data_9KVJ # _entry.id 9KVJ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.407 _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 9KVJ pdb_00009kvj 10.2210/pdb9kvj/pdb WWPDB D_1300049863 ? ? EMDB EMD-62596 ? ? # 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 _pdbx_audit_revision_history.part_number 1 'Structure model' 1 0 2025-12-10 ? 2 'EM metadata' 1 0 2025-12-10 ? 3 'Half map' 1 0 2025-12-10 1 4 'Half map' 1 0 2025-12-10 2 5 Image 1 0 2025-12-10 ? 6 'Primary map' 1 0 2025-12-10 ? # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 2 'EM metadata' repository 'Initial release' ? ? 3 3 'Half map' repository 'Initial release' ? ? 4 4 'Half map' repository 'Initial release' ? ? 5 5 Image repository 'Initial release' ? ? 6 6 'Primary map' repository 'Initial release' ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9KVJ _pdbx_database_status.recvd_initial_deposition_date 2024-12-05 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBC _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 BA.5 spike protein in complex with nAb 1C4 (local refinement)' _pdbx_database_related.db_id EMD-62596 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 3 _pdbx_contact_author.email abing0811@xmu.edu.cn _pdbx_contact_author.name_first Qingbing _pdbx_contact_author.name_last Zheng _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-7516-9965 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Sun, H.' 1 ? 'Jiang, Y.' 2 ? 'Li, S.' 3 ? 'Zheng, Q.' 4 ? # _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 ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Cryo-EM structure of SARS-CoV-2 BA.5 spike protein in complex with nAb 1C4 (local refinement)' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sun, H.' 1 ? primary 'Jiang, Y.' 2 ? primary 'Li, S.' 3 ? primary 'Zheng, Q.' 4 ? # 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 nat 'Heavy chain of nAb 1C4' 13384.900 1 ? ? ? ? 2 polymer nat 'Light chain of nAb 1C4' 11642.854 1 ? ? ? ? 3 polymer man 'Spike protein S1' 22168.045 1 ? ? ? ? 4 branched man ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; 732.682 1 ? ? ? ? # 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 ;QIQLVQSGPELKKPGETVKISCKASGYTFTDYGLNWVKQAPGKGLKWMGWINTYSGEPTYNDEFRGRFAFSLETSTITAY LKINNLKNEDTATYFCARGGNWDWYFDVWGAGTTVTVSS ; ;QIQLVQSGPELKKPGETVKISCKASGYTFTDYGLNWVKQAPGKGLKWMGWINTYSGEPTYNDEFRGRFAFSLETSTITAY LKINNLKNEDTATYFCARGGNWDWYFDVWGAGTTVTVSS ; C ? 2 'polypeptide(L)' no no ;DIVLTQSPATLSVTPGDNVSLSCRASQIISNNLHWYQQKSHESPRLLIKYASQSISGIPSRFSGSGSGTDFTLSINSVET EDFGMYFCQQSNTWPLTCGSGTKLELN ; ;DIVLTQSPATLSVTPGDNVSLSCRASQIISNNLHWYQQKSHESPRLLIKYASQSISGIPSRFSGSGSGTDFTLSINSVET EDFGMYFCQQSNTWPLTCGSGTKLELN ; D ? 3 'polypeptide(L)' no no ;TNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAP GQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGVNCYFPL QSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGKK ; ;TNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAP GQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGVNCYFPL QSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGKK ; G ? # 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 ILE n 1 3 GLN n 1 4 LEU n 1 5 VAL n 1 6 GLN n 1 7 SER n 1 8 GLY n 1 9 PRO n 1 10 GLU n 1 11 LEU n 1 12 LYS n 1 13 LYS n 1 14 PRO n 1 15 GLY n 1 16 GLU n 1 17 THR n 1 18 VAL n 1 19 LYS n 1 20 ILE n 1 21 SER n 1 22 CYS n 1 23 LYS n 1 24 ALA n 1 25 SER n 1 26 GLY n 1 27 TYR n 1 28 THR n 1 29 PHE n 1 30 THR n 1 31 ASP n 1 32 TYR n 1 33 GLY n 1 34 LEU n 1 35 ASN n 1 36 TRP n 1 37 VAL n 1 38 LYS n 1 39 GLN n 1 40 ALA n 1 41 PRO n 1 42 GLY n 1 43 LYS n 1 44 GLY n 1 45 LEU n 1 46 LYS n 1 47 TRP n 1 48 MET n 1 49 GLY n 1 50 TRP n 1 51 ILE n 1 52 ASN n 1 53 THR n 1 54 TYR n 1 55 SER n 1 56 GLY n 1 57 GLU n 1 58 PRO n 1 59 THR n 1 60 TYR n 1 61 ASN n 1 62 ASP n 1 63 GLU n 1 64 PHE n 1 65 ARG n 1 66 GLY n 1 67 ARG n 1 68 PHE n 1 69 ALA n 1 70 PHE n 1 71 SER n 1 72 LEU n 1 73 GLU n 1 74 THR n 1 75 SER n 1 76 THR n 1 77 ILE n 1 78 THR n 1 79 ALA n 1 80 TYR n 1 81 LEU n 1 82 LYS n 1 83 ILE n 1 84 ASN n 1 85 ASN n 1 86 LEU n 1 87 LYS n 1 88 ASN n 1 89 GLU n 1 90 ASP n 1 91 THR n 1 92 ALA n 1 93 THR n 1 94 TYR n 1 95 PHE n 1 96 CYS n 1 97 ALA n 1 98 ARG n 1 99 GLY n 1 100 GLY n 1 101 ASN n 1 102 TRP n 1 103 ASP n 1 104 TRP n 1 105 TYR n 1 106 PHE n 1 107 ASP n 1 108 VAL n 1 109 TRP n 1 110 GLY n 1 111 ALA n 1 112 GLY n 1 113 THR n 1 114 THR n 1 115 VAL n 1 116 THR n 1 117 VAL n 1 118 SER n 1 119 SER n 2 1 ASP n 2 2 ILE n 2 3 VAL n 2 4 LEU n 2 5 THR n 2 6 GLN n 2 7 SER n 2 8 PRO n 2 9 ALA n 2 10 THR n 2 11 LEU n 2 12 SER n 2 13 VAL n 2 14 THR n 2 15 PRO n 2 16 GLY n 2 17 ASP n 2 18 ASN n 2 19 VAL n 2 20 SER n 2 21 LEU n 2 22 SER n 2 23 CYS n 2 24 ARG n 2 25 ALA n 2 26 SER n 2 27 GLN n 2 28 ILE n 2 29 ILE n 2 30 SER n 2 31 ASN n 2 32 ASN n 2 33 LEU n 2 34 HIS n 2 35 TRP n 2 36 TYR n 2 37 GLN n 2 38 GLN n 2 39 LYS n 2 40 SER n 2 41 HIS n 2 42 GLU n 2 43 SER n 2 44 PRO n 2 45 ARG n 2 46 LEU n 2 47 LEU n 2 48 ILE n 2 49 LYS n 2 50 TYR n 2 51 ALA n 2 52 SER n 2 53 GLN n 2 54 SER n 2 55 ILE n 2 56 SER n 2 57 GLY n 2 58 ILE n 2 59 PRO n 2 60 SER n 2 61 ARG n 2 62 PHE n 2 63 SER n 2 64 GLY n 2 65 SER n 2 66 GLY n 2 67 SER n 2 68 GLY n 2 69 THR n 2 70 ASP n 2 71 PHE n 2 72 THR n 2 73 LEU n 2 74 SER n 2 75 ILE n 2 76 ASN n 2 77 SER n 2 78 VAL n 2 79 GLU n 2 80 THR n 2 81 GLU n 2 82 ASP n 2 83 PHE n 2 84 GLY n 2 85 MET n 2 86 TYR n 2 87 PHE n 2 88 CYS n 2 89 GLN n 2 90 GLN n 2 91 SER n 2 92 ASN n 2 93 THR n 2 94 TRP n 2 95 PRO n 2 96 LEU n 2 97 THR n 2 98 CYS n 2 99 GLY n 2 100 SER n 2 101 GLY n 2 102 THR n 2 103 LYS n 2 104 LEU n 2 105 GLU n 2 106 LEU n 2 107 ASN 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 PHE n 3 40 ALA n 3 41 PRO n 3 42 PHE n 3 43 PHE n 3 44 ALA 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 ASN n 3 74 GLU n 3 75 VAL n 3 76 SER 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 GLY n 3 115 GLY n 3 116 ASN n 3 117 TYR n 3 118 ASN n 3 119 TYR n 3 120 ARG 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 VAL 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 GLN n 3 162 SER n 3 163 TYR n 3 164 GLY 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 3 190 ALA n 3 191 THR n 3 192 VAL n 3 193 CYS n 3 194 GLY n 3 195 LYS n 3 196 LYS n # _entity_src_gen.entity_id 3 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 196 _entity_src_gen.gene_src_common_name '2019-nCoV, SARS-CoV-2' _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'S, 2' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'BA.5, Omicron' _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 'Severe acute respiratory syndrome coronavirus 2' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 2697049 _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 'Homo sapiens' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 9606 _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 ? # loop_ _entity_src_nat.entity_id _entity_src_nat.pdbx_src_id _entity_src_nat.pdbx_alt_source_flag _entity_src_nat.pdbx_beg_seq_num _entity_src_nat.pdbx_end_seq_num _entity_src_nat.common_name _entity_src_nat.pdbx_organism_scientific _entity_src_nat.pdbx_ncbi_taxonomy_id _entity_src_nat.genus _entity_src_nat.species _entity_src_nat.strain _entity_src_nat.tissue _entity_src_nat.tissue_fraction _entity_src_nat.pdbx_secretion _entity_src_nat.pdbx_fragment _entity_src_nat.pdbx_variant _entity_src_nat.pdbx_cell_line _entity_src_nat.pdbx_atcc _entity_src_nat.pdbx_cellular_location _entity_src_nat.pdbx_organ _entity_src_nat.pdbx_organelle _entity_src_nat.pdbx_cell _entity_src_nat.pdbx_plasmid_name _entity_src_nat.pdbx_plasmid_details _entity_src_nat.details 1 1 sample 1 119 ? 