data_7YG5 # _model_server_result.job_id 845Mk5xXwWGOPCHhRuhBvg _model_server_result.datetime_utc '2024-11-26 16:25:06' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 7yg5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":1201}' # _entry.id 7YG5 # _exptl.entry_id 7YG5 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 40.078 _entity.id 9 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 7YG5 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YG5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 9 U N N ? 9 Z N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 5 3 2 BMA NAG C1 O1 . O3 HO3 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n D NAG 1 E 1 NAG E 1235 NAG 4 n D NAG 2 E 2 NAG E 1236 NAG 4 n D BMA 3 E 3 BMA E 1237 BMA 4 n E NAG 1 C 1 NAG E 1241 NAG 4 n E NAG 2 C 2 NAG E 1242 NAG 4 n E BMA 3 C 3 BMA E 1243 BMA 5 n F NAG 1 F 1 NAG E 1247 NAG 5 n F NAG 2 F 2 NAG E 1248 NAG 5 n F BMA 3 F 3 BMA E 1249 BMA # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 251 A CYS 251 1_555 A SG CYS 273 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 268 A CYS 268 1_555 A SG CYS 279 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 1318 A CYS 1318 1_555 A SG CYS 1329 A CYS 1329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf4 A SG CYS 1678 A CYS 1678 1_555 A SG CYS 1694 A CYS 1694 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 C SG CYS 303 D CYS 303 1_555 C SG CYS 1044 D CYS 1044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 C SG CYS 354 D CYS 354 1_555 C SG CYS 1059 D CYS 1059 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf7 C SG CYS 404 D CYS 404 1_555 C SG CYS 1071 D CYS 1071 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf8 C SG CYS 667 D CYS 667 1_555 C SG CYS 697 D CYS 697 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 C SG CYS 904 D CYS 904 1_555 C SG CYS 974 D CYS 974 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf10 C SG CYS 996 D CYS 996 1_555 C SG CYS 1026 D CYS 1026 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf11 C SG CYS 999 D CYS 999 1_555 C SG CYS 1024 D CYS 1024 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 C ND2 ASN 92 D ASN 92 1_555 AA C1 NAG . D NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 C ND2 ASN 184 D ASN 184 1_555 HA C1 NAG . D NAG 1209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 C ND2 ASN 324 D ASN 324 1_555 BA C1 NAG . D NAG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 C ND2 ASN 348 D ASN 348 1_555 CA C1 NAG . D NAG 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale5 C ND2 ASN 468 D ASN 468 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale6 C ND2 ASN 604 D ASN 604 1_555 DA C1 NAG . D NAG 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 C ND2 ASN 613 D ASN 613 1_555 EA C1 NAG . D NAG 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale8 C ND2 ASN 675 D ASN 675 1_555 FA C1 NAG . D NAG 1207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 C ND2 ASN 824 D ASN 824 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale10 C ND2 ASN 888 D ASN 888 1_555 GA C1 NAG . D NAG 1208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale11 C ND2 ASN 895 D ASN 895 1_555 D C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale12 D O4 NAG . E NAG 1 1_555 D C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale13 D O4 NAG . E NAG 2 1_555 D C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale14 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale15 E O4 NAG . C NAG 2 1_555 E C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale16 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale17 F O3 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? metalc ? metalc1 A OD2 ASP 116 A ASP 116 1_555 Z CA CA . D CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc2 A OE1 GLU 309 A GLU 309 1_555 U CA CA . A CA 2415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? metalc ? metalc3 A OE2 GLU 309 A GLU 309 1_555 U CA CA . A CA 2415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.976 ? metalc ? metalc4 A OE1 GLU 1372 A GLU 1372 1_555 U CA CA . A CA 2415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc5 A O GLY 1662 A GLY 1662 1_555 U CA CA . A CA 2415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.137 ? metalc ? metalc6 C OG SER 261 D SER 261 1_555 Z CA CA . D CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? metalc ? metalc7 C OG SER 263 D SER 263 1_555 Z CA CA . D CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? metalc ? metalc8 C OG1 THR 331 D THR 331 1_555 Z CA CA . D CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? # _chem_comp.formula 'Ca 2' _chem_comp.formula_weight 40.078 _chem_comp.id CA _chem_comp.mon_nstd_flag . _chem_comp.name 'CALCIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 7YG5 _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code G 6 Y01 A 1 2401 1902 Y01 Y01 . H 7 R16 A 1 2402 1903 R16 R16 . I 7 R16 A 1 2403 1904 R16 R16 . J 8 3PE A 1 2404 1905 3PE 3PE . K 8 3PE A 1 2405 1906 3PE 3PE . L 6 Y01 A 1 2406 1907 Y01 Y01 . M 7 R16 A 1 2407 1908 R16 R16 . N 6 Y01 A 1 2408 1909 Y01 Y01 . O 7 R16 A 1 2409 1910 R16 R16 . P 6 Y01 A 1 2410 1911 Y01 Y01 . Q 6 Y01 A 1 2411 1912 Y01 Y01 . R 6 Y01 A 1 2412 1913 Y01 Y01 . S 6 Y01 A 1 2413 1915 Y01 Y01 . T 6 Y01 A 1 2414 1916 Y01 Y01 . U 9 CA A 1 2415 1917 CA CA . V 10 TOR A 1 2416 1918 TOR TOR . W 6 Y01 A 1 2417 1919 Y01 Y01 . X 7 R16 A 1 2418 1925 R16 R16 . Y 7 R16 A 1 2419 1926 R16 R16 . Z 9 CA D 1 1201 1201 CA CA . AA 11 NAG D 1 1202 1238 NAG NAG . BA 11 NAG D 1 1203 1239 NAG NAG . CA 11 NAG D 1 1204 1240 NAG NAG . DA 11 NAG D 1 1205 1244 NAG NAG . EA 11 NAG D 1 1206 1245 NAG NAG . FA 11 NAG D 1 1207 1246 NAG NAG . GA 11 NAG D 1 1208 1250 NAG NAG . HA 11 NAG D 1 1209 1251 NAG NAG . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CA _atom_site.label_atom_id CA _atom_site.label_comp_id CA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id Z _atom_site.label_entity_id 9 _atom_site.Cartn_x 178.569 _atom_site.Cartn_y 193.914 _atom_site.Cartn_z 191.219 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 46.98 _atom_site.pdbx_formal_charge 0 _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 1201 _atom_site.auth_asym_id D _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #