data_1C8F # _model_server_result.job_id ZbpcHvOyCbGwQxtzqqsILA _model_server_result.datetime_utc '2025-04-18 08:46:03' _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 1c8f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":587}' # _entry.id 1C8F # _exptl.entry_id 1C8F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _entity.pdbx_number_of_molecules 3 _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 1C8F _cell.length_a 380.12 _cell.length_b 379.25 _cell.length_c 350.82 _cell.Z_PDB 240 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1C8F _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 'complete icosahedral assembly' 60 'complete icosahedral assembly' 1 ? monomeric 1 'icosahedral asymmetric unit' 2 ? pentameric 5 'icosahedral pentamer' 3 ? hexameric 6 'icosahedral 23 hexamer' 4 ? monomeric 1 'icosahedral asymmetric unit, std point frame' 5 ? 60-meric 60 'crystal asymmetric unit, crystal frame' 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D 1 (1-60) A,B,C,D 2 1 A,B,C,D 3 (1-5) A,B,C,D 4 (1,2,6,10,23,24) A,B,C,D 5 P A,B,C,D 6 (X0)(1-60) # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] X0 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 P 'transform to point frame' ? ? -0.537169 0.6225 -0.56916 0.732844 0.678523 0.05046 0.417599 -0.39 -0.820677 103.73194 -2.85328 140.41817 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.687921 0.651486 -0.31989 -0.625937 0.309448 -0.715853 -0.367379 0.692681 0.620665 60.6679 118.90606 71.3151 3 'point symmetry operation' ? ? 0.182967 0.42819 -0.884972 -0.3613 -0.807889 -0.465593 -0.914322 0.404929 0.006888 157.05533 66.67589 175.65377 4 'point symmetry operation' ? ? 0.182967 -0.3613 -0.914322 0.428191 -0.807889 0.404929 -0.884972 -0.465593 0.006888 155.95814 -84.5102 168.82352 5 'point symmetry operation' ? ? 0.687921 -0.625937 -0.367379 0.651486 0.309448 0.692681 -0.31989 -0.715853 0.620665 58.89261 -125.71817 60.26352 6 'point symmetry operation' ? ? -0.651221 -0.325728 -0.685428 -0.325728 -0.695799 0.640128 -0.685428 0.640128 0.347021 115.6251 -125.27427 118.36814 7 'point symmetry operation' ? ? 0.007708 -0.999841 0.016071 -0.023719 0.015884 0.999593 -0.999689 -0.008086 -0.023592 -11.49553 -182.11945 177.64761 8 'point symmetry operation' ? ? 0.625236 -0.293245 0.723248 -0.393488 0.681862 0.616629 -0.673979 -0.670128 0.310936 -128.76895 -110.38363 114.3546 9 'point symmetry operation' ? ? 0.347959 0.817569 0.458808 -0.924028 0.381775 0.02048 -0.158418 -0.431078 0.888299 -74.12727 -9.20328 15.9579 10 'point symmetry operation' ? ? -0.440935 0.797493 -0.411802 -0.88215 -0.469666 0.035004 -0.165494 0.378705 0.910601 76.91656 -18.4062 18.4384 11 'point symmetry operation' ? ? 0.074121 0.994503 0.073958 0.994503 -0.079213 0.068476 0.073958 0.068476 -0.994908 -5.83402 -19.62003 348.55605 12 'point symmetry operation' ? ? -0.598677 0.407265 -0.689725 0.708566 0.670825 -0.218926 0.373524 -0.619781 -0.690182 122.18952 36.17881 290.23325 13 'point symmetry operation' ? ? -0.413374 -0.741763 -0.528119 0.147972 0.51756 -0.842755 0.898457 -0.42652 -0.104186 85.10751 143.31846 189.97804 14 'point symmetry operation' ? ? 0.373947 -0.864663 0.335442 0.087444 -0.327201 -0.9409 0.923318 0.381179 -0.046747 -65.83398 153.73556 186.33971 15 'point symmetry operation' ? ? 0.675236 0.208408 0.707547 0.610629 -0.696027 -0.377729 0.41375 0.687104 -0.597243 -122.03894 53.03403 284.3463 16 'point symmetry operation' ? ? -0.4229 -0.668775 0.61147 -0.668775 -0.224987 -0.708605 0.61147 -0.708605 -0.352113 -113.09508 113.3983 230.76382 17 'point symmetry operation' ? ? -0.096952 -0.05891 0.993544 -0.05891 -0.996157 -0.064814 0.993544 -0.064814 0.093109 -174.66589 -4.46143 158.49204 18 'point symmetry operation' ? ? -0.394829 0.606817 0.689843 0.606817 -0.391533 0.691719 0.689843 0.691719 -0.213638 -116.69788 -131.10671 217.70159 19 'point symmetry operation' ? ? -0.904874 0.408394 0.120072 0.408394 0.753315 0.515491 0.120072 0.515491 -0.848441 -19.30088 -91.51807 326.56688 20 'point symmetry operation' ? ? -0.922223 -0.379965 0.071634 -0.379965 0.856246 -0.349956 0.071634 -0.349956 -0.934023 -17.07423 59.59433 334.63978 21 'point symmetry operation' ? ? -0.311947 0.949042 0.044808 -0.390335 -0.085019 -0.916739 -0.866215 -0.303464 0.396966 -1.42642 151.03361 102.07748 22 'point symmetry operation' ? ? -0.825097 0.121488 -0.551775 0.121488 -0.915615 -0.383263 -0.551775 -0.383263 0.740712 95.69079 51.86622 41.75199 23 'point symmetry operation' ? ? -0.440935 -0.88215 -0.165494 0.797494 -0.469666 0.378705 -0.411802 0.035004 0.910601 20.7296 -76.96795 15.52864 24 'point symmetry operation' ? ? 0.309641 -0.674877 0.669824 0.703466 0.636541 0.316151 -0.639733 0.373305 0.671852 -122.71618 -57.42446 59.64721 25 'point symmetry operation' ? ? 0.38936 0.456862 0.799798 -0.030653 0.874266 -0.484478 -0.920576 0.16412 0.354408 -136.40935 83.48825 113.13734 26 'point symmetry operation' ? ? -0.136696 -0.53005 0.836876 0.910246 -0.400532 -0.105004 0.390853 0.747409 0.537228 -151.08204 8.03906 86.92565 27 'point symmetry operation' ? ? -0.069709 0.32661 0.942585 0.915462 0.396335 -0.069629 -0.396321 0.858047 -0.326627 -162.71943 8.14779 237.82179 28 'point symmetry operation' ? ? -0.598677 0.708566 0.373524 0.407265 0.670825 -0.619781 -0.689725 -0.218926 -0.690182 -60.89207 105.84798 292.51135 29 'point symmetry operation' ? ? -0.992585 0.087967 -0.083885 0.087967 0.043602 -0.995169 -0.083885 -0.995169 -0.051017 13.67809 166.1213 175.41521 30 'point symmetry operation' ? ? -0.707065 -0.67754 0.202482 0.398827 -0.618533 -0.677019 0.583949 -0.397941 0.707564 -42.06238 105.67206 48.35626 31 'point symmetry operation' ? ? 0.924018 -0.382341 -0.002664 -0.181284 -0.444229 0.87738 -0.336642 -0.810232 -0.479788 -2.60864 -164.55605 251.44976 32 'point symmetry operation' ? ? 0.875951 0.481825 -0.023538 -0.168981 0.352175 0.920553 0.451835 -0.802382 0.389908 7.79695 -165.80528 100.4688 33 'point symmetry operation' ? ? 0.309641 0.703466 -0.639733 -0.674877 0.636541 0.373305 0.669824 0.316151 0.671852 116.55238 -68.53189 60.27887 34 'point symmetry operation' ? ? 0.007708 -0.023719 -0.999689 -0.999841 0.015884 -0.008086 0.016071 0.999592 -0.023592 173.36135 -7.16439 186.42109 35 'point symmetry operation' ? ? 0.387414 -0.694784 -0.605959 -0.694784 -0.652069 0.30345 -0.605959 0.30345 -0.735345 99.71579 -66.51059 304.5712 36 'point symmetry operation' ? ? -0.475375 -0.036651 -0.87902 -0.338628 0.92978 0.144363 0.812004 0.366287 -0.454405 151.8131 -26.01262 257.23511 37 'point symmetry operation' ? ? 0.018854 -0.929922 -0.367272 -0.867968 0.167104 -0.467661 0.496261 0.327598 -0.803993 55.9277 74.29527 317.64541 38 'point symmetry operation' ? ? 0.729971 -0.529882 0.431703 -0.529882 -0.8377 -0.132229 0.431703 -0.132229 -0.892271 -79.6939 8.15585 329.36913 39 'point symmetry operation' ? ? 0.675236 0.610628 0.41375 0.208408 -0.696027 0.687104 0.707547 -0.377729 -0.597243 -67.62726 -133.02844 276.20448 40 'point symmetry operation' ? ? -0.069709 0.915462 -0.396321 0.32661 0.396335 0.858047 0.942585 -0.069629 -0.326627 75.45193 -154.14572 231.6232 41 'point symmetry operation' ? ? -0.311947 -0.390335 -0.866215 0.949042 -0.085019 -0.303464 0.044808 -0.916739 0.396966 146.92972 45.17128 98.00105 42 'point symmetry operation' ? ? 0.347959 -0.924028 -0.158418 0.817569 0.381775 -0.431078 0.458808 0.02048 0.888299 19.8172 70.99686 20.02329 43 'point symmetry operation' ? ? 0.875951 -0.168981 0.451835 0.481825 0.352175 -0.802382 -0.023538 0.920553 0.389908 -80.24299 135.25013 113.64255 44 'point symmetry operation' ? ? 0.542362 0.831357 0.121195 0.405797 -0.132913 -0.904247 -0.735644 0.53961 -0.409449 -14.97106 149.13525 249.48019 45 'point symmetry operation' ? ? -0.191799 0.694553 -0.693404 0.694553 -0.403114 -0.595899 -0.693404 -0.595899 -0.405087 125.4294 93.46346 239.81322 46 'point symmetry operation' ? ? 0.924018 -0.181284 -0.336642 -0.382341 -0.444229 -0.810232 -0.002664 0.87738 -0.479788 57.22753 129.6346 265.01389 47 'point symmetry operation' ? ? 0.872799 0.312702 -0.374753 0.312702 -0.947788 -0.062573 -0.374753 -0.062573 -0.925011 67.72233 -4.16456 334.96197 48 'point symmetry operation' ? ? 0.542362 0.405797 -0.735644 0.831357 -0.132913 0.53961 0.121195 -0.904247 -0.409449 131.12975 -102.35374 238.819 49 'point symmetry operation' ? ? 0.38936 -0.030653 -0.920576 0.456862 0.874266 0.16412 0.799798 -0.484478 0.354408 159.82289 -29.23884 109.4513 50 'point symmetry operation' ? ? 0.625236 -0.393488 -0.673979 -0.293245 0.681862 -0.670128 0.723248 0.616629 0.310936 114.14881 114.13784 125.64063 51 'point symmetry operation' ? ? -0.475375 -0.338627 0.812004 -0.036651 0.92978 0.366287 -0.87902 0.144363 -0.454405 -145.51634 -64.47162 254.0909 52 'point symmetry operation' ? ? -0.413374 0.147972 0.898457 -0.741763 0.51756 -0.42652 -0.528119 -0.842755 -0.104186 -156.71306 69.98307 185.52226 53 'point symmetry operation' ? ? -0.707065 0.398827 0.583949 -0.67754 -0.618533 -0.397941 0.202482 -0.677019 0.707564 -100.12325 56.10564 45.84371 54 'point symmetry operation' ? ? -0.950576 0.067264 0.303119 0.067264 -0.908458 0.412529 0.303119 0.412529 0.859034 -53.9521 -86.92578 28.08625 55 'point symmetry operation' ? ? -0.807384 -0.388508 0.444064 0.463355 0.048452 0.884847 -0.365286 0.92017 0.140897 -82.00657 -161.44662 156.79009 56 'point symmetry operation' ? ? -0.136696 0.910246 0.390853 -0.53005 -0.400532 0.747409 0.836876 -0.105004 0.537228 -61.94492 -141.83026 80.58216 57 'point symmetry operation' ? ? -0.807384 0.463355 -0.365286 -0.388508 0.048452 0.920171 0.444064 0.884847 0.140897 65.86953 -168.31138 157.18048 58 'point symmetry operation' ? ? -0.711248 -0.635643 -0.30014 -0.635643 0.399271 0.660713 -0.30014 0.660713 -0.688022 45.93249 -120.49803 299.38274 59 'point symmetry operation' ? ? 0.018854 -0.867968 0.496262 -0.929922 0.167104 0.327598 -0.367272 -0.467661 -0.803993 -94.20373 -64.46663 310.67026 60 'point symmetry operation' ? ? 0.373947 0.087444 0.923318 -0.864663 -0.327201 0.381179 0.335442 -0.9409 -0.046747 -160.87564 -77.65068 175.44406 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D N N # 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 454 A CYS 490 1_555 A SG CYS 458 A CYS 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc1 A OD2 ASP 337 A ASP 373 1_555 D CA CA . A CA 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.151 ? metalc ? metalc2 A OD2 ASP 339 A ASP 375 1_555 D CA CA . A CA 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.27 ? metalc ? metalc3 A OD1 ASP 369 A ASP 405 1_555 C CA CA . A CA 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc4 A OD2 ASP 369 A ASP 405 1_555 C CA CA . A CA 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.346 ? # _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 1C8F _atom_sites.fract_transf_matrix[1][1] 0.002631 _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] 0.002637 _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] 0.00285 _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 B 2 CA A 1 585 585 CA CA . C 2 CA A 1 586 586 CA CA . D 2 CA A 1 587 587 CA CA . # _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 D _atom_site.label_entity_id 2 _atom_site.Cartn_x 35.432 _atom_site.Cartn_y -37.845 _atom_site.Cartn_z 67.17 _atom_site.occupancy 0.67 _atom_site.B_iso_or_equiv 30 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 587 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 1 #