'Mus musculus' 10090 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 sample 1 107 ? 'Mus musculus' 10090 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 'DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-' 'Glycam Condensed Sequence' GMML 1.0 2 4 'WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1' WURCS PDB2Glycan 1.1.0 3 4 '[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}' 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 4 2 NAG C1 O1 1 NAG O4 HO4 sing ? 2 4 3 BMA C1 O1 2 NAG O4 HO4 sing ? 3 4 4 FUC C1 O1 1 NAG O6 HO6 sing ? # 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 BMA 'D-saccharide, beta linking' . beta-D-mannopyranose 'beta-D-mannose; D-mannose; mannose' 'C6 H12 O6' 180.156 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 FUC 'L-saccharide, alpha linking' . alpha-L-fucopyranose 'alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose' 'C6 H12 O5' 164.156 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 BMA 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DManpb BMA 'COMMON NAME' GMML 1.0 b-D-mannopyranose BMA 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-Manp BMA 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Man FUC 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 LFucpa FUC 'COMMON NAME' GMML 1.0 a-L-fucopyranose FUC 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-L-Fucp FUC 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Fuc 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 C . n A 1 2 ILE 2 2 2 ILE ILE C . n A 1 3 GLN 3 3 3 GLN GLN C . n A 1 4 LEU 4 4 4 LEU LEU C . n A 1 5 VAL 5 5 5 VAL VAL C . n A 1 6 GLN 6 6 6 GLN GLN C . n A 1 7 SER 7 7 7 SER SER C . n A 1 8 GLY 8 8 8 GLY GLY C . n A 1 9 PRO 9 9 9 PRO PRO C . n A 1 10 GLU 10 10 10 GLU GLU C . n A 1 11 LEU 11 11 11 LEU LEU C . n A 1 12 LYS 12 12 12 LYS LYS C . n A 1 13 LYS 13 13 13 LYS LYS C . n A 1 14 PRO 14 14 14 PRO PRO C . n A 1 15 GLY 15 15 15 GLY GLY C . n A 1 16 GLU 16 16 16 GLU GLU C . n A 1 17 THR 17 17 17 THR THR C . n A 1 18 VAL 18 18 18 VAL VAL C . n A 1 19 LYS 19 19 19 LYS LYS C . n A 1 20 ILE 20 20 20 ILE ILE C . n A 1 21 SER 21 21 21 SER SER C . n A 1 22 CYS 22 22 22 CYS CYS C . n A 1 23 LYS 23 23 23 LYS LYS C . n A 1 24 ALA 24 24 24 ALA ALA C . n A 1 25 SER 25 25 25 SER SER C . n A 1 26 GLY 26 26 26 GLY GLY C . n A 1 27 TYR 27 27 27 TYR TYR C . n A 1 28 THR 28 28 28 THR THR C . n A 1 29 PHE 29 29 29 PHE PHE C . n A 1 30 THR 30 30 30 THR THR C . n A 1 31 ASP 31 31 31 ASP ASP C . n A 1 32 TYR 32 32 32 TYR TYR C . n A 1 33 GLY 33 33 33 GLY GLY C . n A 1 34 LEU 34 34 34 LEU LEU C . n A 1 35 ASN 35 35 35 ASN ASN C . n A 1 36 TRP 36 36 36 TRP TRP C . n A 1 37 VAL 37 37 37 VAL VAL C . n A 1 38 LYS 38 38 38 LYS LYS C . n A 1 39 GLN 39 39 39 GLN GLN C . n A 1 40 ALA 40 40 40 ALA ALA C . n A 1 41 PRO 41 41 41 PRO PRO C . n A 1 42 GLY 42 42 42 GLY GLY C . n A 1 43 LYS 43 43 43 LYS LYS C . n A 1 44 GLY 44 44 44 GLY GLY C . n A 1 45 LEU 45 45 45 LEU LEU C . n A 1 46 LYS 46 46 46 LYS LYS C . n A 1 47 TRP 47 47 47 TRP TRP C . n A 1 48 MET 48 48 48 MET MET C . n A 1 49 GLY 49 49 49 GLY GLY C . n A 1 50 TRP 50 50 50 TRP TRP C . n A 1 51 ILE 51 51 51 ILE ILE C . n A 1 52 ASN 52 52 52 ASN ASN C . n A 1 53 THR 53 53 53 THR THR C . n A 1 54 TYR 54 54 54 TYR TYR C . n A 1 55 SER 55 55 55 SER SER C . n A 1 56 GLY 56 56 56 GLY GLY C . n A 1 57 GLU 57 57 57 GLU GLU C . n A 1 58 PRO 58 58 58 PRO PRO C . n A 1 59 THR 59 59 59 THR THR C . n A 1 60 TYR 60 60 60 TYR TYR C . n A 1 61 ASN 61 61 61 ASN ASN C . n A 1 62 ASP 62 62 62 ASP ASP C . n A 1 63 GLU 63 63 63 GLU GLU C . n A 1 64 PHE 64 64 64 PHE PHE C . n A 1 65 ARG 65 65 65 ARG ARG C . n A 1 66 GLY 66 66 66 GLY GLY C . n A 1 67 ARG 67 67 67 ARG ARG C . n A 1 68 PHE 68 68 68 PHE PHE C . n A 1 69 ALA 69 69 69 ALA ALA C . n A 1 70 PHE 70 70 70 PHE PHE C . n A 1 71 SER 71 71 71 SER SER C . n A 1 72 LEU 72 72 72 LEU LEU C . n A 1 73 GLU 73 73 73 GLU GLU C . n A 1 74 THR 74 74 74 THR THR C . n A 1 75 SER 75 75 75 SER SER C . n A 1 76 THR 76 76 76 THR THR C . n A 1 77 ILE 77 77 77 ILE ILE C . n A 1 78 THR 78 78 78 THR THR C . n A 1 79 ALA 79 79 79 ALA ALA C . n A 1 80 TYR 80 80 80 TYR TYR C . n A 1 81 LEU 81 81 81 LEU LEU C . n A 1 82 LYS 82 82 82 LYS LYS C . n A 1 83 ILE 83 83 83 ILE ILE C . n A 1 84 ASN 84 84 84 ASN ASN C . n A 1 85 ASN 85 85 85 ASN ASN C . n A 1 86 LEU 86 86 86 LEU LEU C . n A 1 87 LYS 87 87 87 LYS LYS C . n A 1 88 ASN 88 88 88 ASN ASN C . n A 1 89 GLU 89 89 89 GLU GLU C . n A 1 90 ASP 90 90 90 ASP ASP C . n A 1 91 THR 91 91 91 THR THR C . n A 1 92 ALA 92 92 92 ALA ALA C . n A 1 93 THR 93 93 93 THR THR C . n A 1 94 TYR 94 94 94 TYR TYR C . n A 1 95 PHE 95 95 95 PHE PHE C . n A 1 96 CYS 96 96 96 CYS CYS C . n A 1 97 ALA 97 97 97 ALA ALA C . n A 1 98 ARG 98 98 98 ARG ARG C . n A 1 99 GLY 99 99 99 GLY GLY C . n A 1 100 GLY 100 100 100 GLY GLY C . n A 1 101 ASN 101 101 101 ASN ASN C . n A 1 102 TRP 102 102 102 TRP TRP C . n A 1 103 ASP 103 103 103 ASP ASP C . n A 1 104 TRP 104 104 104 TRP TRP C . n A 1 105 TYR 105 105 105 TYR TYR C . n A 1 106 PHE 106 106 106 PHE PHE C . n A 1 107 ASP 107 107 107 ASP ASP C . n A 1 108 VAL 108 108 108 VAL VAL C . n A 1 109 TRP 109 109 109 TRP TRP C . n A 1 110 GLY 110 110 110 GLY GLY C . n A 1 111 ALA 111 111 111 ALA ALA C . n A 1 112 GLY 112 112 112 GLY GLY C . n A 1 113 THR 113 113 113 THR THR C . n A 1 114 THR 114 114 114 THR THR C . n A 1 115 VAL 115 115 115 VAL VAL C . n A 1 116 THR 116 116 116 THR THR C . n A 1 117 VAL 117 117 117 VAL VAL C . n A 1 118 SER 118 118 118 SER SER C . n A 1 119 SER 119 119 119 SER SER C . n B 2 1 ASP 1 1 1 ASP ASP D . n B 2 2 ILE 2 2 2 ILE ILE D . n B 2 3 VAL 3 3 3 VAL VAL D . n B 2 4 LEU 4 4 4 LEU LEU D . n B 2 5 THR 5 5 5 THR THR D . n B 2 6 GLN 6 6 6 GLN GLN D . n B 2 7 SER 7 7 7 SER SER D . n B 2 8 PRO 8 8 8 PRO PRO D . n B 2 9 ALA 9 9 9 ALA ALA D . n B 2 10 THR 10 10 10 THR THR D . n B 2 11 LEU 11 11 11 LEU LEU D . n B 2 12 SER 12 12 12 SER SER D . n B 2 13 VAL 13 13 13 VAL VAL D . n B 2 14 THR 14 