GLY n 2 45 LEU n 2 46 GLU n 2 47 TRP n 2 48 VAL n 2 49 ALA n 2 50 VAL n 2 51 MET n 2 52 SER n 2 53 PHE n 2 54 ASP n 2 55 GLY n 2 56 SER n 2 57 ILE n 2 58 LYS n 2 59 TYR n 2 60 TYR n 2 61 GLY n 2 62 ASP n 2 63 SER n 2 64 VAL n 2 65 LYS n 2 66 GLY n 2 67 ARG n 2 68 PHE n 2 69 THR n 2 70 ILE n 2 71 SER n 2 72 ARG n 2 73 ASP n 2 74 ASN n 2 75 SER n 2 76 LYS n 2 77 SER n 2 78 THR n 2 79 LEU n 2 80 TYR n 2 81 LEU n 2 82 GLN n 2 83 MET n 2 84 ASN n 2 85 SER n 2 86 LEU n 2 87 ARG n 2 88 ALA n 2 89 GLU n 2 90 ASP n 2 91 THR n 2 92 ALA n 2 93 VAL n 2 94 TYR n 2 95 TYR n 2 96 CYS n 2 97 ALA n 2 98 ARG n 2 99 GLY n 2 100 VAL n 2 101 GLN n 2 102 GLY n 2 103 TYR n 2 104 TYR n 2 105 ASP n 2 106 ARG n 2 107 SER n 2 108 GLY n 2 109 TYR n 2 110 TYR n 2 111 ASN n 2 112 LEU n 2 113 ASP n 2 114 TYR n 2 115 ASN n 2 116 TYR n 2 117 GLY n 2 118 MET n 2 119 ASP n 2 120 VAL n 2 121 TRP n 2 122 GLY n 2 123 GLN n 2 124 GLY n 2 125 THR n 2 126 THR n 2 127 VAL n 2 128 THR n 2 129 VAL n 2 130 SER n 2 131 SER n 3 1 THR n 3 2 ASN n 3 3 LEU n 3 4 CYS n 3 5 PRO n 3 6 PHE n 3 7 ASP n 3 8 GLU n 3 9 VAL n 3 10 PHE n 3 11 ASN n 3 12 ALA n 3 13 THR n 3 14 ARG n 3 15 PHE n 3 16 ALA n 3 17 SER n 3 18 VAL n 3 19 TYR n 3 20 ALA n 3 21 TRP n 3 22 ASN n 3 23 ARG n 3 24 LYS n 3 25 ARG n 3 26 ILE n 3 27 SER n 3 28 ASN n 3 29 CYS n 3 30 VAL n 3 31 ALA n 3 32 ASP n 3 33 TYR n 3 34 SER n 3 35 VAL n 3 36 LEU n 3 37 TYR n 3 38 ASN n 3 39 LEU n 3 40 ALA n 3 41 PRO n 3 42 PHE n 3 43 PHE n 3 44 THR n 3 45 PHE n 3 46 LYS n 3 47 CYS n 3 48 TYR n 3 49 GLY n 3 50 VAL n 3 51 SER n 3 52 PRO n 3 53 THR n 3 54 LYS n 3 55 LEU n 3 56 ASN n 3 57 ASP n 3 58 LEU n 3 59 CYS n 3 60 PHE n 3 61 THR n 3 62 ASN n 3 63 VAL n 3 64 TYR n 3 65 ALA n 3 66 ASP n 3 67 SER n 3 68 PHE n 3 69 VAL n 3 70 ILE n 3 71 ARG n 3 72 GLY n 3 73 ASP n 3 74 GLU n 3 75 VAL n 3 76 ARG n 3 77 GLN n 3 78 ILE n 3 79 ALA n 3 80 PRO n 3 81 GLY n 3 82 GLN n 3 83 THR n 3 84 GLY n 3 85 ASN n 3 86 ILE n 3 87 ALA n 3 88 ASP n 3 89 TYR n 3 90 ASN n 3 91 TYR n 3 92 LYS n 3 93 LEU n 3 94 PRO n 3 95 ASP n 3 96 ASP n 3 97 PHE n 3 98 THR n 3 99 GLY n 3 100 CYS n 3 101 VAL n 3 102 ILE n 3 103 ALA n 3 104 TRP n 3 105 ASN n 3 106 SER n 3 107 ASN n 3 108 LYS n 3 109 LEU n 3 110 ASP n 3 111 SER n 3 112 LYS n 3 113 VAL n 3 114 SER n 3 115 GLY n 3 116 ASN n 3 117 TYR n 3 118 ASN n 3 119 TYR n 3 120 LEU n 3 121 TYR n 3 122 ARG n 3 123 LEU n 3 124 PHE n 3 125 ARG n 3 126 LYS n 3 127 SER n 3 128 ASN n 3 129 LEU n 3 130 LYS n 3 131 PRO n 3 132 PHE n 3 133 GLU n 3 134 ARG n 3 135 ASP n 3 136 ILE n 3 137 SER n 3 138 THR n 3 139 GLU n 3 140 ILE n 3 141 TYR n 3 142 GLN n 3 143 ALA n 3 144 GLY n 3 145 ASN n 3 146 LYS n 3 147 PRO n 3 148 CYS n 3 149 ASN n 3 150 GLY n 3 151 VAL n 3 152 ALA n 3 153 GLY n 3 154 PHE n 3 155 ASN n 3 156 CYS n 3 157 TYR n 3 158 PHE n 3 159 PRO n 3 160 LEU n 3 161 ARG n 3 162 SER n 3 163 TYR n 3 164 SER n 3 165 PHE n 3 166 ARG n 3 167 PRO n 3 168 THR n 3 169 TYR n 3 170 GLY n 3 171 VAL n 3 172 GLY n 3 173 HIS n 3 174 GLN n 3 175 PRO n 3 176 TYR n 3 177 ARG n 3 178 VAL n 3 179 VAL n 3 180 VAL n 3 181 LEU n 3 182 SER n 3 183 PHE n 3 184 GLU n 3 185 LEU n 3 186 LEU n 3 187 HIS n 3 188 ALA n 3 189 PRO n # loop_ _entity_src_gen.entity_id _entity_src_gen.pdbx_src_id _entity_src_gen.pdbx_alt_source_flag _entity_src_gen.pdbx_seq_type _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.gene_src_species _entity_src_gen.gene_src_strain _entity_src_gen.gene_src_tissue _entity_src_gen.gene_src_tissue_fraction _entity_src_gen.gene_src_details _entity_src_gen.pdbx_gene_src_fragment _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_variant _entity_src_gen.pdbx_gene_src_cell_line _entity_src_gen.pdbx_gene_src_atcc _entity_src_gen.pdbx_gene_src_organ _entity_src_gen.pdbx_gene_src_organelle _entity_src_gen.pdbx_gene_src_cell _entity_src_gen.pdbx_gene_src_cellular_location _entity_src_gen.host_org_common_name _entity_src_gen.pdbx_host_org_scientific_name _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_gen.host_org_genus _entity_src_gen.pdbx_host_org_gene _entity_src_gen.pdbx_host_org_organ _entity_src_gen.host_org_species _entity_src_gen.pdbx_host_org_tissue _entity_src_gen.pdbx_host_org_tissue_fraction _entity_src_gen.pdbx_host_org_strain _entity_src_gen.pdbx_host_org_variant _entity_src_gen.pdbx_host_org_cell_line _entity_src_gen.pdbx_host_org_atcc _entity_src_gen.pdbx_host_org_culture_collection _entity_src_gen.pdbx_host_org_cell _entity_src_gen.pdbx_host_org_organelle _entity_src_gen.pdbx_host_org_cellular_location _entity_src_gen.pdbx_host_org_vector_type _entity_src_gen.pdbx_host_org_vector _entity_src_gen.host_org_details _entity_src_gen.expression_system_id _entity_src_gen.plasmid_name _entity_src_gen.plasmid_details _entity_src_gen.pdbx_description 1 1 sample 'Biological sequence' 1 111 human ? ? ? ? ? ? ? ? 'Homo sapiens' 9606 ? ? ? ? ? ? ? ? 'Homo sapiens' 9606 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 sample 'Biological sequence' 1 131 ? ? ? ? ? ? ? ? ? 'Homo sapiens' 9606 ? ? ? ? ? ? ? ? 'Homo sapiens' 9606 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 3 1 sample 'Biological sequence' 1 189 ? ? 'S, 2' ? ? ? ? ? ? 'Severe acute respiratory syndrome coronavirus 2' 2697049 ? ? ? ? ? ? ? ? 'Homo sapiens' 9606 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # 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 4 DGlcpNAcb1-4DGlcpNAcb1-ROH 'Glycam Condensed Sequence' GMML 1.0 2 4 'WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1' WURCS PDB2Glycan 1.1.0 3 4 '[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}' LINUCS PDB-CARE ? # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.value_order sing _pdbx_entity_branch_link.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 NAG 'D-saccharide, beta linking' . 2-acetamido-2-deoxy-beta-D-glucopyranose ;N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE ; 'C8 H15 N O6' 221.208 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier NAG 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpNAcb NAG 'COMMON NAME' GMML 1.0 N-acetyl-b-D-glucopyranosamine NAG 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpNAc NAG 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcNAc # 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.ndb_seq_num _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 _pdbx_poly_seq_scheme.hetero A 1 1 GLN 1 1 1 GLN GLN L . n A 1 2 SER 2 2 2 SER SER L . n A 1 3 VAL 3 3 3 VAL VAL L . n A 1 4 LEU 4 4 4 LEU LEU L . n A 1 5 THR 5 5 5 THR THR L . n A 1 6 GLN 6 6 6 GLN GLN L . n A 1 7 PRO 7 7 7 PRO PRO L . n A 1 8 PRO 8 8 8 PRO PRO L . n A 1 9 SER 9 9 9 SER SER L . n A 1 10 VAL 10 10 10 VAL VAL L . n A 1 11 SER 11 11 11 SER SER L . n A 1 12 GLY 12 12 12 GLY GLY L . n A 1 13 ALA 13 13 13 ALA ALA L . n A 1 14 PRO 14 14 14 PRO PRO L . n A 1 15 GLY 15 15 15 GLY GLY L . n A 1 16 GLN 16 16 16 GLN GLN L . n A 1 17 ARG 17 17 17 ARG ARG L . n A 1 18 VAL 18 18 18 VAL VAL L . n A 1 19 THR 19 19 19 THR THR L . n A 1 20 ILE 20 20 20 ILE ILE L . n A 1 21 SER 21 21 21 SER SER L . n A 1 22 CYS 22 22 22 CYS CYS L . n A 1 23 THR 23 23 23 THR THR L . n A 1 24 GLY 24 24 24 GLY GLY L . n A 1 25 SER 25 25 25 SER SER L . n A 1 26 SER 26 26 26 SER SER L . n A 1 27 SER 27 27 27 SER SER L . n A 1 28 ASN 28 28 28 ASN ASN L . n A 1 29 ILE 29 29 29 ILE ILE L . n A 1 30 GLY 30 30 30 GLY GLY L . n A 1 31 ALA 31 31 31 ALA ALA L . n A 1 32 GLY 32 32 32 GLY GLY L . n A 1 33 TYR 33 33 33 TYR TYR L . n A 1 34 ASP 34 34 34 ASP ASP L . n A 1 35 VAL 35 35 35 VAL VAL L . n A 1 36 HIS 36 36 36 HIS HIS L . n A 1 37 TRP 37 37 37 TRP TRP L . n A 1 38 TYR 38 38 38 TYR TYR L . n A 1 39 GLN 39 39 39 GLN GLN L . n A 1 40 GLN 40 40 40 GLN GLN L . n A 1 41 LEU 41 41 41 LEU LEU L . n A 1 42 PRO 42 42 42 PRO PRO L . n A 1 43 GLY 43 43 43 GLY GLY L . n A 1 44 THR 44 44 44 THR THR L . n A 1 45 ALA 45 45 45 ALA ALA L . n A 1 46 PRO 46 46 46 PRO PRO L . n A 1 47 LYS 47 47 47 LYS LYS L . n A 1 48 LEU 48 48 48 LEU LEU L . n A 1 49 LEU 49 49 49 LEU LEU L . n A 1 50 ILE 50 50 50 ILE ILE L . n A 1 51 TYR 51 51 51 TYR TYR L . n A 1 52 GLY 52 52 52 GLY GLY L . n A 1 53 ASN 53 53 53 ASN ASN L . n A 1 54 SER 54 54 54 SER SER L . n A 1 55 ASN 55 55 55 ASN ASN L . n A 1 56 ARG 56 56 56 ARG ARG L . n A 1 57 PRO 57 57 57 PRO PRO L . n A 1 58 SER 58 58 58 SER SER L . n A 1 59 GLY 59 59 59 GLY GLY L . n A 1 60 VAL 60 60 60 VAL VAL L . n A 1 61 PRO 61 61 61 PRO PRO L . n A 1 62 ASP 62 62 62 ASP ASP L . n A 1 63 ARG 63 63 63 ARG ARG L . n A 1 64 PHE 64 64 64 PHE PHE L . n A 1 65 SER 65 65 65 SER SER L . n A 1 66 GLY 66 66 66 GLY GLY L . n A 1 67 SER 67 67 67 SER SER L . n A 1 68 LYS 68 68 68 LYS LYS L . n A 1 69 SER 69 69 69 SER SER L . n A 1 70 GLY 70 70 70 GLY GLY L . n A 1 71 THR 71 71 71 THR THR L . n A 1 72 SER 72 72 72 SER SER L . n A 1 73 ALA 73 73 73 ALA ALA L . n A 1 74 SER 74 74 74 SER SER L . n A 1 75 LEU 75 75 75 LEU LEU L . n A 1 76 ALA 76 76 76 ALA ALA L . n A 1 77 ILE 77 77 77 ILE ILE L . n A 1 78 THR 78 78 78 THR THR L . n A 1 79 GLY 79 79 79 GLY GLY L . n A 1 80 LEU 80 80 80 LEU LEU L . n A 1 81 GLN 81 81 81 GLN GLN L . n A 1 82 ALA 82 82 82 ALA ALA L . n A 1 83 GLU 83 83 83 GLU GLU L . n A 1 84 ASP 84 84 84 ASP ASP L . n A 1 85 GLU 85 85 85 GLU GLU L . n A 1 86 ALA 86 86 86 ALA ALA L . n A 1 87 ASP 87 87 87 ASP ASP L . n A 1 88 TYR 88 88 88 TYR TYR L . n A 1 89 TYR 89 89 89 TYR TYR L . n A 1 90 CYS 90 90 90 CYS CYS L . n A 1 91 GLN 91 91 91 GLN GLN L . n A 1 92 SER 92 92 92 SER SER L . n A 1 93 TYR 93 93 93 TYR TYR L . n A 1 94 ASP 94 94 94 ASP ASP L . n A 1 95 SER 95 95 95 SER SER L . n A 1 96 SER 96 96 96 SER SER L . n A 1 97 LEU 97 97 97 LEU LEU L . n A 1 98 SER 98 98 98 SER SER L . n A 1 99 GLY 99 99 99 GLY GLY L . n A 1 100 TRP 100 100 100 TRP TRP L . n A 1 101 VAL 101 101 101 VAL VAL L . n A 1 102 PHE 102 102 102 PHE PHE L . n A 1 103 GLY 103 103 103 GLY GLY L . n A 1 104 GLY 104 104 104 GLY GLY L . n A 1 105 GLY 105 105 105 GLY GLY L . n A 1 106 THR 106 106 106 THR THR L . n A 1 107 LYS 107 107 107 LYS LYS L . n A 1 108 LEU 108 108 108 LEU LEU L . n A 1 109 THR 109 109 109 THR THR L . n A 1 110 VAL 110 110 110 VAL VAL L . n A 1 111 LEU 111 111 111 LEU LEU L . n B 2 1 GLN 1 1 1 GLN GLN H . n B 2 2 VAL 2 2 2 VAL VAL H . n B 2 3 GLN 3 3 3 GLN GLN H . n B 2 4 LEU 4 4 4 LEU LEU H . n B 2 5 VAL 5 5 5 VAL VAL H . n B 2 6 GLU 6 6 6 GLU GLU H . n B 2 7 SER 7 7 7 SER SER H . n B 2 8 GLY 8 8 8 GLY GLY H . n B 2 9 GLY 9 9 9 GLY GLY H . n B 2 10 GLY 10 10 10 GLY GLY H . n B 2 11 VAL 11 11 11 VAL VAL H . n B 2 12 VAL 12 12 12 VAL VAL H . n B 2 13 GLN 13 13 13 GLN GLN H . n B 2 14 PRO 14 14 14 PRO PRO H . n B 2 15 GLY 15 15 15 GLY GLY H . n B 2 16 ARG 16 16 16 ARG ARG H . n B 2 17 SER 17 17 17 SER SER H . n B 2 18 LEU 18 18 18 LEU LEU H . n B 2 19 ARG 19 19 19 ARG ARG H . n B 2 20 LEU 20 20 20 LEU LEU H . n B 2 21 SER 21 21 21 SER SER H . n B 2 22 CYS 22 22 22 CYS CYS H . n B 2 23 ALA 23 23 23 ALA ALA H . n B 2 24 ALA 24 24 24 ALA ALA H . n B 2 25 SER 25 25 25 SER SER H . n B 2 26 GLY 26 26 26 GLY GLY H . n B 2 27 PHE 27 27 27 PHE PHE H . n B 2 28 THR 28 28 28 THR THR H . n B 2 29 PHE 29 29 29 PHE PHE H . n B 2 30 SER 30 30 30 SER SER H . n B 2 31 SER 31 31 31 SER SER H . n B 2 32 ILE 32 32 32 ILE ILE H . n B 2 33 ALA 33 33 33 ALA ALA H . n B 2 34 MET 34 34 34 MET MET H . n B 2 35 HIS 35 35 35 HIS HIS H . n B 2 36 TRP 36 36 36 TRP TRP H . n B 2 37 VAL 37 37 37 VAL VAL H . n B 2 38 ARG 38 38 38 ARG ARG H . n B 2 39 GLN 39 39 39 GLN GLN H . n B 2 40 ALA 40 40 40 ALA ALA H . n B 2 41 PRO 41 41 41 PRO PRO H . n B 2 42 GLY 42 42 42 GLY GLY H . n B 2 43 LYS 43 43 43 LYS LYS H . n B 2 44 GLY 44 44 44 GLY GLY H . n B 2 45 LEU 45 45 45 LEU LEU H . n B 2 46 GLU 46 46 46 GLU GLU H . n B 2 47 TRP 47 47 47 TRP TRP H . n B 2 48 VAL 48 48 48 VAL VAL H . n B 2 49 ALA 49 49 49 ALA ALA H . n B 2 50 VAL 50 50 50 VAL VAL H . n B 2 51 MET 51 51 51 MET MET H . n B 2 52 SER 52 52 52 SER SER H . n B 2 53 PHE 53 53 53 PHE PHE H . n B 2 54 ASP 54 54 54 ASP ASP H . n B 2 55 GLY 55 55 55 GLY GLY H . n B 2 56 SER 56 56 56 SER SER H . n B 2 57 ILE 57 57 57 ILE ILE H . n B 2 58 LYS 58 58 58 LYS LYS H . n B 2 59 TYR 59 59 59 TYR TYR H . n B 2 60 TYR 60 60 60 TYR TYR H . n B 2 61 GLY 61 61 61 GLY GLY H . n B 2 62 ASP 62 62 62 ASP ASP H . n B 2 63 SER 63 63 63 SER SER H . n B 2 64 VAL 64 64 64 VAL VAL H . n B 2 65 LYS 65 65 65 LYS LYS H . n B 2 66 GLY 66 66 66 GLY GLY H . n B 2 67 ARG 67 67 67 ARG ARG H . n B 2 68 PHE 68 68 68 PHE PHE H . n B 2 69 THR 69 69 69 THR THR H . n B 2 70 ILE 70 70 70 ILE ILE H . n B 2 71 SER 71 71 71 SER SER H . n B 2 72 ARG 72 72 72 ARG ARG H . n B 2 73 ASP 73 73 73 ASP ASP H . n B 2 74 ASN 74 74 74 ASN ASN H . n B 2 75 SER 75 75 75 SER SER H . n B 2 76 LYS 76 76 76 LYS LYS H . n B 2 77 SER 77 77 77 SER SER H . n B 2 78 THR 78 78 78 THR THR H . n B 2 79 LEU 79 79 79 LEU LEU H . n B 2 80 TYR 80 80 80 TYR TYR H . n B 2 81 LEU 81 81 81 LEU LEU H . n B 2 82 GLN 82 82 82 GLN GLN H . n B 2 83 MET 83 83 83 MET MET H . n B 2 84 ASN 84 84 84 ASN ASN H . n B 2 85 SER 85 85 85 SER SER H . n B 2 86 LEU 86 86 86 LEU LEU H . n B 2 87 ARG 87 87 87 ARG ARG H . n B 2 88 ALA 88 88 88 ALA ALA H . n B 2 89 GLU 89 89 89 GLU GLU H . n B 2 90 ASP 90 90 90 ASP ASP H . n B 2 91 THR 91 91 91 THR THR H . n B 2 92 ALA 92 92 92 ALA ALA H . n B 2 93 VAL 93 93 93 VAL VAL H . n B 2 94 TYR 94 94 94 TYR TYR H . n B 2 95 TYR 95 95 95 TYR TYR H . n B 2 96 CYS 96 96 96 CYS CYS H . n B 2 97 ALA 97 97 97 ALA ALA H . n B 2 98 ARG 98 98 98 ARG ARG H . n B 2 99 GLY 99 99 99 GLY GLY H . n B 2 100 VAL 100 100 100 VAL VAL H . n B 2 101 GLN 101 101 101 GLN GLN H . n B 2 102 GLY 102 102 102 GLY GLY H . n B 2 103 TYR 103 103 103 TYR TYR H . n B 2 104 TYR 104 104 104 TYR TYR H . n B 2 105 ASP 105 105 105 ASP ASP H . n B 2 106 ARG 106 106 106 ARG ARG H . n B 2 107 SER 107 107 107 SER SER H . n B 2 108 GLY 108 108 108 GLY GLY H . n B 2 109 TYR 109 109 109 TYR TYR H . n B 2 110 TYR 110 110 110 TYR TYR H . n B 2 111 ASN 111 111 111 ASN ASN H . n B 2 112 LEU 112 112 112 LEU LEU H . n B 2 113 ASP 113 113 113 ASP ASP H . n B 2 114 TYR 114 114 114 TYR TYR H . n B 2 115 ASN 115 115 115 ASN ASN H . n B 2 116 TYR 116 116 116 TYR TYR H . n B 2 117 GLY 117 117 117 GLY GLY H . n B 2 118 MET 118 118 118 MET MET H . n B 2 119 ASP 119 119 119 ASP ASP H . n B 2 120 VAL 120 120 120 VAL VAL H . n B 2 121 TRP 121 121 121 TRP TRP H . n B 2 122 GLY 122 122 122 GLY GLY H . n B 2 123 GLN 123 123 123 GLN GLN H . n B 2 124 GLY 124 124 124 GLY GLY H . n B 2 125 THR 125 125 125 THR THR H . n B 2 126 THR 126 126 126 THR THR H . n B 2 127 VAL 127 127 127 VAL VAL H . n B 2 128 THR 128 128 128 THR THR H . n B 2 129 VAL 129 129 129 VAL VAL H . n B 2 130 SER 130 130 130 SER SER H . n B 2 131 SER 131 131 131 SER SER H . n C 3 1 THR 1 333 ? ? ? F . n C 3 2 ASN 2 334 ? ? ? F . n C 3 3 LEU 3 335 ? ? ? F . n C 3 4 CYS 4 336 336 CYS CYS F . n C 3 5 PRO 5 337 337 PRO PRO F . n C 3 6 PHE 6 338 338 PHE PHE F . n C 3 7 ASP 7 339 339 ASP ASP F . n C 3 8 GLU 8 340 340 GLU GLU F . n C 3 9 VAL 9 341 341 VAL VAL F . n C 3 10 PHE 10 342 342 PHE PHE F . n C 3 11 ASN 11 343 343 ASN ASN F . n C 3 12 ALA 12 344 344 ALA ALA F . n C 3 13 THR 13 345 345 THR THR F . n C 3 14 ARG 14 346 346 ARG ARG F . n C 3 15 PHE 15 347 347 PHE PHE F . n C 3 16 ALA 16 348 348 ALA ALA F . n C 3 17 SER 17 349 349 SER SER F . n C 3 18 VAL 18 350 350 VAL VAL F . n C 3 19 TYR 19 351 351 TYR TYR F . n C 3 20 ALA 20 352 352 ALA ALA F . n C 3 21 TRP 21 353 353 TRP TRP F . n C 3 22 ASN 22 354 354 ASN ASN F . n C 3 23 ARG 23 355 355 ARG ARG F . n C 3 24 LYS 24 356 356 LYS LYS F . n C 3 25 ARG 25 357 357 ARG ARG F . n C 3 26 ILE 26 358 358 ILE ILE F . n C 3 27 SER 27 359 359 SER SER F . n C 3 28 ASN 28 360 360 ASN ASN F . n C 3 29 CYS 29 361 361 CYS CYS F . n C 3 30 VAL 30 362 362 VAL VAL F . n C 3 31 ALA 31 363 363 ALA ALA F . n C 3 32 ASP 32 364 364 ASP ASP F . n C 3 33 TYR 33 365 365 TYR TYR F . n C 3 34 SER 34 366 366 SER SER F . n C 3 35 VAL 35 367 367 VAL VAL F . n C 3 36 LEU 36 368 368 LEU LEU F . n C 3 37 TYR 37 369 369 TYR TYR F . n C 3 38 ASN 38 370 370 ASN ASN F . n C 3 39 LEU 39 371 371 LEU LEU F . n C 3 40 ALA 40 372 372 ALA ALA F . n C 3 41 PRO 41 373 373 PRO PRO F . n C 3 42 PHE 42 374 374 PHE PHE F . n C 3 43 PHE 43 375 375 PHE PHE F . n C 3 44 THR 44 376 376 THR THR F . n C 3 45 PHE 45 377 377 PHE PHE F . n C 3 46 LYS 46 378 378 LYS LYS F . n C 3 47 CYS 47 379 379 CYS CYS F . n C 3 48 TYR 48 380 380 TYR TYR F . n C 3 49 GLY 49 381 381 GLY GLY F . n C 3 50 VAL 50 382 382 VAL VAL F . n C 3 51 SER 51 383 383 SER SER F . n C 3 52 PRO 52 384 384 PRO PRO F . n C 3 53 THR 53 385 385 THR THR F . n C 3 54 LYS 54 386 386 LYS LYS F . n C 3 55 LEU 55 387 387 LEU LEU F . n C 3 56 ASN 56 388 388 ASN ASN F . n C 3 57 ASP 57 389 389 ASP ASP F . n C 3 58 LEU 58 390 390 LEU LEU F . n C 3 59 CYS 59 391 391 CYS CYS F . n C 3 60 PHE 60 392 392 PHE PHE F . n C 3 61 THR 61 393 393 THR THR F . n C 3 62 ASN 62 394 394 ASN ASN F . n C 3 63 VAL 63 395 395 VAL VAL F . n C 3 64 TYR 64 396 396 TYR TYR F . n C 3 65 ALA 65 397 397 ALA ALA F . n C 3 66 ASP 66 398 398 ASP ASP F . n C 3 67 SER 67 399 399 SER SER F . n C 3 68 PHE 68 400 400 PHE PHE F . n C 3 69 VAL 69 401 401 VAL VAL F . n C 3 70 ILE 70 402 402 ILE ILE F . n C 3 71 ARG 71 403 403 ARG ARG F . n C 3 72 GLY 72 404 404 GLY GLY F . n C 3 73 ASP 73 405 405 ASP ASP F . n C 3 74 GLU 74 406 406 GLU GLU F . n C 3 75 VAL 75 407 407 VAL VAL F . n C 3 76 ARG 76 408 408 ARG ARG F . n C 3 77 GLN 77 409 409 GLN GLN F . n C 3 78 ILE 78 410 410 ILE ILE F . n C 3 79 ALA 79 411 411 ALA ALA F . n C 3 80 PRO 80 412 412 PRO PRO F . n C 3 81 GLY 81 413 413 GLY GLY F . n C 3 82 GLN 82 414 414 GLN GLN F . n C 3 83 THR 83 415 415 THR THR F . n C 3 84 GLY 84 416 416 GLY GLY F . n C 3 85 ASN 85 417 417 ASN ASN F . n C 3 86 ILE 86 418 418 ILE ILE F . n C 3 87 ALA 87 419 419 ALA ALA F . n C 3 88 ASP 88 420 420 ASP ASP F . n C 3 89 TYR 89 421 421 TYR TYR F . n C 3 90 ASN 90 422 422 ASN ASN F . n C 3 91 TYR 91 423 423 TYR TYR F . n C 3 92 LYS 92 424 424 LYS LYS F . n C 3 93 LEU 93 425 425 LEU LEU F . n C 3 94 PRO 94 426 426 PRO PRO F . n C 3 95 ASP 95 427 427 ASP ASP F . n C 3 96 ASP 96 428 428 ASP ASP F . n C 3 97 PHE 97 429 429 PHE PHE F . n C 3 98 THR 98 430 430 THR THR F . n C 3 99 GLY 99 431 431 GLY GLY F . n C 3 100 CYS 100 432 432 CYS CYS F . n C 3 101 VAL 101 433 433 VAL VAL F . n C 3 102 ILE 102 434 434 ILE ILE F . n C 3 103 ALA 103 435 435 ALA ALA F . n C 3 104 TRP 104 436 436 TRP TRP F . n C 3 105 ASN 105 437 437 ASN ASN F . n C 3 106 SER 106 438 438 SER SER F . n C 3 107 ASN 107 439 439 ASN ASN F . n C 3 108 LYS 108 440 440 LYS LYS F . n C 3 109 LEU 109 441 441 LEU LEU F . n C 3 110 ASP 110 442 442 ASP ASP F . n C 3 111 SER 111 443 443 SER SER F . n C 3 112 LYS 112 444 444 LYS LYS F . n C 3 113 VAL 113 445 445 VAL VAL F . n C 3 114 SER 114 446 446 SER SER F . n C 3 115 GLY 115 447 447 GLY GLY F . n C 3 116 ASN 116 448 448 ASN ASN F . n C 3 117 TYR 117 449 449 TYR TYR F . n C 3 118 ASN 118 450 450 ASN ASN F . n C 3 119 TYR 119 451 451 TYR TYR F . n C 3 120 LEU 120 452 452 LEU LEU F . n C 3 121 TYR 121 453 453 TYR TYR F . n C 3 122 ARG 122 454 454 ARG ARG F . n C 3 123 LEU 123 455 455 LEU LEU F . n C 3 124 PHE 124 456 456 PHE PHE F . n C 3 125 ARG 125 457 457 ARG ARG F . n C 3 126 LYS 126 458 458 LYS LYS F . n C 3 127 SER 127 459 459 SER SER F . n C 3 128 ASN 128 460 460 ASN ASN F . n C 3 129 LEU 129 461 461 LEU LEU F . n C 3 130 LYS 130 462 462 LYS LYS F . n C 3 131 PRO 131 463 463 PRO PRO F . n C 3 132 PHE 132 464 464 PHE PHE F . n C 3 133 GLU 133 465 465 GLU GLU F . n C 3 134 ARG 134 466 466 ARG ARG F . n C 3 135 ASP 135 467 467 ASP ASP F . n C 3 136 ILE 136 468 468 ILE ILE F . n C 3 137 SER 137 469 469 SER SER F . n C 3 138 THR 138 470 470 THR THR F . n C 3 139 GLU 139 471 471 GLU GLU F . n C 3 140 ILE 140 472 472 ILE ILE F . n C 3 141 TYR 141 473 473 TYR TYR F . n C 3 142 GLN 142 474 474 GLN GLN F . n C 3 143 ALA 143 475 475 ALA ALA F . n C 3 144 GLY 144 476 476 GLY GLY F . n C 3 145 ASN 145 477 477 ASN ASN F . n C 3 146 LYS 146 478 478 LYS LYS F . n C 3 147 PRO 147 479 479 PRO PRO F . n C 3 148 CYS 148 480 480 CYS CYS F . n C 3 149 ASN 149 481 481 ASN ASN F . n C 3 150 GLY 150 482 482 GLY GLY F . n C 3 151 VAL 151 483 483 VAL VAL F . n C 3 152 ALA 152 484 484 ALA ALA F . n C 3 153 GLY 153 485 485 GLY GLY F . n C 3 154 PHE 154 486 486 PHE PHE F . n C 3 155 ASN 155 487 487 ASN ASN F . n C 3 156 CYS 156 488 488 CYS CYS F . n C 3 157 TYR 157 489 489 TYR TYR F . n C 3 158 PHE 158 490 490 PHE PHE F . n C 3 159 PRO 159 491 491 PRO PRO F . n C 3 160 LEU 160 492 492 LEU LEU F . n C 3 161 ARG 161 493 493 ARG ARG F . n C 3 162 SER 162 494 494 SER SER F . n C 3 163 TYR 163 495 495 TYR TYR F . n C 3 164 SER 164 496 496 SER SER F . n C 3 165 PHE 165 497 497 PHE PHE F . n C 3 166 ARG 166 498 498 ARG ARG F . n C 3 167 PRO 167 499 499 PRO PRO F . n C 3 168 THR 168 500 500 THR THR F . n C 3 169 TYR 169 501 501 TYR TYR F . n C 3 170 GLY 170 502 502 GLY GLY F . n C 3 171 VAL 171 503 503 VAL VAL F . n C 3 172 GLY 172 504 504 GLY GLY F . n C 3 173 HIS 173 505 505 HIS HIS F . n C 3 174 GLN 174 506 506 GLN GLN F . n C 3 175 PRO 175 507 507 PRO PRO F . n C 3 176 TYR 176 508 508 TYR TYR F . n C 3 177 ARG 177 509 509 ARG ARG F . n C 3 178 VAL 178 510 510 VAL VAL F . n C 3 179 VAL 179 511 511 VAL VAL F . n C 3 180 VAL 180 512 512 VAL VAL F . n C 3 181 LEU 181 513 513 LEU LEU F . n C 3 182 SER 182 514 514 SER SER F . n C 3 183 PHE 183 515 515 PHE PHE F . n C 3 184 GLU 184 516 516 GLU GLU F . n C 3 185 LEU 185 517 517 LEU LEU F . n C 3 186 LEU 186 518 518 LEU LEU F . n C 3 187 HIS 187 519 ? ? ? F . n C 3 188 ALA 188 520 ? ? ? F . n C 3 189 PRO 189 521 ? ? ? F . n # loop_ _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_mon_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.hetero D 4 NAG 1 A NAG 1 F NAG 519 n D 4 NAG 2 A NAG 2 F NAG 520 n # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id NAG _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id NAG _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # _software.citation_id ? _software.classification refinement _software.compiler_name ? _software.compiler_version ? _software.contact_author ? _software.contact_author_email ? _software.date ? _software.description ? _software.dependencies ? _software.hardware ? _software.language ? _software.location ? _software.mods ? _software.name PHENIX _software.os ? _software.os_version ? _software.type ? _software.version 1.14_3259: _software.pdbx_ordinal 1 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 7WP5 _cell.details ? _cell.formula_units_Z ? _cell.length_a 1.00 _cell.length_a_esd ? _cell.length_b 1.00 _cell.length_b_esd ? _cell.length_c 1.00 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB ? _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7WP5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 7WP5 _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _struct.entry_id 7WP5 _struct.title 'Cryo-EM structure of SARS-CoV-2 Omicron S6P trimer in complex with neutralizing antibody VacW-209 (local refinement)' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7WP5 _struct_keywords.text 'SARS-CoV-2, Omicron variant, spike, neutralizing antibody, Cryo-EM, VIRAL PROTEIN, IMMUNE SYSTEM-VIRAL PROTEIN complex' _struct_keywords.pdbx_keywords 'IMMUNE SYSTEM/VIRAL PROTEIN' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 UNP A0A5C2GQT9_HUMAN A0A5C2GQT9 ? 1 ;QSVLTQPPSVSGAPGQRVTISCTGSSSNIGAGYDVHWYQQLPGTAPKLLIYGNSNRPSGVPDRFSGSKSGTSASLAITGL QAEDEADYYCQSYDSSLSGWVFGGGTKLTVL ; 1 2 PDB 7WP5 7WP5 ? 2 ? 1 3 UNP SPIKE_SARS2 P0DTC2 ? 3 ;TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAP GQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPL QSYGFQPTNGVGYQPYRVVVLSFELLHAP ; 333 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 7WP5 L 1 ? 111 ? A0A5C2GQT9 1 ? 111 ? 1 111 2 2 7WP5 H 1 ? 131 ? 7WP5 1 ? 131 ? 1 131 3 3 7WP5 F 1 ? 189 ? P0DTC2 333 ? 521 ? 333 521 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 3 7WP5 ASP F 7 ? UNP P0DTC2 GLY 339 variant 339 1 3 7WP5 LEU F 39 ? UNP P0DTC2 SER 371 variant 371 2 3 7WP5 PRO F 41 ? UNP P0DTC2 SER 373 variant 373 3 3 7WP5 PHE F 43 ? UNP P0DTC2 SER 375 variant 375 4 3 7WP5 ASN F 85 ? UNP P0DTC2 LYS 417 variant 417 5 3 7WP5 LYS F 108 ? UNP P0DTC2 ASN 440 variant 440 6 3 7WP5 SER F 114 ? UNP P0DTC2 GLY 446 variant 446 7 3 7WP5 ASN F 145 ? UNP P0DTC2 SER 477 variant 477 8 3 7WP5 LYS F 146 ? UNP P0DTC2 THR 478 variant 478 9 3 7WP5 ALA F 152 ? UNP P0DTC2 GLU 484 variant 484 10 3 7WP5 ARG F 161 ? UNP P0DTC2 GLN 493 variant 493 11 3 7WP5 SER F 164 ? UNP P0DTC2 GLY 496 variant 496 12 3 7WP5 ARG F 166 ? UNP P0DTC2 GLN 498 variant 498 13 3 7WP5 TYR F 169 ? UNP P0DTC2 ASN 501 variant 501 14 3 7WP5 HIS F 173 ? UNP P0DTC2 TYR 505 variant 505 15 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 AA1 CYS C 4 ? GLU C 8 ? CYS F 336 GLU F 340 5 ? 5 HELX_P HELX_P2 AA2 GLU C 74 ? ILE C 78 ? GLU F 406 ILE F 410 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 22 SG ? ? ? 1_555 A CYS 90 SG ? ? L CYS 22 L CYS 90 1_555 ? ? ? ? ? ? ? 2.036 ? ? disulf2 disulf ? ? B CYS 22 SG ? ? ? 1_555 B CYS 96 SG ? ? H CYS 22 H CYS 96 1_555 ? ? ? ? ? ? ? 2.037 ? ? disulf3 disulf ? ? C CYS 47 SG ? ? ? 1_555 C CYS 100 SG ? ? F CYS 379 F CYS 432 1_555 ? ? ? ? ? ? ? 2.029 ? ? covale1 covale one ? C ASN 11 ND2 ? ? ? 1_555 D NAG . C1 ? ? F ASN 343 A NAG 1 1_555 ? ? ? ? ? ? ? 1.442 ? N-Glycosylation covale2 covale both ? D NAG . O4 ? ? ? 1_555 D NAG . C1 ? ? A NAG 1 A NAG 2 1_555 ? ? ? ? ? ? ? 1.446 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # loop_ _pdbx_modification_feature.ordinal _pdbx_modification_feature.label_comp_id _pdbx_modification_feature.label_asym_id _pdbx_modification_feature.label_seq_id _pdbx_modification_feature.label_alt_id _pdbx_modification_feature.modified_residue_label_comp_id _pdbx_modification_feature.modified_residue_label_asym_id _pdbx_modification_feature.modified_residue_label_seq_id _pdbx_modification_feature.modified_residue_label_alt_id _pdbx_modification_feature.auth_comp_id _pdbx_modification_feature.auth_asym_id _pdbx_modification_feature.auth_seq_id _pdbx_modification_feature.PDB_ins_code _pdbx_modification_feature.symmetry _pdbx_modification_feature.modified_residue_auth_comp_id _pdbx_modification_feature.modified_residue_auth_asym_id _pdbx_modification_feature.modified_residue_auth_seq_id _pdbx_modification_feature.modified_residue_PDB_ins_code _pdbx_modification_feature.modified_residue_symmetry _pdbx_modification_feature.comp_id_linking_atom _pdbx_modification_feature.modified_residue_id_linking_atom _pdbx_modification_feature.modified_residue_id _pdbx_modification_feature.ref_pcm_id _pdbx_modification_feature.ref_comp_id _pdbx_modification_feature.type _pdbx_modification_feature.category 1 NAG D . ? ASN C 11 ? NAG A 1 ? 