data_5ABJ # _model_server_result.job_id i3v-xPP46JNLGSu7mOiBWg _model_server_result.datetime_utc '2024-11-22 20:59:34' _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 5abj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1243}' # _entry.id 5ABJ # _exptl.entry_id 5ABJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 1 _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 5ABJ _cell.length_a 491.6 _cell.length_b 491.6 _cell.length_c 709.56 _cell.Z_PDB 480 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ABJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 240-MERIC 240 'complete icosahedral assembly' 1 ? tetrameric 4 'icosahedral asymmetric unit' 2 ? eicosameric 20 'icosahedral pentamer' 3 ? 24-meric 24 'icosahedral 23 hexamer' 4 ? tetrameric 4 'icosahedral asymmetric unit, std point frame' 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K 1 (1-60) A,B,C,D,E,F,G,H,I,J,K 2 1 A,B,C,D,E,F,G,H,I,J,K 3 (1-5) A,B,C,D,E,F,G,H,I,J,K 4 (1,2,6,10,23,24) A,B,C,D,E,F,G,H,I,J,K 5 P # 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] P 'transform to point frame' ? ? 0.572233 -0.20061 -0.795176 -0.796661 -0.366099 -0.48094 -0.194632 0.908696 -0.369311 94.37804 228.63091 -22.92136 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.544998 0.304835 0.781059 -0.773664 0.541875 0.328353 -0.323143 -0.783228 0.531161 -119.25209 94.27612 219.43301 3 'point symmetry operation' ? ? -0.191211 -0.280431 0.940637 -0.946979 -0.199386 -0.251943 0.258202 -0.938938 -0.227437 15.88449 309.67446 300.68295 4 'point symmetry operation' ? ? -0.191211 -0.946979 0.258202 -0.280431 -0.199386 -0.938938 0.940637 -0.251943 -0.227437 218.65558 348.52184 131.46516 5 'point symmetry operation' ? ? 0.544998 -0.773664 -0.323143 0.304835 0.541875 -0.783228 0.781059 0.328353 0.531161 208.83843 157.1325 -54.36712 6 'point symmetry operation' ? ? -0.924237 -0.353722 0.143759 -0.353722 0.651455 -0.671183 0.143759 -0.671183 -0.727218 256.27008 205.26916 370.01006 7 'point symmetry operation' ? ? -0.2765 -0.586009 -0.76167 -0.479897 0.770871 -0.418877 0.832614 0.249703 -0.49437 364.68531 161.58814 130.01423 8 'point symmetry operation' ? ? 0.54881 0.19473 -0.81295 -0.72258 0.599502 -0.344201 0.420339 0.776323 0.469721 175.27643 199.57619 -54.21681 9 'point symmetry operation' ? ? 0.411144 0.909542 0.060786 -0.746392 0.374176 -0.550356 -0.523316 0.180905 0.832715 -50.19992 266.73512 71.91797 10 'point symmetry operation' ? ? -0.49925 0.57058 0.652065 -0.518425 0.406284 -0.752442 -0.694252 -0.713703 0.092965 -0.1431 270.25357 334.1046 11 'point symmetry operation' ? ? 0.269336 0.583313 0.766293 0.583313 -0.731944 0.352143 0.766293 0.352143 -0.537393 -116.93486 79.52337 133.16413 12 'point symmetry operation' ? ? -0.552122 -0.201996 0.808924 0.77039 -0.494617 0.40231 0.318842 0.845312 0.428705 74.08856 18.22914 -42.94086 13 'point symmetry operation' ? ? -0.406026 -0.911336 -0.067897 0.672524 -0.34828 0.653003 -0.618752 0.219474 0.754306 298.39154 -31.99186 92.80124 14 'point symmetry operation' ? ? 0.505724 -0.564422 -0.652434 0.424963 -0.495165 0.757772 -0.750766 -0.660484 -0.010559 245.99499 -1.73591 352.79946 15 'point symmetry operation' ? ? 0.923121 0.359321 -0.136877 0.369827 -0.732283 0.57183 0.105238 -0.57849 -0.808873 -10.69084 67.18428 377.7451 16 'point symmetry operation' ? ? -0.345099 -0.229591 -0.910052 -0.229591 -0.919512 0.31904 -0.910052 0.31904 0.264611 355.36005 209.05995 202.98546 17 'point symmetry operation' ? ? 0.283625 0.483171 -0.828313 0.483171 -0.818129 -0.311786 -0.828313 -0.311786 -0.465496 175.17349 219.75908 399.65326 18 'point symmetry operation' ? ? 0.048427 0.997036 -0.05979 0.997036 -0.051837 -0.056859 -0.05979 -0.056859 -0.99659 5.14281 16.59369 366.89227 19 'point symmetry operation' ? ? -0.725657 0.60186 0.333446 0.60186 0.320376 0.731522 0.333446 0.731522 -0.594719 80.24463 -119.66857 149.97706 20 'point symmetry operation' ? ? -0.96887 -0.156237 -0.192045 -0.156237 -0.215877 0.96384 -0.192045 0.96384 0.184747 296.69079 -0.71787 48.67708 21 'point symmetry operation' ? ? -0.412195 0.751058 0.51576 -0.894371 -0.441522 -0.071828 0.173772 -0.490888 0.853717 -9.1286 301.2656 64.94023 22 'point symmetry operation' ? ? -0.972375 -0.12263 0.198615 -0.12263 -0.455628 -0.881683 0.198615 -0.881683 0.428003 224.00798 350.53469 185.2722 23 'point symmetry operation' ? ? -0.49925 -0.518425 -0.694252 0.57058 0.406284 -0.713703 0.652065 -0.752442 0.092965 371.98742 128.7333 172.38328 24 'point symmetry operation' ? ? 0.353339 0.110647 -0.928929 0.227265 0.953081 0.19997 0.90747 -0.28177 0.311614 230.30715 -57.61659 44.08551 25 'point symmetry operation' ? ? 0.407142 0.895231 -0.1811 -0.678124 0.429107 0.59667 0.611869 -0.120121 0.781785 -5.2355 49.01424 -22.31794 26 'point symmetry operation' ? ? 0.189445 0.288913 -0.938424 0.972461 0.076936 0.220003 0.13576 -0.954259 -0.266382 230.24353 -45.14287 324.59265 27 'point symmetry operation' ? ? 0.182971 0.949305 -0.25562 0.399374 0.165817 0.901668 0.898344 -0.267067 -0.348788 28.96819 -105.58167 159.9862 28 'point symmetry operation' ? ? -0.552122 0.77039 0.318842 -0.201996 -0.494617 0.845312 0.808924 0.40231 0.428705 40.55375 60.28047 -48.85685 29 'point symmetry operation' ? ? -0.99996 -0.000577 -0.008924 -0.000577 -0.991668 0.128817 -0.008924 0.128817 0.991628 248.98936 223.2277 -13.32251 30 'point symmetry operation' ? ? -0.541646 -0.298146 -0.785957 0.725277 -0.638429 -0.257645 -0.424962 -0.709589 0.562041 366.22409 158.07249 217.48197 31 'point symmetry operation' ? ? 0.722305 -0.608549 -0.328547 -0.553473 -0.223822 -0.802229 0.414659 0.761296 -0.498483 167.47865 361.17243 119.26761 32 'point symmetry operation' ? ? 0.970635 0.147754 0.189833 0.130756 0.338327 -0.9319 -0.201917 0.929357 0.309072 -48.12354 230.03876 32.20698 33 'point symmetry operation' ? ? 0.353339 0.227265 0.90747 0.110647 0.953081 -0.28177 -0.928929 0.19997 0.311614 -108.28855 41.85236 211.72283 34 'point symmetry operation' ? ? -0.2765 -0.479897 0.832614 -0.586009 0.770871 0.249703 -0.76167 -0.418877 -0.49437 70.12961 56.68043 409.73036 35 'point symmetry operation' ? ? -0.048467 -0.996458 0.068713 -0.996458 0.043505 -0.071958 0.068713 -0.071958 -0.995038 240.56311 254.03109 352.58989 36 'point symmetry operation' ? ? -0.499556 -0.431422 0.751212 0.475383 0.588408 0.654054 -0.724192 0.68385 -0.088852 106.1017 -123.44268 197.35917 37 'point symmetry operation' ? ? -0.18123 -0.974429 -0.132827 -0.4075 -0.048516 0.911916 -0.895042 0.219394 -0.388287 289.84264 18.86069 328.69428 38 'point symmetry operation' ? ? 0.698033 -0.47923 -0.532061 -0.47923 -0.864748 0.150162 -0.532061 0.150162 -0.833284 190.44266 262.98635 370.9104 39 'point symmetry operation' ? ? 0.923121 0.369827 0.105238 0.359321 -0.732283 -0.57849 -0.136877 0.57183 -0.808873 -54.73084 271.56093 265.66629 40 'point symmetry operation' ? ? 0.182971 0.399374 0.898344 0.949305 0.165817 -0.267067 -0.25562 0.901668 -0.348788 -106.85642 32.73466 158.40573 41 'point symmetry operation' ? ? -0.412195 -0.894371 0.173772 0.751058 -0.441522 -0.490888 0.51576 -0.071828 0.853717 254.39552 171.74994 -29.09305 42 'point symmetry operation' ? ? 0.411144 -0.746392 -0.523316 0.909542 0.374176 0.180905 0.060786 -0.550356 0.832715 257.36419 -67.15719 89.9635 43 'point symmetry operation' ? ? 0.970635 0.130756 -0.201917 0.147754 0.338327 0.929357 0.189833 -0.9319 0.309072 23.13468 -100.6496 213.5543 44 'point symmetry operation' ? ? 