14 14 THR THR D . n B 2 15 PRO 15 15 15 PRO PRO D . n B 2 16 GLY 16 16 16 GLY GLY D . n B 2 17 ASP 17 17 17 ASP ASP D . n B 2 18 ASN 18 18 18 ASN ASN D . n B 2 19 VAL 19 19 19 VAL VAL D . n B 2 20 SER 20 20 20 SER SER D . n B 2 21 LEU 21 21 21 LEU LEU D . n B 2 22 SER 22 22 22 SER SER D . n B 2 23 CYS 23 23 23 CYS CYS D . n B 2 24 ARG 24 24 24 ARG ARG D . n B 2 25 ALA 25 25 25 ALA ALA D . n B 2 26 SER 26 26 26 SER SER D . n B 2 27 GLN 27 27 27 GLN GLN D . n B 2 28 ILE 28 28 28 ILE ILE D . n B 2 29 ILE 29 29 29 ILE ILE D . n B 2 30 SER 30 30 30 SER SER D . n B 2 31 ASN 31 31 31 ASN ASN D . n B 2 32 ASN 32 32 32 ASN ASN D . n B 2 33 LEU 33 33 33 LEU LEU D . n B 2 34 HIS 34 34 34 HIS HIS D . n B 2 35 TRP 35 35 35 TRP TRP D . n B 2 36 TYR 36 36 36 TYR TYR D . n B 2 37 GLN 37 37 37 GLN GLN D . n B 2 38 GLN 38 38 38 GLN GLN D . n B 2 39 LYS 39 39 39 LYS LYS D . n B 2 40 SER 40 40 40 SER SER D . n B 2 41 HIS 41 41 41 HIS HIS D . n B 2 42 GLU 42 42 42 GLU GLU D . n B 2 43 SER 43 43 43 SER SER D . n B 2 44 PRO 44 44 44 PRO PRO D . n B 2 45 ARG 45 45 45 ARG ARG D . n B 2 46 LEU 46 46 46 LEU LEU D . n B 2 47 LEU 47 47 47 LEU LEU D . n B 2 48 ILE 48 48 48 ILE ILE D . n B 2 49 LYS 49 49 49 LYS LYS D . n B 2 50 TYR 50 50 50 TYR TYR D . n B 2 51 ALA 51 51 51 ALA ALA D . n B 2 52 SER 52 52 52 SER SER D . n B 2 53 GLN 53 53 53 GLN GLN D . n B 2 54 SER 54 54 54 SER SER D . n B 2 55 ILE 55 55 55 ILE ILE D . n B 2 56 SER 56 56 56 SER SER D . n B 2 57 GLY 57 57 57 GLY GLY D . n B 2 58 ILE 58 58 58 ILE ILE D . n B 2 59 PRO 59 59 59 PRO PRO D . n B 2 60 SER 60 60 60 SER SER D . n B 2 61 ARG 61 61 61 ARG ARG D . n B 2 62 PHE 62 62 62 PHE PHE D . n B 2 63 SER 63 63 63 SER SER D . n B 2 64 GLY 64 64 64 GLY GLY D . n B 2 65 SER 65 65 65 SER SER D . n B 2 66 GLY 66 66 66 GLY GLY D . n B 2 67 SER 67 67 67 SER SER D . n B 2 68 GLY 68 68 68 GLY GLY D . n B 2 69 THR 69 69 69 THR THR D . n B 2 70 ASP 70 70 70 ASP ASP D . n B 2 71 PHE 71 71 71 PHE PHE D . n B 2 72 THR 72 72 72 THR THR D . n B 2 73 LEU 73 73 73 LEU LEU D . n B 2 74 SER 74 74 74 SER SER D . n B 2 75 ILE 75 75 75 ILE ILE D . n B 2 76 ASN 76 76 76 ASN ASN D . n B 2 77 SER 77 77 77 SER SER D . n B 2 78 VAL 78 78 78 VAL VAL D . n B 2 79 GLU 79 79 79 GLU GLU D . n B 2 80 THR 80 80 80 THR THR D . n B 2 81 GLU 81 81 81 GLU GLU D . n B 2 82 ASP 82 82 82 ASP ASP D . n B 2 83 PHE 83 83 83 PHE PHE D . n B 2 84 GLY 84 84 84 GLY GLY D . n B 2 85 MET 85 85 85 MET MET D . n B 2 86 TYR 86 86 86 TYR TYR D . n B 2 87 PHE 87 87 87 PHE PHE D . n B 2 88 CYS 88 88 88 CYS CYS D . n B 2 89 GLN 89 89 89 GLN GLN D . n B 2 90 GLN 90 90 90 GLN GLN D . n B 2 91 SER 91 91 91 SER SER D . n B 2 92 ASN 92 92 92 ASN ASN D . n B 2 93 THR 93 93 93 THR THR D . n B 2 94 TRP 94 94 94 TRP TRP D . n B 2 95 PRO 95 95 95 PRO PRO D . n B 2 96 LEU 96 96 96 LEU LEU D . n B 2 97 THR 97 97 97 THR THR D . n B 2 98 CYS 98 98 98 CYS CYS D . n B 2 99 GLY 99 99 99 GLY GLY D . n B 2 100 SER 100 100 100 SER SER D . n B 2 101 GLY 101 101 101 GLY GLY D . n B 2 102 THR 102 102 102 THR THR D . n B 2 103 LYS 103 103 103 LYS LYS D . n B 2 104 LEU 104 104 104 LEU LEU D . n B 2 105 GLU 105 105 105 GLU GLU D . n B 2 106 LEU 106 106 106 LEU LEU D . n B 2 107 ASN 107 107 107 ASN ASN D . n C 3 1 THR 1 333 333 THR THR G . n C 3 2 ASN 2 334 334 ASN ASN G . n C 3 3 LEU 3 335 335 LEU LEU G . n C 3 4 CYS 4 336 336 CYS CYS G . n C 3 5 PRO 5 337 337 PRO PRO G . n C 3 6 PHE 6 338 338 PHE PHE G . n C 3 7 ASP 7 339 339 ASP ASP G . n C 3 8 GLU 8 340 340 GLU GLU G . n C 3 9 VAL 9 341 341 VAL VAL G . n C 3 10 PHE 10 342 342 PHE PHE G . n C 3 11 ASN 11 343 343 ASN ASN G . n C 3 12 ALA 12 344 344 ALA ALA G . n C 3 13 THR 13 345 345 THR THR G . n C 3 14 ARG 14 346 346 ARG ARG G . n C 3 15 PHE 15 347 347 PHE PHE G . n C 3 16 ALA 16 348 348 ALA ALA G . n C 3 17 SER 17 349 349 SER SER G . n C 3 18 VAL 18 350 350 VAL VAL G . n C 3 19 TYR 19 351 351 TYR TYR G . n C 3 20 ALA 20 352 352 ALA ALA G . n C 3 21 TRP 21 353 353 TRP TRP G . n C 3 22 ASN 22 354 354 ASN ASN G . n C 3 23 ARG 23 355 355 ARG ARG G . n C 3 24 LYS 24 356 356 LYS LYS G . n C 3 25 ARG 25 357 357 ARG ARG G . n C 3 26 ILE 26 358 358 ILE ILE G . n C 3 27 SER 27 359 359 SER SER G . n C 3 28 ASN 28 360 360 ASN ASN G . n C 3 29 CYS 29 361 361 CYS CYS G . n C 3 30 VAL 30 362 362 VAL VAL G . n C 3 31 ALA 31 363 363 ALA ALA G . n C 3 32 ASP 32 364 364 ASP ASP G . n C 3 33 TYR 33 365 365 TYR TYR G . n C 3 34 SER 34 366 366 SER SER G . n C 3 35 VAL 35 367 367 VAL VAL G . n C 3 36 LEU 36 368 368 LEU LEU G . n C 3 37 TYR 37 369 369 TYR TYR G . n C 3 38 ASN 38 370 370 ASN ASN G . n C 3 39 PHE 39 371 371 PHE PHE G . n C 3 40 ALA 40 372 372 ALA ALA G . n C 3 41 PRO 41 373 373 PRO PRO G . n C 3 42 PHE 42 374 374 PHE PHE G . n C 3 43 PHE 43 375 375 PHE PHE G . n C 3 44 ALA 44 376 376 ALA ALA G . n C 3 45 PHE 45 377 377 PHE PHE G . n C 3 46 LYS 46 378 378 LYS LYS G . n C 3 47 CYS 47 379 379 CYS CYS G . n C 3 48 TYR 48 380 380 TYR TYR G . n C 3 49 GLY 49 381 381 GLY GLY G . n C 3 50 VAL 50 382 382 VAL VAL G . n C 3 51 SER 51 383 383 SER SER G . n C 3 52 PRO 52 384 384 PRO PRO G . n C 3 53 THR 53 385 385 THR THR G . n C 3 54 LYS 54 386 386 LYS LYS G . n C 3 55 LEU 55 387 387 LEU LEU G . n C 3 56 ASN 56 388 388 ASN ASN G . n C 3 57 ASP 57 389 389 ASP ASP G . n C 3 58 LEU 58 390 390 LEU LEU G . n C 3 59 CYS 59 391 391 CYS CYS G . n C 3 60 PHE 60 392 392 PHE PHE G . n C 3 61 THR 61 393 393 THR THR G . n C 3 62 ASN 62 394 394 ASN ASN G . n C 3 63 VAL 63 395 395 VAL VAL G . n C 3 64 TYR 64 396 396 TYR TYR G . n C 3 65 ALA 65 397 397 ALA ALA G . n C 3 66 ASP 66 398 398 ASP ASP G . n C 3 67 SER 67 399 399 SER SER G . n C 3 68 PHE 68 400 400 PHE PHE G . n C 3 69 VAL 69 401 401 VAL VAL G . n C 3 70 ILE 70 402 402 ILE ILE G . n C 3 71 ARG 71 403 403 ARG ARG G . n C 3 72 GLY 72 404 404 GLY GLY G . n C 3 73 ASN 73 405 405 ASN ASN G . n C 3 74 GLU 74 406 406 GLU GLU G . n C 3 75 VAL 75 407 407 VAL VAL G . n C 3 76 SER 76 408 408 SER SER G . n C 3 77 GLN 77 409 409 GLN GLN G . n C 3 78 ILE 78 410 410 ILE ILE G . n C 3 79 ALA 79 411 411 ALA ALA G . n C 3 80 PRO 80 412 412 PRO PRO G . n C 3 81 GLY 81 413 413 GLY GLY G . n C 3 82 GLN 82 414 414 GLN GLN G . n C 3 83 THR 83 415 415 THR THR G . n C 3 84 GLY 84 416 416 GLY GLY G . n C 3 85 ASN 85 417 417 ASN ASN G . n C 3 86 ILE 86 418 418 ILE ILE G . n C 3 87 ALA 87 419 419 ALA ALA G . n C 3 88 ASP 88 420 420 ASP ASP G . n C 3 89 TYR 89 421 421 TYR TYR G . n C 3 90 ASN 90 422 422 ASN ASN G . n C 3 91 TYR 91 423 423 TYR TYR G . n C 3 92 LYS 92 424 424 LYS LYS G . n C 3 93 LEU 93 425 425 LEU LEU G . n C 3 94 PRO 94 426 426 PRO PRO G . n C 3 95 ASP 95 427 427 ASP ASP G . n C 3 96 ASP 96 428 428 ASP ASP G . n C 3 97 PHE 97 429 429 PHE PHE G . n C 3 98 THR 98 430 430 THR THR G . n C 3 99 GLY 99 431 431 GLY GLY G . n C 3 100 CYS 100 432 432 CYS CYS G . n C 3 101 VAL 101 433 433 