1_555 ASN F 343 ? 1_555 C1 ND2 ASN 1 NAG N-Glycosylation Carbohydrate 2 CYS A 22 ? CYS A 90 ? CYS L 22 ? 1_555 CYS L 90 ? 1_555 SG SG . . . None 'Disulfide bridge' 3 CYS B 22 ? CYS B 96 ? CYS H 22 ? 1_555 CYS H 96 ? 1_555 SG SG . . . None 'Disulfide bridge' 4 CYS C 47 ? CYS C 100 ? CYS F 379 ? 1_555 CYS F 432 ? 1_555 SG SG . . . None 'Disulfide bridge' # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 3 ? AA2 ? 3 ? AA3 ? 4 ? AA4 ? 6 ? AA5 ? 2 ? AA6 ? 2 ? AA7 ? 4 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? anti-parallel AA1 2 3 ? anti-parallel AA2 1 2 ? anti-parallel AA2 2 3 ? anti-parallel AA3 1 2 ? anti-parallel AA3 2 3 ? anti-parallel AA3 3 4 ? anti-parallel AA4 1 2 ? parallel AA4 2 3 ? anti-parallel AA4 3 4 ? anti-parallel AA4 4 5 ? anti-parallel AA4 5 6 ? anti-parallel AA5 1 2 ? anti-parallel AA6 1 2 ? anti-parallel AA7 1 2 ? anti-parallel AA7 2 3 ? anti-parallel AA7 3 4 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 ARG A 17 ? THR A 23 ? ARG L 17 THR L 23 AA1 2 SER A 72 ? THR A 78 ? SER L 72 THR L 78 AA1 3 PHE A 64 ? SER A 69 ? PHE L 64 SER L 69 AA2 1 LYS A 47 ? ILE A 50 ? LYS L 47 ILE L 50 AA2 2 HIS A 36 ? GLN A 39 ? HIS L 36 GLN L 39 AA2 3 CYS A 90 ? GLN A 91 ? CYS L 90 GLN L 91 AA3 1 GLN B 3 ? SER B 7 ? GLN H 3 SER H 7 AA3 2 LEU B 18 ? SER B 25 ? LEU H 18 SER H 25 AA3 3 THR B 78 ? MET B 83 ? THR H 78 MET H 83 AA3 4 PHE B 68 ? ASP B 73 ? PHE H 68 ASP H 73 AA4 1 GLY B 10 ? VAL B 12 ? GLY H 10 VAL H 12 AA4 2 THR B 125 ? VAL B 129 ? THR H 125 VAL H 129 AA4 3 ALA B 92 ? ARG B 98 ? ALA H 92 ARG H 98 AA4 4 MET B 34 ? GLN B 39 ? MET H 34 GLN H 39 AA4 5 LEU B 45 ? MET B 51 ? LEU H 45 MET H 51 AA4 6 LYS B 58 ? TYR B 60 ? LYS H 58 TYR H 60 AA5 1 TYR B 103 ? TYR B 104 ? TYR H 103 TYR H 104 AA5 2 TYR B 110 ? ASN B 111 ? TYR H 110 ASN H 111 AA6 1 ILE C 26 ? SER C 27 ? ILE F 358 SER F 359 AA6 2 THR C 61 ? VAL C 63 ? THR F 393 VAL F 395 AA7 1 THR C 44 ? CYS C 47 ? THR F 376 CYS F 379 AA7 2 CYS C 100 ? ASN C 105 ? CYS F 432 ASN F 437 AA7 3 TYR C 176 ? VAL C 180 ? TYR F 508 VAL F 512 AA7 4 ASP C 66 ? ILE C 70 ? ASP F 398 ILE F 402 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 N CYS A 22 ? N CYS L 22 O ALA A 73 ? O ALA L 73 AA1 2 3 O SER A 72 ? O SER L 72 N SER A 69 ? N SER L 69 AA2 1 2 O ILE A 50 ? O ILE L 50 N TRP A 37 ? N TRP L 37 AA2 2 3 N HIS A 36 ? N HIS L 36 O GLN A 91 ? O GLN L 91 AA3 1 2 N SER B 7 ? N SER H 7 O SER B 21 ? O SER H 21 AA3 2 3 N LEU B 18 ? N LEU H 18 O MET B 83 ? O MET H 83 AA3 3 4 O TYR B 80 ? O TYR H 80 N SER B 71 ? N SER H 71 AA4 1 2 N VAL B 12 ? N VAL H 12 O THR B 128 ? O THR H 128 AA4 2 3 O THR B 125 ? O THR H 125 N TYR B 94 ? N TYR H 94 AA4 3 4 O ALA B 97 ? O ALA H 97 N HIS B 35 ? N HIS H 35 AA4 4 5 N TRP B 36 ? N TRP H 36 O ALA B 49 ? O ALA H 49 AA4 5 6 N VAL B 50 ? N VAL H 50 O TYR B 59 ? O TYR H 59 AA5 1 2 N TYR B 103 ? N TYR H 103 O ASN B 111 ? O ASN H 111 AA6 1 2 N ILE C 26 ? N ILE F 358 O VAL C 63 ? O VAL F 395 AA7 1 2 N LYS C 46 ? N LYS F 378 O VAL C 101 ? O VAL F 433 AA7 2 3 N ILE C 102 ? N ILE F 434 O VAL C 179 ? O VAL F 511 AA7 3 4 O TYR C 176 ? O TYR F 508 N ILE C 70 ? N ILE F 402 # _pdbx_entry_details.entry_id 7WP5 _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_protein_modification Y # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 CA _pdbx_validate_rmsd_angle.auth_asym_id_1 F _pdbx_validate_rmsd_angle.auth_comp_id_1 LEU _pdbx_validate_rmsd_angle.auth_seq_id_1 371 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 CB _pdbx_validate_rmsd_angle.auth_asym_id_2 F _pdbx_validate_rmsd_angle.auth_comp_id_2 LEU _pdbx_validate_rmsd_angle.auth_seq_id_2 371 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 CG _pdbx_validate_rmsd_angle.auth_asym_id_3 F _pdbx_validate_rmsd_angle.auth_comp_id_3 LEU _pdbx_validate_rmsd_angle.auth_seq_id_3 371 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 129.31 _pdbx_validate_rmsd_angle.angle_target_value 115.30 _pdbx_validate_rmsd_angle.angle_deviation 14.01 _pdbx_validate_rmsd_angle.angle_standard_deviation 2.30 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ASN L 53 ? ? 72.13 -12.90 2 1 SER L 54 ? ? -150.80 -1.26 3 1 SER H 52 ? ? -77.56 -165.85 4 1 TYR F 365 ? ? 67.71 -3.45 5 1 PHE F 400 ? ? -161.99 -168.60 6 1 ASP F 428 ? ? -150.04 -157.34 7 1 PHE F 429 ? ? -84.20 31.04 8 1 SER F 459 ? ? 58.46 71.49 9 1 ASN F 460 ? ? -47.11 152.41 10 1 ASN F 477 ? ? -72.04 -148.41 11 1 LYS F 478 ? ? -28.36 133.47 12 1 VAL F 483 ? ? -140.08 -16.10 13 1 ASN F 487 ? ? 58.30 16.26 14 1 SER F 494 ? ? -78.07 -168.04 15 1 ARG F 498 ? ? -170.98 140.30 # _pdbx_validate_peptide_omega.id 1 _pdbx_validate_peptide_omega.PDB_model_num 1 _pdbx_validate_peptide_omega.auth_comp_id_1 ASN _pdbx_validate_peptide_omega.auth_asym_id_1 F _pdbx_validate_peptide_omega.auth_seq_id_1 460 _pdbx_validate_peptide_omega.PDB_ins_code_1 ? _pdbx_validate_peptide_omega.label_alt_id_1 ? _pdbx_validate_peptide_omega.auth_comp_id_2 LEU _pdbx_validate_peptide_omega.auth_asym_id_2 F _pdbx_validate_peptide_omega.auth_seq_id_2 461 _pdbx_validate_peptide_omega.PDB_ins_code_2 ? _pdbx_validate_peptide_omega.label_alt_id_2 ? _pdbx_validate_peptide_omega.omega -147.27 # _em_3d_fitting.entry_id 7WP5 _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_protocol ? _em_3d_fitting.ref_space ? _em_3d_fitting.target_criteria ? _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 7WP5 _em_3d_reconstruction.id 1 _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.details ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.num_particles 451606 _em_3d_reconstruction.resolution 3.9 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.symmetry_type POINT _em_3d_reconstruction.method ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.magnification_calibration ? # _em_buffer.id 1 _em_buffer.details ? _em_buffer.pH 7.4 _em_buffer.specimen_id 1 _em_buffer.name ? # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.details ? _em_entity_assembly.name 'SARS-CoV-2 Omicron S6P trimer in complex with neutralizing antibody VacW-209' _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type COMPLEX _em_entity_assembly.entity_id_list '1, 2, 3' _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_imaging.id 1 _em_imaging.entry_id 7WP5 _em_imaging.accelerating_voltage 300 _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.calibrated_defocus_max ? _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_magnification ? _em_imaging.cryogen ? _em_imaging.details ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.microscope_model 'FEI TECNAI F30' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_max 3500 _em_imaging.nominal_defocus_min 1200 _em_imaging.nominal_magnification ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.residual_tilt ? _em_imaging.specimen_holder_model ? _em_imaging.specimen_id 1 _em_imaging.citation_id ? _em_imaging.date ? _em_imaging.temperature ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.astigmatism ? _em_imaging.detector_distance ? _em_imaging.electron_beam_tilt_params ? _em_imaging.specimen_holder_type ? # _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature ? _em_vitrification.cryogen_name ETHANE _em_vitrification.details ? _em_vitrification.humidity ? _em_vitrification.instrument ? _em_vitrification.entry_id 7WP5 _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 7WP5 _em_experiment.id 1 _em_experiment.aggregation_state PARTICLE _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.entity_assembly_id 1 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 F THR 333 ? C THR 1 2 1 Y 1 F ASN 334 ? C ASN 2 3 1 Y 1 F LEU 335 ? C LEU 3 4 1 Y 1 F HIS 519 ? C HIS 187 5 1 Y 1 F ALA 520 ? C ALA 188 6 1 Y 1 F PRO 521 ? C PRO 189 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ARG N N N N 14 ARG CA C N S 15 ARG C C N N 16 ARG O O N N 17 ARG CB C N N 18 ARG CG C N N 19 ARG CD C N N 20 ARG NE N N N 21 ARG CZ C N N 22 ARG NH1 N N N 23 ARG NH2 N N N 24 ARG OXT O N N 25 ARG H H N N 26 ARG H2 H N N 27 ARG HA H N N 28 ARG HB2 H N N 29 ARG HB3 H N N 30 ARG HG2 H N N 31 ARG HG3 H N N 32 ARG HD2 H N N 33 ARG HD3 H N N 34 ARG HE H N N 35 ARG HH11 H N N 36 ARG HH12 H N N 37 ARG HH21 H N N 38 ARG HH22 H N N 39 ARG HXT H N N 40 ASN N N N N 41 ASN CA C N S 42 ASN C C N N 43 ASN O O N N 44 ASN CB C N N 45 ASN CG C N N 46 ASN OD1 O N N 47 ASN ND2 N N N 48 ASN OXT O N N 49 ASN H H N N 50 ASN H2 H N N 51 ASN HA H N N 52 ASN HB2 H N N 53 ASN HB3 H N N 54 ASN HD21 H N N 55 ASN HD22 H N N 56 ASN HXT H N N 57 ASP N N N N 58 ASP CA C N S 59 ASP C C N N 60 ASP O O N N 61 ASP CB C N N 62 ASP CG C N N 63 ASP OD1 O N N 64 ASP OD2 O N N 65 ASP OXT O N N 66 ASP H H N N 67 ASP H2 H N N 68 ASP HA H N N 69 ASP HB2 H N N 70 ASP HB3 H N N 71 ASP HD2 H N N 72 ASP HXT H N N 73 CYS N N N N 74 CYS CA C N R 75 CYS C C N N 76 CYS O O N N 77 CYS CB C N N 78 CYS SG S N N 79 CYS OXT O N N 80 CYS H H N N 81 CYS H2 H N N 82 CYS HA H N N 83 CYS HB2 H N N 84 CYS HB3 H N N 85 CYS HG H N N 86 CYS HXT H N N 87 GLN N N N N 88 GLN CA C N S 89 GLN C C N N 90 GLN O O N N 91 GLN CB C N N 92 GLN CG C N N 93 GLN CD C N N 94 GLN OE1 O N N 95 GLN NE2 N N N 96 GLN OXT O N N 97 GLN H H N N 98 GLN H2 H N N 99 GLN HA H N N 100 GLN HB2 H N N 101 GLN HB3 H N N 102 GLN HG2 H N N 103 GLN HG3 H N N 104 GLN HE21 H N N 105 GLN HE22 H N N 106 GLN HXT H N N 107 GLU N N N N 108 GLU CA C N S 109 GLU C C N N 110 GLU O O N N 111 GLU CB C N N 112 GLU CG C N N 113 GLU CD C N N 114 GLU OE1 O N N 115 GLU OE2 O N N 116 GLU OXT O N N 117 GLU H H N N 118 GLU H2 H N N 119 GLU HA H N N 120 GLU HB2 H N N 121 GLU HB3 H N N 122 GLU HG2 H N N 123 GLU HG3 H N N 124 GLU HE2 H N N 125 GLU HXT H N N 126 GLY N N N N 127 GLY CA C N N 128 GLY C C N N 129 GLY O O N N 130 GLY OXT O N N 131 GLY H H N N 132 GLY H2 H N N 133 GLY HA2 H N N 134 GLY HA3 H N N 135 GLY HXT H N N 136 HIS N N N N 137 HIS CA C N S 138 HIS C C N N 139 HIS O O N N 140 HIS CB C N N 141 HIS CG C Y N 142 HIS ND1 N Y N 143 HIS CD2 C Y N 144 HIS CE1 C Y N 145 HIS NE2 N Y N 146 HIS OXT O N N 147 HIS H H N N 148 HIS H2 H N N 149 HIS HA H N N 150 HIS HB2 H N N 151 HIS HB3 H N N 152 HIS HD1 H N N 153 HIS HD2 H N N 154 HIS HE1 H N N 155 HIS HE2 H N N 156 HIS HXT H N N 157 ILE N N N N 158 ILE CA C N S 159 ILE C C N N 160 ILE O O N N 161 ILE CB C N S 162 ILE CG1 C N N 163 ILE CG2 C N N 164 ILE CD1 C N N 165 ILE OXT O N N 166 ILE H H N N 167 ILE H2 H N N 168 ILE HA H N N 169 ILE HB H N N 170 ILE HG12 H N N 171 ILE HG13 H N N 172 ILE HG21 H N N 173 ILE HG22 H N N 174 ILE HG23 H N N 175 ILE HD11 H N N 176 ILE HD12 H N N 177 ILE HD13 H N N 178 ILE HXT H N N 179 LEU N N N N 180 LEU CA C N S 181 LEU C C N N 182 LEU O O N N 183 LEU CB C N N 184 LEU CG C N N 185 LEU CD1 C N N 186 LEU CD2 C N N 187 LEU OXT O N N 188 LEU H H N N 189 LEU H2 H N N 190 LEU HA H N N 191 LEU HB2 H N N 192 LEU HB3 H N N 193 LEU HG H N N 194 LEU HD11 H N N 195 LEU HD12 H N N 196 LEU HD13 H N N 197 LEU HD21 H N N 198 LEU HD22 H N N 199 LEU HD23 H N N 200 LEU HXT H N N 201 LYS N N N N 202 LYS CA C N S 203 LYS C C N N 204 LYS O O N N 205 LYS CB C N N 206 LYS CG C N N 207 LYS CD C N N 208 LYS CE C N N 209 LYS NZ N N N 210 LYS OXT O N N 211 LYS H H N N 212 LYS H2 H N N 213 LYS HA H N N 214 LYS HB2 H N N 215 LYS HB3 H N N 216 LYS HG2 H N N 217 LYS HG3 H N N 218 LYS HD2 H N N 219 LYS HD3 H N N 220 LYS HE2 H N N 221 LYS HE3 H N N 222 LYS HZ1 H N N 223 LYS HZ2 H N N 224 LYS HZ3 H N N 225 LYS HXT H N N 226 MET N N N N 227 MET CA C N S 228 MET C C N N 229 MET O O N N 230 MET CB C N N 231 MET CG C N N 232 MET SD S N N 233 MET CE C N N 234 MET OXT O N N 235 MET H H N N 236 MET H2 H N N 237 MET HA H N N 238 MET HB2 H N N 239 MET HB3 H N N 240 MET HG2 H N N 241 MET HG3 H N N 242 MET HE1 H N N 243 MET HE2 H N N 244 MET HE3 H N N 245 MET HXT H N N 246 NAG C1 C N R 247 NAG C2 C N R 248 NAG C3 C N R 249 NAG C4 C N S 250 NAG C5 C N R 251 NAG C6 C N N 252 NAG C7 C N N 253 NAG C8 C N N 254 NAG N2 N N N 255 NAG O1 O N N 256 NAG O3 O N N 257 NAG O4 O N N 258 NAG O5 O N N 259 NAG O6 O N N 260 NAG O7 O N N 261 NAG H1 H N N 262 NAG H2 H N N 263 NAG H3 H N N 264 NAG H4 H N N 265 NAG H5 H N N 266 NAG H61 H N N 267 NAG H62 H N N 268 NAG H81 H N N 269 NAG H82 H N N 270 NAG H83 H N N 271 NAG HN2 H N N 272 NAG HO1 H N N 273 NAG HO3 H N N 274 NAG HO4 H N N 275 NAG HO6 H N N 276 PHE N N N N 277 PHE CA C N S 278 PHE C C N N 279 PHE O O N N 280 PHE CB C N N 281 PHE CG C Y N 282 PHE CD1 C Y N 283 PHE CD2 C Y N 284 PHE CE1 C Y N 285 PHE CE2 C Y N 286 PHE CZ C Y N 287 PHE OXT O N N 288 PHE H H N N 289 PHE H2 H N N 290 PHE HA H N N 291 PHE HB2 H N N 292 PHE HB3 H N N 293 PHE HD1 H N N 294 PHE HD2 H N N 295 PHE HE1 H N N 296 PHE HE2 H N N 297 PHE HZ H N N 298 PHE HXT H N N 299 PRO N N N N 300 PRO CA C N S 301 PRO C C N N 302 PRO O O N N 303 PRO CB C N N 304 PRO CG C N N 305 PRO