VAL VAL G . n C 3 102 ILE 102 434 434 ILE ILE G . n C 3 103 ALA 103 435 435 ALA ALA G . n C 3 104 TRP 104 436 436 TRP TRP G . n C 3 105 ASN 105 437 437 ASN ASN G . n C 3 106 SER 106 438 438 SER SER G . n C 3 107 ASN 107 439 439 ASN ASN G . n C 3 108 LYS 108 440 440 LYS LYS G . n C 3 109 LEU 109 441 441 LEU LEU G . n C 3 110 ASP 110 442 442 ASP ASP G . n C 3 111 SER 111 443 443 SER SER G . n C 3 112 LYS 112 444 444 LYS LYS G . n C 3 113 VAL 113 445 445 VAL VAL G . n C 3 114 GLY 114 446 446 GLY GLY G . n C 3 115 GLY 115 447 447 GLY GLY G . n C 3 116 ASN 116 448 448 ASN ASN G . n C 3 117 TYR 117 449 449 TYR TYR G . n C 3 118 ASN 118 450 450 ASN ASN G . n C 3 119 TYR 119 451 451 TYR TYR G . n C 3 120 ARG 120 452 452 ARG ARG G . n C 3 121 TYR 121 453 453 TYR TYR G . n C 3 122 ARG 122 454 454 ARG ARG G . n C 3 123 LEU 123 455 455 LEU LEU G . n C 3 124 PHE 124 456 456 PHE PHE G . n C 3 125 ARG 125 457 457 ARG ARG G . n C 3 126 LYS 126 458 458 LYS LYS G . n C 3 127 SER 127 459 459 SER SER G . n C 3 128 ASN 128 460 460 ASN ASN G . n C 3 129 LEU 129 461 461 LEU LEU G . n C 3 130 LYS 130 462 462 LYS LYS G . n C 3 131 PRO 131 463 463 PRO PRO G . n C 3 132 PHE 132 464 464 PHE PHE G . n C 3 133 GLU 133 465 465 GLU GLU G . n C 3 134 ARG 134 466 466 ARG ARG G . n C 3 135 ASP 135 467 467 ASP ASP G . n C 3 136 ILE 136 468 468 ILE ILE G . n C 3 137 SER 137 469 469 SER SER G . n C 3 138 THR 138 470 470 THR THR G . n C 3 139 GLU 139 471 471 GLU GLU G . n C 3 140 ILE 140 472 472 ILE ILE G . n C 3 141 TYR 141 473 473 TYR TYR G . n C 3 142 GLN 142 474 474 GLN GLN G . n C 3 143 ALA 143 475 475 ALA ALA G . n C 3 144 GLY 144 476 476 GLY GLY G . n C 3 145 ASN 145 477 477 ASN ASN G . n C 3 146 LYS 146 478 478 LYS LYS G . n C 3 147 PRO 147 479 479 PRO PRO G . n C 3 148 CYS 148 480 480 CYS CYS G . n C 3 149 ASN 149 481 481 ASN ASN G . n C 3 150 GLY 150 482 482 GLY GLY G . n C 3 151 VAL 151 483 483 VAL VAL G . n C 3 152 ALA 152 484 484 ALA ALA G . n C 3 153 GLY 153 485 485 GLY GLY G . n C 3 154 VAL 154 486 486 VAL VAL G . n C 3 155 ASN 155 487 487 ASN ASN G . n C 3 156 CYS 156 488 488 CYS CYS G . n C 3 157 TYR 157 489 489 TYR TYR G . n C 3 158 PHE 158 490 490 PHE PHE G . n C 3 159 PRO 159 491 491 PRO PRO G . n C 3 160 LEU 160 492 492 LEU LEU G . n C 3 161 GLN 161 493 493 GLN GLN G . n C 3 162 SER 162 494 494 SER SER G . n C 3 163 TYR 163 495 495 TYR TYR G . n C 3 164 GLY 164 496 496 GLY GLY G . n C 3 165 PHE 165 497 497 PHE PHE G . n C 3 166 ARG 166 498 498 ARG ARG G . n C 3 167 PRO 167 499 499 PRO PRO G . n C 3 168 THR 168 500 500 THR THR G . n C 3 169 TYR 169 501 501 TYR TYR G . n C 3 170 GLY 170 502 502 GLY GLY G . n C 3 171 VAL 171 503 503 VAL VAL G . n C 3 172 GLY 172 504 504 GLY GLY G . n C 3 173 HIS 173 505 505 HIS HIS G . n C 3 174 GLN 174 506 506 GLN GLN G . n C 3 175 PRO 175 507 507 PRO PRO G . n C 3 176 TYR 176 508 508 TYR TYR G . n C 3 177 ARG 177 509 509 ARG ARG G . n C 3 178 VAL 178 510 510 VAL VAL G . n C 3 179 VAL 179 511 511 VAL VAL G . n C 3 180 VAL 180 512 512 VAL VAL G . n C 3 181 LEU 181 513 513 LEU LEU G . n C 3 182 SER 182 514 514 SER SER G . n C 3 183 PHE 183 515 515 PHE PHE G . n C 3 184 GLU 184 516 516 GLU GLU G . n C 3 185 LEU 185 517 517 LEU LEU G . n C 3 186 LEU 186 518 ? ? ? G . n C 3 187 HIS 187 519 ? ? ? G . n C 3 188 ALA 188 520 520 ALA ALA G . n C 3 189 PRO 189 521 521 PRO PRO G . n C 3 190 ALA 190 522 522 ALA ALA G . n C 3 191 THR 191 523 523 THR THR G . n C 3 192 VAL 192 524 524 VAL VAL G . n C 3 193 CYS 193 525 525 CYS CYS G . n C 3 194 GLY 194 526 526 GLY GLY G . n C 3 195 LYS 195 527 ? ? ? G . n C 3 196 LYS 196 528 ? ? ? G . 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 G NAG 601 n D 4 NAG 2 A NAG 2 G NAG 602 n D 4 BMA 3 A BMA 3 G BMA 603 n D 4 FUC 4 A FUC 4 G FUC 604 n # loop_ _pdbx_entity_instance_feature.ordinal _pdbx_entity_instance_feature.comp_id _pdbx_entity_instance_feature.asym_id _pdbx_entity_instance_feature.seq_num _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.auth_asym_id _pdbx_entity_instance_feature.auth_seq_num _pdbx_entity_instance_feature.feature_type _pdbx_entity_instance_feature.details 1 BMA ? ? BMA ? ? 'SUBJECT OF INVESTIGATION' ? 2 FUC ? ? FUC ? ? 'SUBJECT OF INVESTIGATION' ? 3 NAG ? ? NAG ? ? 'SUBJECT OF INVESTIGATION' ? # _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 9KVJ _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 ? _cell.pdbx_esd_method ? # _symmetry.entry_id 9KVJ _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 9KVJ _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 9KVJ _refine.pdbx_diffrn_id ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low ? _refine.ls_d_res_high . _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'ELECTRON MICROSCOPY' ? 0.004 ? 3417 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 0.532 ? 4647 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 5.085 ? 1980 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.043 ? 502 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.004 ? 597 ? f_plane_restr ? ? # _struct.entry_id 9KVJ _struct.title 'Cryo-EM structure of SARS-CoV-2 BA.5 spike protein in complex with nAb 1C4 (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 9KVJ _struct_keywords.text 'SARS-CoV-2, Neutralizing antibody, Cryo-EM, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex' _struct_keywords.pdbx_keywords 'VIRAL PROTEIN/IMMUNE SYSTEM' # 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 PDB 9KVJ 9KVJ ? 1 ? 1 2 PDB 9KVJ 9KVJ ? 2 ? 1 3 UNP SPIKE_SARS2 P0DTC2 ? 3 ;TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAP GQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPL QSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK ; 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 9KVJ C 1 ? 119 ? 9KVJ 1 ? 119 ? 1 119 2 2 9KVJ D 1 ? 107 ? 9KVJ 1 ? 107 ? 1 107 3 3 9KVJ G 1 ? 196 ? P0DTC2 333 ? 528 ? 333 528 # 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 9KVJ ASP G 7 ? UNP P0DTC2 GLY 339 variant 339 1 3 9KVJ PHE G 39 ? UNP P0DTC2 SER 371 variant 371 2 3 9KVJ PRO G 41 ? UNP P0DTC2 SER 373 variant 373 3 3 9KVJ PHE G 43 ? UNP P0DTC2 SER 375 variant 375 4 3 9KVJ ALA G 44 ? UNP P0DTC2 THR 376 variant 376 5 3 9KVJ ASN G 73 ? UNP P0DTC2 ASP 405 variant 405 6 3 9KVJ SER G 76 ? UNP P0DTC2 ARG 408 variant 408 7 3 9KVJ ASN G 85 ? UNP P0DTC2 LYS 417 variant 417 8 3 9KVJ LYS G 108 ? UNP P0DTC2 ASN 440 variant 440 9 3 9KVJ ARG G 120 ? UNP P0DTC2 LEU 452 variant 452 10 3 9KVJ ASN G 145 ? UNP P0DTC2 SER 477 variant 477 11 3 9KVJ LYS G 146 ? UNP P0DTC2 THR 478 variant 478 12 3 9KVJ ALA G 152 ? UNP P0DTC2 GLU 484 variant 484 13 3 9KVJ VAL G 154 ? UNP P0DTC2 PHE 486 variant 486 14 3 9KVJ ARG G 166 ? UNP P0DTC2 GLN 498 variant 498 15 3 9KVJ TYR G 169 ? UNP P0DTC2 ASN 501 variant 501 16 3 9KVJ HIS G 173 ? UNP P0DTC2 TYR 505 variant 505 17 3 9KVJ LYS G 195 ? UNP P0DTC2 PRO 527 conflict 527 18 # _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 'electron microscopy' _pdbx_struct_assembly_auth_evidence.details 'not applicable' # _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 THR A 28 ? TYR A 32 ? THR C 28 TYR C 32 5 ? 5 HELX_P HELX_P2 AA2 GLU B 79 ? PHE B 83 ? GLU D 79 PHE D 83 5 ? 5 HELX_P HELX_P3 AA3 PHE C 6 ? ASN C 11 ? PHE G 338 ASN G 343 1 ? 6 HELX_P HELX_P4 AA4 TYR C 33 ? PHE C 39 ? TYR G 365 PHE G 371 1 ? 7 HELX_P HELX_P5 AA5 SER C 51 ? ASN C 56 ? SER G 383 ASN G 388 5 ? 6 HELX_P HELX_P6 AA6 GLY C 72 ? ILE C 78 ? GLY G 404 ILE G 410 5 ? 7 HELX_P HELX_P7 AA7 ASN C 85 ? ASN C 90 ? ASN G 417 ASN G 422 1 ? 6 # _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 96 SG ? ? C CYS 22 C CYS 96 1_555 ? ? ? ? ? ? ? 2.034 ? ? disulf2 disulf ? ? B CYS 23 SG ? ? ? 1_555 B CYS 88 SG ? ? D CYS 23 D CYS 88 1_555 ? ? ? ? ? ? ? 2.036 ? ? disulf3 disulf ? ? C CYS 4 SG ? ? ? 1_555 C CYS 29 SG ? ? G CYS 336 G CYS 361 1_555 ? ? ? ? ? ? ? 2.026 ? ? disulf4 disulf ? ? C CYS 47 SG ? ? ? 1_555 C CYS 100 SG ? ? G CYS 379 G CYS 432 1_555 ? ? ? ? ? ? ? 2.030 ? ? disulf5 disulf ? ? C CYS 148 SG ? ? ? 1_555 C CYS 156 SG ? ? G CYS 480 G CYS 488 1_555 ? ? ? ? ? ? ? 2.036 ? ? covale1 covale one ? C ASN 11 ND2 ? ? ? 1_555 D NAG . C1 ? ? G ASN 343 A NAG 1 1_555 ? ? ? ? ? ? ? 1.463 ? N-Glycosylation covale2 covale both ? D NAG . O4 ? ? ? 1_555 D NAG . C1 ? ? A NAG 1 A NAG 2 1_555 ? ? ? ? ? ? ? 1.438 ? ? covale3 covale both ? D NAG . O6 ? ? ? 1_555 D FUC . C1 ? ? A NAG 1 A FUC 4 1_555 ? ? ? ? ? ? ? 1.433 ? ? covale4 covale both ? D NAG . O4 ? ? ? 1_555 D BMA . C1 ? ? A NAG 2 A BMA 3 1_555 ? ? ? ? ? ? ? 1.441 ? ? # 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 G 343 ? 1_555 C1 ND2 ASN 1 NAG N-Glycosylation Carbohydrate 2 CYS A 22 ? CYS A 96 ? CYS C 22 ? 1_555 CYS C 96 ? 1_555 SG SG . . . None 'Disulfide bridge' 3 CYS B 23 ? CYS B 88 ? CYS D 23 ? 1_555 CYS D 88 ? 1_555 SG SG . . . None 'Disulfide bridge' 4 CYS C 4 ? CYS C 29 ? CYS G 336 ? 1_555 CYS G 361 ? 1_555 SG SG . . . None 'Disulfide bridge' 5 CYS C 47 ? CYS C 100 ? CYS G 379 ? 1_555 CYS G 432 ? 1_555 SG SG . . . None 'Disulfide bridge' 6 CYS C 148 ? CYS C 156 ? CYS G 480 ? 1_555 CYS G 488 ? 1_555 SG SG . . . None 'Disulfide bridge' # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 SER 7 B . ? SER 7 D PRO 8 B ? PRO 8 D 1 -2.08 2 TRP 94 B . ? TRP 94 D PRO 95 B ? PRO 95 D 1 -1.69 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 4 ? AA2 ? 4 ? AA3 ? 5 ? AA4 ? 2 ? AA5 ? 4 ? AA6 ? 6 ? AA7 ? 5 ? AA8 ? 2 ? # 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 AA1 3 4 ? anti-parallel AA2 1 2 ? anti-parallel AA2 2 3 ? anti-parallel AA2 3 4 ? anti-parallel AA3 1 2 ? parallel AA3 2 3 ? anti-parallel AA3 3 4 ? anti-parallel AA3 4 5 ? anti-parallel AA4 1 2 ? anti-parallel AA5 1 2 ? anti-parallel AA5 2 3 ? anti-parallel AA5 3 4 ? anti-parallel AA6 1 2 ? parallel AA6 2 3 ? anti-parallel AA6 3 4 ? anti-parallel AA6 4 5 ? anti-parallel AA6 5 6 ? anti-parallel AA7 1 2 ? anti-parallel AA7 2 3 ? anti-parallel AA7 3 4 ? anti-parallel AA7 4 5 ? anti-parallel AA8 1 2 ? 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 GLN A 3 ? GLN A 6 ? GLN C 3 GLN C 6 AA1 2 VAL A 18 ? SER A 25 ? VAL C 18 SER C 25 AA1 3 THR A 78 ? ILE A 83 ? THR C 78 ILE C 83 AA1 4 PHE A 68 ? ALA A 69 ? PHE C 68 ALA C 69 AA2 1 GLN A 3 ? GLN A 6 ? GLN C 3 GLN C 6 AA2 2 VAL A 18 ? SER A 25 ? VAL C 18 SER C 25 AA2 3 THR A 78 ? ILE A 83 ? THR C 78 ILE C 83 AA2 4 LEU A 72 ? GLU A 73 ? LEU C 72 GLU C 73 AA3 1 GLU A 10 ? LYS A 12 ? GLU C 10 LYS C 12 AA3 2 THR A 113 ? VAL A 117 ? THR C 113 VAL C 117 AA3 3 ALA A 92 ? TYR A 94 ? ALA C 92 TYR C 94 AA3 4 VAL A 37 ? GLN A 39 ? VAL C 37 GLN C 39 AA3 5 LEU A 45 ? TRP A 47 ? LEU C 45 TRP C 47 AA4 1 ARG A 98 ? GLY A 99 ? ARG C 98 GLY C 99 AA4 2 PHE A 106 ? VAL A 108 ? PHE C 106 VAL C 108 AA5 1 THR B 5 ? SER B 7 ? THR D 5 SER D 7 AA5 2 VAL B 19 ? ARG B 24 ? VAL D 19 ARG D 24 AA5 3 THR B 72 ? ILE B 75 ? THR D 72 ILE D 75 AA5 4 PHE B 62 ? SER B 65 ? PHE D 62 SER D 65 AA6 1 SER B 12 ? VAL B 13 ? SER D 12 VAL D 13 AA6 2 THR B 102 ? LEU B 106 ? THR D 102 LEU D 106 AA6 3 GLY B 84 ? GLN B 90 ? GLY D 84 GLN D 90 AA6 4 LEU B 33 ? GLN B 38 ? LEU D 33 GLN D 38 AA6 5 ARG B 45 ? LYS B 49 ? ARG D 45 LYS D 49 AA6 6 GLN B 53 ? SER B 54 ? GLN D 53 SER D 54 AA7 1 ASN C 22 ? ILE C 26 ? ASN G 354 ILE G 358 AA7 2 VAL C 63 ? ILE C 70 ? VAL G 395 ILE G 402 AA7 3 TYR C 176 ? SER C 182 ? TYR G 508 SER G 514 AA7 4 CYS C 100 ? ALA C 103 ? CYS G 432 ALA G 435 AA7 5 LYS C 46 ? CYS C 47 ? LYS G 378 CYS G 379 AA8 1 ARG C 120 ? ARG C 122 ? ARG G 452 ARG G 454 AA8 2 LEU C 160 ? SER C 162 ? LEU G 492 SER G 494 # 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 VAL A 5 ? N VAL C 5 O LYS A 23 ? O LYS C 23 AA1 2 3 N ILE A 20 ? N ILE C 20 O LEU A 81 ? O LEU C 81 AA1 3 4 O LYS A 82 ? O LYS C 82 N ALA A 69 ? N ALA C 69 AA2 1 2 N VAL A 5 ? N VAL C 5 O LYS A 23 ? O LYS C 23 AA2 2 3 N ILE A 20 ? N ILE C 20 O LEU A 81 ? O LEU C 81 AA2 3 4 O THR A 78 ? O THR C 78 N GLU A 73 ? N GLU C 73 AA3 1 2 N GLU A 10 ? N GLU C 10 O THR A 114 ? O THR C 114 AA3 2 3 O THR A 113 ? O THR C 113 N TYR A 94 ? N TYR C 94 AA3 3 4 O THR A 93 ? O THR C 93 N GLN A 39 ? N GLN C 39 AA3 4 5 N LYS A 38 ? N LYS C 38 O LYS A 46 ? O LYS C 46 AA4 1 2 N ARG A 98 ? N ARG C 98 O VAL A 108 ? O VAL C 108 AA5 1 2 N SER B 7 ? N SER D 7 O SER B 22 ? O SER D 22 AA5 2 3 N LEU B 21 ? N LEU D 21 O LEU B 73 ? O LEU D 73 AA5 3 4 O THR B 72 ? O THR D 72 N SER B 65 ? N SER D 65 AA6 1 2 N VAL B 13 ? N VAL D 13 O GLU B 105 ? O GLU D 105 AA6 2 3 O THR B 102 ? O THR D 102 N TYR B 86 ? N TYR D 86 AA6 3 4 O PHE B 87 ? O PHE D 87 N TYR B 36 ? N TYR D 36 AA6 4 5 N GLN B 37 ? N GLN D 37 O ARG B 45 ? O ARG D 45 AA6 5 6 N LYS B 49 ? N LYS D 49 O GLN B 53 ? O GLN D 53 AA7 1 2 N ILE C 26 ? N ILE G 358 O VAL C 63 ? O VAL G 395 AA7 2 3 N ILE C 70 ? N ILE G 402 O TYR C 176 ? O TYR G 508 AA7 3 4 O LEU C 181 ? O LEU G 513 N CYS C 100 ? N CYS G 432 AA7 4 5 O VAL C 101 ? O VAL G 433 N LYS C 46 ? N LYS G 378 AA8 1 2 N TYR C 121 ? N TYR G 453 O GLN C 161 ? O GLN G 493 # _pdbx_entry_details.entry_id 9KVJ _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 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 OG1 D THR 14 ? ? OD2 D ASP 17 ? ? 2.15 2 1 O D SER 7 ? ? OG D SER 22 ? ? 2.19 # 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 LEU C 11 ? ? -160.78 116.12 2 1 PHE C 64 ? ? -94.11 53.99 3 1 ARG C 67 ? ? 68.03 -3.85 4 1 ASP C 90 ? ? -96.93 36.07 5 1 LEU D 47 ? ? -94.39 -61.82 6 1 ALA D 51 ? ? 