CD C N N 306 PRO OXT O N N 307 PRO H H N N 308 PRO HA H N N 309 PRO HB2 H N N 310 PRO HB3 H N N 311 PRO HG2 H N N 312 PRO HG3 H N N 313 PRO HD2 H N N 314 PRO HD3 H N N 315 PRO HXT H N N 316 SER N N N N 317 SER CA C N S 318 SER C C N N 319 SER O O N N 320 SER CB C N N 321 SER OG O N N 322 SER OXT O N N 323 SER H H N N 324 SER H2 H N N 325 SER HA H N N 326 SER HB2 H N N 327 SER HB3 H N N 328 SER HG H N N 329 SER HXT H N N 330 THR N N N N 331 THR CA C N S 332 THR C C N N 333 THR O O N N 334 THR CB C N R 335 THR OG1 O N N 336 THR CG2 C N N 337 THR OXT O N N 338 THR H H N N 339 THR H2 H N N 340 THR HA H N N 341 THR HB H N N 342 THR HG1 H N N 343 THR HG21 H N N 344 THR HG22 H N N 345 THR HG23 H N N 346 THR HXT H N N 347 TRP N N N N 348 TRP CA C N S 349 TRP C C N N 350 TRP O O N N 351 TRP CB C N N 352 TRP CG C Y N 353 TRP CD1 C Y N 354 TRP CD2 C Y N 355 TRP NE1 N Y N 356 TRP CE2 C Y N 357 TRP CE3 C Y N 358 TRP CZ2 C Y N 359 TRP CZ3 C Y N 360 TRP CH2 C Y N 361 TRP OXT O N N 362 TRP H H N N 363 TRP H2 H N N 364 TRP HA H N N 365 TRP HB2 H N N 366 TRP HB3 H N N 367 TRP HD1 H N N 368 TRP HE1 H N N 369 TRP HE3 H N N 370 TRP HZ2 H N N 371 TRP HZ3 H N N 372 TRP HH2 H N N 373 TRP HXT H N N 374 TYR N N N N 375 TYR CA C N S 376 TYR C C N N 377 TYR O O N N 378 TYR CB C N N 379 TYR CG C Y N 380 TYR CD1 C Y N 381 TYR CD2 C Y N 382 TYR CE1 C Y N 383 TYR CE2 C Y N 384 TYR CZ C Y N 385 TYR OH O N N 386 TYR OXT O N N 387 TYR H H N N 388 TYR H2 H N N 389 TYR HA H N N 390 TYR HB2 H N N 391 TYR HB3 H N N 392 TYR HD1 H N N 393 TYR HD2 H N N 394 TYR HE1 H N N 395 TYR HE2 H N N 396 TYR HH H N N 397 TYR HXT H N N 398 VAL N N N N 399 VAL CA C N S 400 VAL C C N N 401 VAL O O N N 402 VAL CB C N N 403 VAL CG1 C N N 404 VAL CG2 C N N 405 VAL OXT O N N 406 VAL H H N N 407 VAL H2 H N N 408 VAL HA H N N 409 VAL HB H N N 410 VAL HG11 H N N 411 VAL HG12 H N N 412 VAL HG13 H N N 413 VAL HG21 H N N 414 VAL HG22 H N N 415 VAL HG23 H N N 416 VAL HXT H N N 417 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ARG N CA sing N N 13 ARG N H sing N N 14 ARG N H2 sing N N 15 ARG CA C sing N N 16 ARG CA CB sing N N 17 ARG CA HA sing N N 18 ARG C O doub N N 19 ARG C OXT sing N N 20 ARG CB CG sing N N 21 ARG CB HB2 sing N N 22 ARG CB HB3 sing N N 23 ARG CG CD sing N N 24 ARG CG HG2 sing N N 25 ARG CG HG3 sing N N 26 ARG CD NE sing N N 27 ARG CD HD2 sing N N 28 ARG CD HD3 sing N N 29 ARG NE CZ sing N N 30 ARG NE HE sing N N 31 ARG CZ NH1 sing N N 32 ARG CZ NH2 doub N N 33 ARG NH1 HH11 sing N N 34 ARG NH1 HH12 sing N N 35 ARG NH2 HH21 sing N N 36 ARG NH2 HH22 sing N N 37 ARG OXT HXT sing N N 38 ASN N CA sing N N 39 ASN N H sing N N 40 ASN N H2 sing N N 41 ASN CA C sing N N 42 ASN CA CB sing N N 43 ASN CA HA sing N N 44 ASN C O doub N N 45 ASN C OXT sing N N 46 ASN CB CG sing N N 47 ASN CB HB2 sing N N 48 ASN CB HB3 sing N N 49 ASN CG OD1 doub N N 50 ASN CG ND2 sing N N 51 ASN ND2 HD21 sing N N 52 ASN ND2 HD22 sing N N 53 ASN OXT HXT sing N N 54 ASP N CA sing N N 55 ASP N H sing N N 56 ASP N H2 sing N N 57 ASP CA C sing N N 58 ASP CA CB sing N N 59 ASP CA HA sing N N 60 ASP C O doub N N 61 ASP C OXT sing N N 62 ASP CB CG sing N N 63 ASP CB HB2 sing N N 64 ASP CB HB3 sing N N 65 ASP CG OD1 doub N N 66 ASP CG OD2 sing N N 67 ASP OD2 HD2 sing N N 68 ASP OXT HXT sing N N 69 CYS N CA sing N N 70 CYS N H sing N N 71 CYS N H2 sing N N 72 CYS CA C sing N N 73 CYS CA CB sing N N 74 CYS CA HA sing N N 75 CYS C O doub N N 76 CYS C OXT sing N N 77 CYS CB SG sing N N 78 CYS CB HB2 sing N N 79 CYS CB HB3 sing N N 80 CYS SG HG sing N N 81 CYS OXT HXT sing N N 82 GLN N CA sing N N 83 GLN N H sing N N 84 GLN N H2 sing N N 85 GLN CA C sing N N 86 GLN CA CB sing N N 87 GLN CA HA sing N N 88 GLN C O doub N N 89 GLN C OXT sing N N 90 GLN CB CG sing N N 91 GLN CB HB2 sing N N 92 GLN CB HB3 sing N N 93 GLN CG CD sing N N 94 GLN CG HG2 sing N N 95 GLN CG HG3 sing N N 96 GLN CD OE1 doub N N 97 GLN CD NE2 sing N N 98 GLN NE2 HE21 sing N N 99 GLN NE2 HE22 sing N N 100 GLN OXT HXT sing N N 101 GLU N CA sing N N 102 GLU N H sing N N 103 GLU N H2 sing N N 104 GLU CA C sing N N 105 GLU CA CB sing N N 106 GLU CA HA sing N N 107 GLU C O doub N N 108 GLU C OXT sing N N 109 GLU CB CG sing N N 110 GLU CB HB2 sing N N 111 GLU CB HB3 sing N N 112 GLU CG CD sing N N 113 GLU CG HG2 sing N N 114 GLU CG HG3 sing N N 115 GLU CD OE1 doub N N 116 GLU CD OE2 sing N N 117 GLU OE2 HE2 sing N N 118 GLU OXT HXT sing N N 119 GLY N CA sing N N 120 GLY N H sing N N 121 GLY N H2 sing N N 122 GLY CA C sing N N 123 GLY CA HA2 sing N N 124 GLY CA HA3 sing N N 125 GLY C O doub N N 126 GLY C OXT sing N N 127 GLY OXT HXT sing N N 128 HIS N CA sing N N 129 HIS N H sing N N 130 HIS N H2 sing N N 131 HIS CA C sing N N 132 HIS CA CB sing N N 133 HIS CA HA sing N N 134 HIS C O doub N N 135 HIS C OXT sing N N 136 HIS CB CG sing N N 137 HIS CB HB2 sing N N 138 HIS CB HB3 sing N N 139 HIS CG ND1 sing Y N 140 HIS CG CD2 doub Y N 141 HIS ND1 CE1 doub Y N 142 HIS ND1 HD1 sing N N 143 HIS CD2 NE2 sing Y N 144 HIS CD2 HD2 sing N N 145 HIS CE1 NE2 sing Y N 146 HIS CE1 HE1 sing N N 147 HIS NE2 HE2 sing N N 148 HIS OXT HXT sing N N 149 ILE N CA sing N N 150 ILE N H sing N N 151 ILE N H2 sing N N 152 ILE CA C sing N N 153 ILE CA CB sing N N 154 ILE CA HA sing N N 155 ILE C O doub N N 156 ILE C OXT sing N N 157 ILE CB CG1 sing N N 158 ILE CB CG2 sing N N 159 ILE CB HB sing N N 160 ILE CG1 CD1 sing N N 161 ILE CG1 HG12 sing N N 162 ILE CG1 HG13 sing N N 163 ILE CG2 HG21 sing N N 164 ILE CG2 HG22 sing N N 165 ILE CG2 HG23 sing N N 166 ILE CD1 HD11 sing N N 167 ILE CD1 HD12 sing N N 168 ILE CD1 HD13 sing N N 169 ILE OXT HXT sing N N 170 LEU N CA sing N N 171 LEU N H sing N N 172 LEU N H2 sing N N 173 LEU CA C sing N N 174 LEU CA CB sing N N 175 LEU CA HA sing N N 176 LEU C O doub N N 177 LEU C OXT sing N N 178 LEU CB CG sing N N 179 LEU CB HB2 sing N N 180 LEU CB HB3 sing N N 181 LEU CG CD1 sing N N 182 LEU CG CD2 sing N N 183 LEU CG HG sing N N 184 LEU CD1 HD11 sing N N 185 LEU CD1 HD12 sing N N 186 LEU CD1 HD13 sing N N 187 LEU CD2 HD21 sing N N 188 LEU CD2 HD22 sing N N 189 LEU CD2 HD23 sing N N 190 LEU OXT HXT sing N N 191 LYS N CA sing N N 192 LYS N H sing N N 193 LYS N H2 sing N N 194 LYS CA C sing N N 195 LYS CA CB sing N N 196 LYS CA HA sing N N 197 LYS C O doub N N 198 LYS C OXT sing N N 199 LYS CB CG sing N N 200 LYS CB HB2 sing N N 201 LYS CB HB3 sing N N 202 LYS CG CD sing N N 203 LYS CG HG2 sing N N 204 LYS CG HG3 sing N N 205 LYS CD CE sing N N 206 LYS CD HD2 sing N N 207 LYS CD HD3 sing N N 208 LYS CE NZ sing N N 209 LYS CE HE2 sing N N 210 LYS CE HE3 sing N N 211 LYS NZ HZ1 sing N N 212 LYS NZ HZ2 sing N N 213 LYS NZ HZ3 sing N N 214 LYS OXT HXT sing N N 215 MET N CA sing N N 216 MET N H sing N N 217 MET N H2 sing N N 218 MET CA C sing N N 219 MET CA CB sing N N 220 MET CA HA sing N N 221 MET C O doub N N 222 MET C OXT sing N N 223 MET CB CG sing N N 224 MET CB HB2 sing N N 225 MET CB HB3 sing N N 226 MET CG SD sing N N 227 MET CG HG2 sing N N 228 MET CG HG3 sing N N 229 MET SD CE sing N N 230 MET CE HE1 sing N N 231 MET CE HE2 sing N N 232 MET CE HE3 sing N N 233 MET OXT HXT sing N N 234 NAG C1 C2 sing N N 235 NAG C1 O1 sing N N 236 NAG C1 O5 sing N N 237 NAG C1 H1 sing N N 238 NAG C2 C3 sing N N 239 NAG C2 N2 sing N N 240 NAG C2 H2 sing N N 241 NAG C3 C4 sing N N 242 NAG C3 O3 sing N N 243 NAG C3 H3 sing N N 244 NAG C4 C5 sing N N 245 NAG C4 O4 sing N N 246 NAG C4 H4 sing N N 247 NAG C5 C6 sing N N 248 NAG C5 O5 sing N N 249 NAG C5 H5 sing N N 250 NAG C6 O6 sing N N 251 NAG C6 H61 sing N N 252 NAG C6 H62 sing N N 253 NAG C7 C8 sing N N 254 NAG C7 N2 sing N N 255 NAG C7 O7 doub N N 256 NAG C8 H81 sing N N 257 NAG C8 H82 sing N N 258 NAG C8 H83 sing N N 259 NAG N2 HN2 sing N N 260 NAG O1 HO1 sing N N 261 NAG O3 HO3 sing N N 262 NAG O4 HO4 sing N N 263 NAG O6 HO6 sing N N 264 PHE N CA sing N N 265 PHE N H sing N N 266 PHE N H2 sing N N 267 PHE CA C sing N N 268 PHE CA CB sing N N 269 PHE CA HA sing N N 270 PHE C O doub N N 271 PHE C OXT sing N N 272 PHE CB CG sing N N 273 PHE CB HB2 sing N N 274 PHE CB HB3 sing N N 275 PHE CG CD1 doub Y N 276 PHE CG CD2 sing Y N 277 PHE CD1 CE1 sing Y N 278 PHE CD1 HD1 sing N N 279 PHE CD2 CE2 doub Y N 280 PHE CD2 HD2 sing N N 281 PHE CE1 CZ doub Y N 282 PHE CE1 HE1 sing N N 283 PHE CE2 CZ sing Y N 284 PHE CE2 HE2 sing N N 285 PHE CZ HZ sing N N 286 PHE OXT HXT sing N N 287 PRO N CA sing N N 288 PRO N CD sing N N 289 PRO N H sing N N 290 PRO CA C sing N N 291 PRO CA CB sing N N 292 PRO CA HA sing N N 293 PRO C O doub N N 294 PRO C OXT sing N N 295 PRO CB CG sing N N 296 PRO CB HB2 sing N N 297 PRO CB HB3 sing N N 298 PRO CG CD sing N N 299 PRO CG HG2 sing N N 300 PRO CG HG3 sing N N 301 PRO CD HD2 sing N N 302 PRO CD HD3 sing N N 303 PRO OXT HXT sing N N 304 SER N CA sing N N 305 SER N H sing N N 306 SER N H2 sing N N 307 SER CA C sing N N 308 SER CA CB sing N N 309 SER CA HA sing N N 310 SER C O doub N N 311 SER C OXT sing N N 312 SER CB OG sing N N 313 SER CB HB2 sing N N 314 SER CB HB3 sing N N 315 SER OG HG sing N N 316 SER OXT HXT sing N N 317 THR N CA sing N N 318 THR N H sing N N 319 THR N H2 sing N N 320 THR CA C sing N N 321 THR CA CB sing N N 322 THR CA HA sing N N 323 THR C O doub N N 324 THR C OXT sing N N 325 THR CB OG1 sing N N 326 THR CB CG2 sing N N 327 THR CB HB sing N N 328 THR OG1 HG1 sing N N 329 THR CG2 HG21 sing N N 330 THR CG2 HG22 sing N N 331 THR CG2 HG23 sing N N 332 THR OXT HXT sing N N 333 TRP N CA sing N N 334 TRP N H sing N N 335 TRP N H2 sing N N 336 TRP CA C sing N N 337 TRP CA CB sing N N 338 TRP CA HA sing N N 339 TRP C O doub N N 340 TRP C OXT sing N N 341 TRP CB CG sing N N 342 TRP CB HB2 sing N N 343 TRP CB HB3 sing N N 344 TRP CG CD1 doub Y N 345 TRP CG CD2 sing Y N 346 TRP CD1 NE1 sing Y N 347 TRP CD1 HD1 sing N N 348 TRP CD2 CE2 doub Y N 349 TRP CD2 CE3 sing Y N 350 TRP NE1 CE2 sing Y N 351 TRP NE1 HE1 sing N N 352 TRP CE2 CZ2 sing Y N 353 TRP CE3 CZ3 doub Y N 354 TRP CE3 HE3 sing N N 355 TRP CZ2 CH2 doub Y N 356 TRP CZ2 HZ2 sing N N 357 TRP CZ3 CH2 sing Y N 358 TRP CZ3 HZ3 sing N N 359 TRP CH2 HH2 sing N N 360 TRP OXT HXT sing N N 361 TYR N CA sing N N 362 TYR N H sing N N 363 TYR N H2 sing N N 364 TYR CA C sing N N 365 TYR CA CB sing N N 366 TYR CA HA sing N N 367 TYR C O doub N N 368 TYR C OXT sing N N 369 TYR CB CG sing N N 370 TYR CB HB2 sing N N 371 TYR CB HB3 sing N N 372 TYR CG CD1 doub Y N 373 TYR CG CD2 sing Y N 374 TYR CD1 CE1 sing Y N 375 TYR CD1 HD1 sing N N 376 TYR CD2 CE2 doub Y N 377 TYR CD2 HD2 sing N N 378 TYR CE1 CZ doub Y N 379 TYR CE1 HE1 sing N N 380 TYR CE2 CZ sing Y N 381 TYR CE2 HE2 sing N N 382 TYR CZ OH sing N N 383 TYR OH HH sing N N 384 TYR OXT HXT sing N N 385 VAL N CA sing N N 386 VAL N H sing N N 387 VAL N H2 sing N N 388 VAL CA C sing N N 389 VAL CA CB sing N N 390 VAL CA HA sing N N 391 VAL C O doub N N 392 VAL C OXT sing N N 393 VAL CB CG1 sing N N 394 VAL CB CG2 sing N N 395 VAL CB HB sing N N 396 VAL CG1 HG11 sing N N 397 VAL CG1 HG12 sing N N 398 VAL CG1 HG13 sing N N 399 VAL CG2 HG21 sing N N 400 VAL CG2 HG22 sing N N 401 VAL CG2 HG23 sing N N 402 VAL OXT HXT sing N N 403 # _em_admin.entry_id 7WP5 _em_admin.current_status REL _em_admin.deposition_date 2022-01-22 _em_admin.deposition_site PDBJ _em_admin.last_update 2024-10-16 _em_admin.map_release_date 2022-07-13 _em_admin.title 'Cryo-EM structure of SARS-CoV-2 Omicron S6P trimer in complex with neutralizing antibody VacW-209 (local refinement)' # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' _em_ctf_correction.details ? # _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.ncbi_tax_id 9606 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'Homo sapiens' _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? # _em_entity_assembly_recombinant.id 2 _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.ncbi_tax_id 9606 _em_entity_assembly_recombinant.organism 'Homo sapiens' _em_entity_assembly_recombinant.plasmid ? _em_entity_assembly_recombinant.strain ? # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.avg_electron_dose_per_image 60 _em_image_recording.average_exposure_time ? _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 (6k x 4k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? _em_image_recording.avg_electron_dose_per_subtomogram ? # loop_ _em_software.id _em_software.category _em_software.details _em_software.name _em_software.version _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id 1 'CRYSTALLOGRAPHY MERGING' ? ? ? 1 1 1 2 'IMAGE ACQUISITION' ? ? ? ? ? 1 3 MASKING ? ? ? ? ? ? 4 'CTF CORRECTION' ? ? ? 1 ? ? 5 'LAYERLINE INDEXING' ? ? ? ? ? ? 6 'DIFFRACTION INDEXING' ? ? ? ? ? ? 7 'MODEL FITTING' ? ? ? ? ? ? 8 'MODEL REFINEMENT' ? ? ? ? ? ? 9 OTHER ? ? ? ? ? ? 10 'INITIAL EULER ASSIGNMENT' ? ? ? 1 ? ? 11 'FINAL EULER ASSIGNMENT' ? ? ? 1 ? ? 12 CLASSIFICATION ? ? ? 1 ? ? 13 RECONSTRUCTION ? ? ? 1 ? ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # _pdbx_audit_support.funding_organization 'Not funded' _pdbx_audit_support.country ? _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.hetero 4 NAG 1 n 4 NAG 2 n # _atom_sites.entry_id 7WP5 _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O S # loop_