71.96 -8.83 7 1 SER D 91 ? ? -141.27 10.33 8 1 PRO G 337 ? ? -66.24 77.19 9 1 ASN G 343 ? ? -91.83 41.08 10 1 PRO G 373 ? ? -56.70 9.17 11 1 ASN G 422 ? ? -120.31 -54.49 # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 9KVJ _em_3d_fitting.method ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_space ? _em_3d_fitting.ref_protocol ? # _em_3d_reconstruction.entry_id 9KVJ _em_3d_reconstruction.id 1 _em_3d_reconstruction.method ? _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.citation_id ? _em_3d_reconstruction.details ? _em_3d_reconstruction.resolution 3.82 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.num_particles 148009 _em_3d_reconstruction.euler_angles_details ? _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.symmetry_type POINT # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details ? _em_buffer.pH 7.4 # loop_ _em_entity_assembly.id _em_entity_assembly.parent_id _em_entity_assembly.source _em_entity_assembly.type _em_entity_assembly.name _em_entity_assembly.details _em_entity_assembly.synonym _em_entity_assembly.oligomeric_details _em_entity_assembly.entity_id_list 1 0 'MULTIPLE SOURCES' COMPLEX 'Cryo-EM structure of SARS-CoV-2 BA.5 spike protein in complex with nAb 1C4' ? ? ? '1, 2, 3' 2 1 RECOMBINANT COMPLEX 'SARS-CoV-2 spike protein of BA.5 variant' ? ? ? 3 3 1 NATURAL COMPLEX 'The fragment of nAb 1C4' ? ? ? '1, 2' # _em_imaging.entry_id 9KVJ _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'FEI TECNAI F30' _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model ? _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 300 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_min 1000 _em_imaging.nominal_defocus_max 2200 _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_defocus_max ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_magnification ? _em_imaging.calibrated_magnification ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.citation_id ? _em_imaging.temperature ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_minimum ? _em_imaging.recording_temperature_maximum ? _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.specimen_id 1 _em_imaging.cryogen ? # _em_vitrification.entry_id 9KVJ _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity ? _em_vitrification.temp ? _em_vitrification.chamber_temperature ? _em_vitrification.instrument ? _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details ? # _em_experiment.entry_id 9KVJ _em_experiment.id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.aggregation_state 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 G LEU 518 ? C LEU 186 2 1 Y 1 G HIS 519 ? C HIS 187 3 1 Y 1 G LYS 527 ? C LYS 195 4 1 Y 1 G LYS 528 ? C LYS 196 # 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 BMA C1 C N R 74 BMA C2 C N S 75 BMA C3 C N S 76 BMA C4 C N S 77 BMA C5 C N R 78 BMA C6 C N N 79 BMA O1 O N N 80 BMA O2 O N N 81 BMA O3 O N N 82 BMA O4 O N N 83 BMA O5 O N N 84 BMA O6 O N N 85 BMA H1 H N N 86 BMA H2 H N N 87 BMA H3 H N N 88 BMA H4 H N N 89 BMA H5 H N N 90 BMA H61 H N N 91 BMA H62 H N N 92 BMA HO1 H N N 93 BMA HO2 H N N 94 BMA HO3 H N N 95 BMA HO4 H N N 96 BMA HO6 H N N 97 CYS N N N N 98 CYS CA C N R 99 CYS C C N N 100 CYS O O N N 101 CYS CB C N N 102 CYS SG S N N 103 CYS OXT O N N 104 CYS H H N N 105 CYS H2 H N N 106 CYS HA H N N 107 CYS HB2 H N N 108 CYS HB3 H N N 109 CYS HG H N N 110 CYS HXT H N N 111 FUC C1 C N R 112 FUC C2 C N S 113 FUC C3 C N R 114 FUC C4 C N S 115 FUC C5 C N S 116 FUC C6 C N N 117 FUC O1 O N N 118 FUC O2 O N N 119 FUC O3 O N N 120 FUC O4 O N N 121 FUC O5 O N N 122 FUC H1 H N N 123 FUC H2 H N N 124 FUC H3 H N N 125 FUC H4 H N N 126 FUC H5 H N N 127 FUC H61 H N N 128 FUC H62 H N N 129 FUC H63 H N N 130 FUC HO1 H N N 131 FUC HO2 H N N 132 FUC HO3 H N N 133 FUC HO4 H N N 134 GLN N N N N 135 GLN CA C N S 136 GLN C C N N 137 GLN O O N N 138 GLN CB C N N 139 GLN CG C N N 140 GLN CD C N N 141 GLN OE1 O N N 142 GLN NE2 N N N 143 GLN OXT O N N 144 GLN H H N N 145 GLN H2 H N N 146 GLN HA H N N 147 GLN HB2 H N N 148 GLN HB3 H N N 149 GLN HG2 H N N 150 GLN HG3 H N N 151 GLN HE21 H N N 152 GLN HE22 H N N 153 GLN HXT H N N 154 GLU N N N N 155 GLU CA C N S 156 GLU C C N N 157 GLU O O N N 158 GLU CB C N N 159 GLU CG C N N 160 GLU CD C N N 161 GLU OE1 O N N 162 GLU OE2 O N N 163 GLU OXT O N N 164 GLU H H N N 165 GLU H2 H N N 166 GLU HA H N N 167 GLU HB2 H N N 168 GLU HB3 H N N 169 GLU HG2 H N N 170 GLU HG3 H N N 171 GLU HE2 H N N 172 GLU HXT H N N 173 GLY N N N N 174 GLY CA C N N 175 GLY C C N N 176 GLY O O N N 177 GLY OXT O N N 178 GLY H H N N 179 GLY H2 H N N 180 GLY HA2 H N N 181 GLY HA3 H N N 182 GLY HXT H N N 183 HIS N N N N 184 HIS CA C N S 185 HIS C C N N 186 HIS O O N N 187 HIS CB C N N 188 HIS CG C Y N 189 HIS ND1 N Y N 190 HIS CD2 C Y N 191 HIS CE1 C Y N 192 HIS NE2 N Y N 193 HIS OXT O N N 194 HIS H H N N 195 HIS H2 H N N 196 HIS HA H N N 197 HIS HB2 H N N 198 HIS HB3 H N N 199 HIS HD1 H N N 200 HIS HD2 H N N 201 HIS HE1 H N N 202 HIS HE2 H N N 203 HIS HXT H N N 204 ILE N N N N 205 ILE CA C N S 206 ILE C C N N 207 ILE O O N N 208 ILE CB C N S 209 ILE CG1 C N N 210 ILE CG2 C N N 211 ILE CD1 C N N 212 ILE OXT O N N 213 ILE H H N N 214 ILE H2 H N N 215 ILE HA H N N 216 ILE HB H N N 217 ILE HG12 H N N 218 ILE HG13 H N N 219 ILE HG21 H N N 220 ILE HG22 H N N 221 ILE HG23 H N N 222 ILE HD11 H N N 223 ILE HD12 H N N 224 ILE HD13 H N N 225 ILE HXT H N N 226 LEU N N N N 227 LEU CA C N S 228 LEU C C N N 229 LEU O O N N 230 LEU CB C N N 231 LEU CG C N N 232 LEU CD1 C N N 233 LEU CD2 C N N 234 LEU OXT O N N 235 LEU H H N N 236 LEU H2 H N N 237 LEU HA H N N 238 LEU HB2 H N N 239 LEU HB3 H N N 240 LEU HG H N N 241 LEU HD11 H N N 242 LEU HD12 H N N 243 LEU HD13 H N N 244 LEU HD21 H N N 245 LEU HD22 H N N 246 LEU HD23 H N N 247 LEU HXT H N N 248 LYS N N N N 249 LYS CA C N S 250 LYS C C N N 251 LYS O O N N 252 LYS CB C N N 253 LYS CG C N N 254 LYS CD C N N 255 LYS CE C N N 256 LYS NZ N N N 257 LYS OXT O N N 258 LYS H H N N 259 LYS H2 H N N 260 LYS HA H N N 261 LYS HB2 H N N 262 LYS HB3 H N N 263 LYS HG2 H N N 264 LYS HG3 H N N 265 LYS HD2 H N N 266 LYS HD3 H N N 267 LYS HE2 H N N 268 LYS HE3 H N N 269 LYS HZ1 H N N 270 LYS HZ2 H N N 271 LYS HZ3 H N N 272 LYS HXT H N N 273 MET N N N N 274 MET CA C N S 275 MET C C N N 276 MET O O N N 277 MET CB C N N 278 MET CG C N N 279 MET SD S N N 280 MET CE C N N 281 MET OXT O N N 282 MET H H N N 283 MET H2 H N N 284 MET HA H N N 285 MET HB2 H N N 286 MET HB3 H N N 287 MET HG2 H N N 288 MET HG3 H N N 289 MET HE1 H N N 290 MET HE2 H N N 291 MET HE3 H N N 292 MET HXT H N N 293 NAG C1 C N R 294 NAG C2 C N R 295 NAG C3 C N R 296 NAG C4 C N S 297 NAG C5 C N R 298 NAG C6 C N N 299 NAG C7 C N N 300 NAG C8 C N N 301 NAG N2 N N N 302 NAG O1 O N N 303 NAG O3 O N N 304 NAG O4 O N N 305 NAG O5 O N N 306 NAG O6 O N N 307 NAG O7 O N N 308 NAG H1 H N N 309 NAG H2 H N N 310 NAG H3 H N N 311 NAG H4 H N N 312 NAG H5 H N N 313 NAG H61 H N N 314 NAG H62 H N N 315 NAG H81 H N N 316 NAG H82 H N N 317 NAG H83 H N N 318 NAG HN2 H N N 319 NAG HO1 H N N 320 NAG HO3 H N N 321 NAG HO4 H N N 322 NAG HO6 H N N 323 PHE N N N N 324 PHE CA C N S 325 PHE C C N N 326 PHE O O N N 327 PHE CB C N N 328 PHE CG C Y N 329 PHE CD1 C Y N 330 PHE CD2 C Y N 331 PHE CE1 C Y N 332 PHE CE2 C Y N 333 PHE CZ C Y N 334 PHE OXT O N N 335 PHE H H N N 336 PHE H2 H N N 337 PHE HA H N N 338 PHE HB2 H N N 339 PHE HB3 H N N 340 PHE HD1 H N N 341 PHE HD2 H N N 342 PHE HE1 H N N 343 PHE HE2 H N N 344 PHE HZ H N N 345 PHE HXT H N N 346 PRO N N N N 347 PRO CA C N S 348 PRO C C N N 349 PRO O O N N 350 PRO CB C N N 351 PRO CG C N N 352 PRO CD C N N 353 PRO OXT O N N 354 PRO H H N N 355 PRO HA H N N 356 PRO HB2 H N N 357 PRO HB3 H N N 358 PRO HG2 H N N 359 PRO HG3 H N N 360 PRO HD2 H N N 361 PRO HD3 H N N 362 PRO HXT H N N 363 SER N N N N 364 SER CA C N S 365 SER C C N N 366 SER O O N N 367 SER CB C N N 368 SER OG O N N 369 SER OXT O N N 370 SER H H N N 371 SER H2 H N N 372 SER HA H N N 373 SER HB2 H N N 374 SER HB3 H N N 375 SER HG H N N 376 SER HXT H N N 377 THR N N N N 378 THR CA C N S 379 THR C C N N 380 THR O O N N 381 THR CB C N R 382 THR OG1 O N N 383 THR CG2 C N N 384 THR OXT O N N 385 THR H H N N 386 THR H2 H N N 387 THR HA H N N 388 THR HB H N N 389 THR HG1 H N N 390 THR HG21 H N N 391 THR HG22 H N N 392 THR HG23 H N N 393 THR HXT H N N 394 TRP N N N N 395 TRP CA C N S 396 TRP C C N N 397 TRP O O N N 398 TRP CB C N N 399 TRP CG C Y N 400 TRP CD1 C Y N 401 TRP CD2 C Y N 402 TRP NE1 N Y N 403 TRP CE2 C Y N 404 TRP CE3 C Y N 405 TRP CZ2 C Y N 406 TRP CZ3 C Y N 407 TRP CH2 C Y N 408 TRP OXT O N N 409 TRP H H N N 410 TRP H2 H N N 411 TRP HA H N N 412 TRP HB2 H N N 413 TRP HB3 H N N 414 TRP HD1 H N N 415 TRP HE1 H N N 416 TRP HE3 H N N 417 TRP HZ2 H N N 418 TRP HZ3 H N N 419 TRP HH2 H N N 420 TRP HXT H N N 421 TYR N N N N 422 TYR CA C N S 423 TYR C C N N 424 TYR O O N N 425 TYR CB C N N 426 TYR CG C Y N 427 TYR CD1 C Y N 428 TYR CD2 C Y N 429 TYR CE1 C Y N 430 TYR CE2 C Y N 431 TYR CZ C Y N 432 TYR OH O N N 433 TYR OXT O N N 434 TYR H H N N 435 TYR H2 H N N 436 TYR HA H N N 437 TYR HB2 H N N 438 TYR HB3 H N N 439 TYR HD1 H N N 440 TYR HD2 H N N 441 TYR HE1 H N N 442 TYR HE2 H N N 443 TYR HH H N N 444 TYR HXT H N N 445 VAL N N N N 446 VAL CA C N S 447 VAL C C N N 448 VAL O O N N 449 VAL CB C N N 450 VAL CG1 C N N 451 VAL CG2 C N N 452 VAL OXT O N N 453 VAL H H N N 454 VAL H2 H N N 455 VAL HA H N N 456 VAL HB H N N 457 VAL HG11 H N N 458 VAL HG12 H N N 459 VAL HG13 H N N 460 VAL HG21 H N N 461 VAL HG22 H N N 462 VAL HG23 H N N 463 VAL HXT H N N 464 # 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 BMA C1 C2 sing N N 70 BMA C1 O1 sing N N 71 BMA C1 O5 sing N N 72 BMA C1 H1 sing N N 73 BMA C2 C3 sing N N 74 BMA C2 O2 sing N N 75 BMA C2 H2 sing N N 76 BMA C3 C4 sing N N 77 BMA C3 O3 sing N N 78 BMA C3 H3 sing N N 79 BMA C4 C5 sing N N 80 BMA C4 O4 sing N N 81 BMA C4 H4 sing N N 82 BMA C5 C6 sing N N 83 BMA C5 O5 sing N N 84 BMA C5 H5 sing N N 85 BMA C6 O6 sing N N 86 BMA C6 H61 sing N N 87 BMA C6 H62 sing N N 88 BMA O1 HO1 sing N N 89 BMA O2 HO2 sing N N 90 BMA O3 HO3 sing N N 91 BMA O4 HO4 sing N N 92 BMA O6 HO6 sing N N 93 CYS N CA sing N N 94 CYS N H sing N N 95 CYS N H2 sing N N 96 CYS CA C sing N N 97 CYS CA CB sing N N 98 CYS CA HA sing N N 99 CYS C O doub N N 100 CYS C OXT sing N N 101 CYS CB SG sing N N 102 CYS CB HB2 sing N N 103 CYS CB HB3 sing N N 104 CYS SG HG sing N N 105 CYS OXT HXT sing N N 106 FUC C1 C2 sing N N 107 FUC C1 O1 sing N N 108 FUC C1 O5 sing N N 109 FUC C1 H1 sing N N 110 FUC C2 C3 sing N N 111 FUC C2 O2 sing N N 112 FUC C2 H2 sing N N 113 FUC C3 C4 sing N N 114 FUC C3 O3 sing N N 115 FUC C3 H3 sing N N 116 FUC C4 C5 sing N N 117 FUC C4 O4 sing N N 118 FUC C4 H4 sing N N 119 FUC C5 C6 sing N N 120 FUC C5 O5 sing N N 121 FUC C5 H5 sing N N 122 FUC C6 H61 sing N N 123 FUC C6 H62 sing N N 124 FUC C6 H63 sing N N 125 FUC O1 HO1 sing N N 126 FUC O2 HO2 sing N N 127 FUC O3 HO3 sing N N 128 FUC O4 HO4 sing N N 129 GLN N CA sing N N 130 GLN N H sing N N 131 GLN N H2 sing N N 132 GLN CA C sing N N 133 GLN CA CB sing N N 134 GLN CA HA sing N N 135 GLN C O doub N N 136 GLN C OXT sing N N 137 GLN CB CG sing N N 138 GLN CB HB2 sing N N 139 GLN CB HB3 sing N N 140 GLN CG CD sing N N 141 GLN CG HG2 sing N N 142 GLN CG HG3 sing N N 143 GLN CD OE1 doub N N 144 GLN CD NE2 sing N N 145 GLN NE2 HE21 sing N N 146 GLN NE2 HE22 sing N N 147 GLN OXT HXT sing N N 148 GLU N CA sing N N 149 GLU N H sing N N 150 GLU N H2 sing N N 151 GLU CA C sing N N 152 GLU CA CB sing N N 153 GLU CA HA sing N N 154 GLU C O doub N N 155 GLU C OXT sing N N 156 GLU CB CG sing N N 157 GLU CB HB2 sing N N 158 GLU CB HB3 sing N N 159 GLU CG CD sing N N 160 GLU CG HG2 sing N N 161 GLU CG HG3 sing N N 162 GLU CD OE1 doub N N 163 GLU CD OE2 sing N N 164 GLU OE2 HE2 sing N N 165 GLU OXT HXT sing N N 166 GLY N CA sing N N 167 GLY N H sing N N 168 GLY N H2 sing N N 169 GLY CA C sing N N 170 GLY CA HA2 sing N N 171 GLY CA HA3 sing N N 172 GLY C O doub N N 173 GLY C OXT sing N N 174 GLY OXT HXT sing N N 175 HIS N CA sing N N 176 HIS N H sing N N 177 HIS N H2 sing N N 178 HIS CA C sing N N 179 HIS CA CB sing N N 180 HIS CA HA sing N N 181 HIS C O doub N N 182 HIS C OXT sing N N 183 HIS CB CG sing N N 184 HIS CB HB2 sing N N 185 HIS CB HB3 sing N N 186 HIS CG ND1 sing Y N 187 HIS CG CD2 doub Y N 188 HIS ND1 CE1 doub Y N 189 HIS ND1 HD1 sing N N 190 HIS CD2 NE2 sing Y N 191 HIS CD2 HD2 sing N N 192 HIS CE1 NE2 sing Y N 193 HIS CE1 HE1 sing N N 194 HIS NE2 HE2 sing N N 195 HIS OXT HXT sing N N 196 ILE N CA sing N N 197 ILE N H sing N N 198 ILE N H2 sing N N 199 ILE CA C sing N N 200 ILE CA CB sing N N 201 ILE CA HA sing N N 202 ILE C O doub N N 203 ILE C OXT sing N N 204 ILE CB CG1 sing N N 205 ILE CB CG2 sing N N 206 ILE CB HB sing N N 207 ILE CG1 CD1 sing N N 208 ILE CG1 HG12 sing N N 209 ILE CG1 HG13 sing N N 210 ILE CG2 HG21 sing N N 211 ILE CG2 HG22 sing N N 212 ILE CG2 HG23 sing N N 213 ILE CD1 HD11 sing N N 214 ILE CD1 HD12 sing N N 215 ILE CD1 HD13 sing N N 216 ILE OXT HXT sing N N 217 LEU N CA sing N N 218 LEU N H sing N N 219 LEU N H2 sing N N 220 LEU CA C sing N N 221 LEU CA CB sing N N 222 LEU CA HA sing N N 223 LEU C O doub N N 224 LEU C OXT sing N N 225 LEU CB CG sing N N 226 LEU CB HB2 sing N N 227 LEU CB HB3 sing N N 228 LEU CG CD1 sing N N 229 LEU CG CD2 sing N N 230 LEU CG HG sing N N 231 LEU CD1 HD11 sing N N 232 LEU CD1 HD12 sing N N 233 LEU CD1 HD13 sing N N 234 LEU CD2 HD21 sing N N 235 LEU CD2 HD22 sing N N 236 LEU CD2 HD23 sing N N 237 LEU OXT HXT sing N N 238 LYS N CA sing N N 239 LYS N H sing N N 240 LYS N H2 sing N N 241 LYS CA C sing N N 242 LYS CA CB sing N N 243 LYS CA HA sing N N 244 LYS C O doub N N 245 LYS C OXT sing N N 246 LYS CB CG sing N N 247 LYS CB HB2 sing N N 248 LYS CB HB3 sing N N 249 LYS CG CD sing N N 250 LYS CG HG2 sing N N 251 LYS CG HG3 sing N N 252 LYS CD CE sing N N 253 LYS CD HD2 sing N N 254 LYS CD HD3 sing N N 255 LYS CE NZ sing N N 256 LYS CE HE2 sing N N 257 LYS CE HE3 sing N N 258 LYS NZ HZ1 sing N N 259 LYS NZ HZ2 sing N N 260 LYS NZ HZ3 sing N N 261 LYS OXT HXT sing N N 262 MET N CA sing N N 263 MET N H sing N N 264 MET N H2 sing N N 265 MET CA C sing N N 266 MET CA CB sing N N 267 MET CA HA sing N N 268 MET C O doub N N 269 MET C OXT sing N N 270 MET CB CG sing N N 271 MET CB HB2 sing N N 272 MET CB HB3 sing N N 273 MET CG SD sing N N 274 MET CG HG2 sing N N 275 MET CG HG3 sing N N 276 MET SD CE sing N N 277 MET CE HE1 sing N N 278 MET CE HE2 sing N N 279 MET CE HE3 sing N N 280 MET OXT HXT sing N N 281 NAG C1 C2 sing N N 282 NAG C1 O1 sing N N 283 NAG C1 O5 sing N N 284 NAG C1 H1 sing N N 285 NAG C2 C3 sing N N 286 NAG C2 N2 sing N N 287 NAG C2 H2 sing N N 288 NAG C3 C4 sing N N 289 NAG C3 O3 sing N N 290 NAG C3 H3 sing N N 291 NAG C4 C5 sing N N 292 NAG C4 O4 sing N N 293 NAG C4 H4 sing N N 294 NAG C5 C6 sing N N 295 NAG C5 O5 sing N N 296 NAG C5 H5 sing N N 297 NAG C6 O6 sing N N 298 NAG C6 H61 sing N N 299 NAG C6 H62 sing N N 300 NAG C7 C8 sing N N 301 NAG C7 N2 sing N N 302 NAG C7 O7 doub N N 303 NAG C8 H81 sing N N 304 NAG C8 H82 sing N N 305 NAG C8 H83 sing N N 306 NAG N2 HN2 sing N N 307 NAG O1 HO1 sing N N 308 NAG O3 HO3 sing N N 309 NAG O4 HO4 sing N N 310 NAG O6 HO6 sing N N 311 PHE N CA sing N N 312 PHE N H sing N N 313 PHE N H2 sing N N 314 PHE CA C sing N N 315 PHE CA CB sing N N 316 PHE CA HA sing N N 317 PHE C O doub N N 318 PHE C OXT sing N N 319 PHE CB CG sing N N 320 PHE CB HB2 sing N N 321 PHE CB HB3 sing N N 322 PHE CG CD1 doub Y N 323 PHE CG CD2 sing Y N 324 PHE CD1 CE1 sing Y N 325 PHE CD1 HD1 sing N N 326 PHE CD2 CE2 doub Y N 327 PHE CD2 HD2 sing N N 328 PHE CE1 CZ doub Y N 329 PHE CE1 HE1 sing N N 330 PHE CE2 CZ sing Y N 331 PHE CE2 HE2 sing N N 332 PHE CZ HZ sing N N 333 PHE OXT HXT sing N N 334 PRO N CA sing N N 335 PRO N CD sing N N 336 PRO N H sing N N 337 PRO CA C sing N N 338 PRO CA CB sing N N 339 PRO CA HA sing N N 340 PRO C O doub N N 341 PRO C OXT sing N N 342 PRO CB CG sing N N 343 PRO CB HB2 sing N N 344 PRO CB HB3 sing N N 345 PRO CG CD sing N N 346 PRO CG HG2 sing N N 347 PRO CG HG3 sing N N 348 PRO CD HD2 sing N N 349 PRO CD HD3 sing N N 350 PRO OXT HXT sing N N 351 SER N CA sing N N 352 SER N H sing N N 353 SER N H2 sing N N 354 SER CA C sing N N 355 SER CA CB sing N N 356 SER CA HA sing N N 357 SER C O doub N N 358 SER C OXT sing N N 359 SER CB OG sing N N 360 SER CB HB2 sing N N 361 SER CB HB3 sing N N 362 SER OG HG sing N N 363 SER OXT HXT sing N N 364 THR N CA sing N N 365 THR N H sing N N 366 THR N H2 sing N N 367 THR CA C sing N N 368 THR CA CB sing N N 369 THR CA HA sing N N 370 THR C O doub N N 371 THR C OXT sing N N 372 THR CB OG1 sing N N 373 THR CB CG2 sing N N 374 THR CB HB sing N N 375 THR OG1 HG1 sing N N 376 THR CG2 HG21 sing N N 377 THR CG2 HG22 sing N N 378 THR CG2 HG23 sing N N 379 THR OXT HXT sing N N 380 TRP N CA sing N N 381 TRP N H sing N N 382 TRP N H2 sing N N 383 TRP CA C sing N N 384 TRP CA CB sing N N 385 TRP CA HA sing N N 386 TRP C O doub N N 387 TRP C OXT sing N N 388 TRP CB CG sing N N 389 TRP CB HB2 sing N N 390 TRP CB HB3 sing N N 391 TRP CG CD1 doub Y N 392 TRP CG CD2 sing Y N 393 TRP CD1 NE1 sing Y N 394 TRP CD1 HD1 sing N N 395 TRP CD2 CE2 doub Y N 396 TRP CD2 CE3 sing Y N 397 TRP NE1 CE2 sing Y N 398 TRP NE1 HE1 sing N N 399 TRP CE2 CZ2 sing Y N 400 TRP CE3 CZ3 doub Y N 401 TRP CE3 HE3 sing N N 402 TRP CZ2 CH2 doub Y N 403 TRP CZ2 HZ2 sing N N 404 TRP CZ3 CH2 sing Y N 405 TRP CZ3 HZ3 sing N N 406 TRP CH2 HH2 sing N N 407 TRP OXT HXT sing N N 408 TYR N CA sing N N 409 TYR N H sing N N 410 TYR N H2 sing N N 411 TYR CA C sing N N 412 TYR CA CB sing N N 413 TYR CA HA sing N N 414 TYR C O doub N N 415 TYR C OXT sing N N 416 TYR CB CG sing N N 417 TYR CB HB2 sing N N 418 TYR CB HB3 sing N N 419 TYR CG CD1 doub Y N 420 TYR CG CD2 sing Y N 421 TYR CD1 CE1 sing Y N 422 TYR CD1 HD1 sing N N 423 TYR CD2 CE2 doub Y N 424 TYR CD2 HD2 sing N N 425 TYR CE1 CZ doub Y N 426 TYR CE1 HE1 sing N N 427 TYR CE2 CZ sing Y N 428 TYR CE2 HE2 sing N N 429 TYR CZ OH sing N N 430 TYR OH HH sing N N 431 TYR OXT HXT sing N N 432 VAL N CA sing N N 433 VAL N H sing N N 434 VAL N H2 sing N N 435 VAL CA C sing N N 436 VAL CA CB sing N N 437 VAL CA HA sing N N 438 VAL C O doub N N 439 VAL C OXT sing N N 440 VAL CB CG1 sing N N 441 VAL CB CG2 sing N N 442 VAL CB HB sing N N 443 VAL CG1 HG11 sing N N 444 VAL CG1 HG12 sing N N 445 VAL CG1 HG13 sing N N 446 VAL CG2 HG21 sing N N 447 VAL CG2 HG22 sing N N 448 VAL CG2 HG23 sing N N 449 VAL OXT HXT sing N N 450 # _em_admin.current_status REL _em_admin.deposition_date 2024-12-05 _em_admin.deposition_site PDBJ _em_admin.entry_id 9KVJ _em_admin.last_update 2025-12-10 _em_admin.map_release_date 2025-12-10 _em_admin.title 'Cryo-EM structure of SARS-CoV-2 BA.5 spike protein in complex with nAb 1C4 (local refinement)' # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' # loop_ _em_entity_assembly_naturalsource.cell _em_entity_assembly_naturalsource.cellular_location _em_entity_assembly_naturalsource.entity_assembly_id _em_entity_assembly_naturalsource.id _em_entity_assembly_naturalsource.ncbi_tax_id _em_entity_assembly_naturalsource.organism _em_entity_assembly_naturalsource.organelle _em_entity_assembly_naturalsource.organ _em_entity_assembly_naturalsource.strain _em_entity_assembly_naturalsource.tissue _em_entity_assembly_naturalsource.details ? ? 2 1 2697049 'Severe acute respiratory syndrome coronavirus 2' ? ? ? ? ? ? ? 3 2 10090 'Mus musculus' ? ? ? ? ? # _em_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.entity_assembly_id 2 _em_entity_assembly_recombinant.id 2 _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.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time ? _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 60 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 (6k x 4k)' _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.category _em_software.details _em_software.id _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id _em_software.name _em_software.version 'PARTICLE SELECTION' ? 1 1 ? ? ? ? 'IMAGE ACQUISITION' ? 2 ? ? 1 ? ? MASKING ? 3 ? ? ? ? ? 'CTF CORRECTION' ? 4 1 ? ? ? ? 'LAYERLINE INDEXING' ? 5 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 6 ? ? ? ? ? 'MODEL FITTING' ? 7 ? ? ? ? ? 'MODEL REFINEMENT' ? 8 ? ? ? PHENIX ? OTHER ? 9 ? ? ? ? ? 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? ? ? 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? ? ? CLASSIFICATION ? 12 1 ? ? ? ? RECONSTRUCTION ? 13 1 ? ? ? ? # _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.experiment_id 1 _em_specimen.id 1 _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 4 BMA 3 n 4 FUC 4 n # _atom_sites.entry_id 9KVJ _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.Cartn_transform_axes ? _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_ #