0.493081 0.524884 0.693806 -0.481541 -0.499527 0.720133 0.724561 -0.68918 0.006446 -124.5958 117.55808 170.88106 45 'point symmetry operation' ? ? -0.361554 -0.108679 0.925995 -0.108679 -0.9815 -0.157626 0.925995 -0.157626 0.343055 18.33126 285.91026 20.91675 46 'point symmetry operation' ? ? 0.722305 -0.553473 0.414659 -0.608549 -0.223822 0.761296 -0.328547 -0.802229 -0.498483 29.47321 91.95925 404.2205 47 'point symmetry operation' ? ? 0.687863 -0.404503 0.602679 -0.404503 -0.903059 -0.144434 0.602679 -0.144434 -0.784804 -17.85259 310.48245 258.38575 48 'point symmetry operation' ? ? 0.493081 -0.481541 0.724561 0.524884 -0.499527 -0.68918 0.693806 0.720133 0.006446 -5.76894 241.88965 0.68649 49 'point symmetry operation' ? ? 0.407142 -0.678124 0.611869 0.895231 0.429107 -0.120121 -0.1811 0.59667 0.781785 49.02496 -19.02624 -12.74566 50 'point symmetry operation' ? ? 0.54881 -0.72258 0.420339 0.19473 0.599502 0.776323 -0.81295 -0.344201 0.469721 70.80581 -111.68832 236.65207 51 'point symmetry operation' ? ? -0.499556 0.475383 -0.724192 -0.431422 0.588408 0.68385 0.751212 0.654054 -0.088852 254.61232 -16.55483 18.5691 52 'point symmetry operation' ? ? -0.406026 0.672524 -0.618752 -0.911336 -0.34828 0.219474 -0.067897 0.653003 0.754306 200.09107 240.42527 -28.84985 53 'point symmetry operation' ? ? -0.541646 0.725277 -0.424962 -0.298146 -0.638429 -0.709589 -0.785957 -0.257645 0.562041 176.13901 364.42929 206.32922 54 'point symmetry operation' ? ? -0.718993 0.560739 -0.410634 0.560739 0.118936 -0.819406 -0.410634 -0.819406 -0.399943 215.85707 184.0879 399.09683 55 'point symmetry operation' ? ? -0.69298 0.406297 -0.595568 0.47837 0.877163 0.041787 0.539389 -0.255944 -0.802217 264.35625 -51.37324 283.05469 56 'point symmetry operation' ? ? 0.189445 0.972461 0.13576 0.288913 0.076936 -0.954259 -0.938424 0.220003 -0.266382 -43.78578 246.69812 312.46311 57 'point symmetry operation' ? ? -0.69298 0.47837 0.539389 0.406297 0.877163 -0.255944 -0.595568 0.041787 -0.802217 55.09259 10.10195 386.66025 58 'point symmetry operation' ? ? -0.92207 -0.374492 -0.097682 -0.374492 0.799629 0.469413 -0.097682 0.469413 -0.877559 301.19052 -11.81686 285.58964 59 'point symmetry operation' ? ? -0.18123 -0.4075 -0.895042 -0.974429 -0.048516 0.219394 -0.132827 0.911916 -0.388287 354.40904 211.23273 148.92742 60 'point symmetry operation' ? ? 0.505724 0.424963 -0.750766 -0.564422 -0.495165 -0.660484 -0.652434 0.757772 -0.010559 141.20196 371.00378 165.53614 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id C _struct_conn.ptnr1_label_atom_id O _struct_conn.ptnr1_label_comp_id PRO _struct_conn.ptnr1_label_seq_id 8 _struct_conn.ptnr1_auth_asym_id C _struct_conn.ptnr1_auth_comp_id PRO _struct_conn.ptnr1_auth_seq_id 8 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id G _struct_conn.ptnr2_label_atom_id NA _struct_conn.ptnr2_label_comp_id NA _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id C _struct_conn.ptnr2_auth_comp_id NA _struct_conn.ptnr2_auth_seq_id 1243 _struct_conn.ptnr2_symmetry 1_555 _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 2.691 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5ABJ _atom_sites.fract_transf_matrix[1][1] 0.002034 _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] 0.002034 _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] 0.001409 _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 E 5 CL A 1 1298 1298 CL CL . F 6 YM2 A 1 1299 1299 YM2 YM2 . G 7 NA C 1 1243 1243 NA NA . H 8 HOH A 1 2001 2001 HOH HOH . H 8 HOH A 2 2002 2002 HOH HOH . H 8 HOH A 3 2003 2003 HOH HOH . I 8 HOH B 1 2001 2001 HOH HOH . I 8 HOH B 2 2002 2002 HOH HOH . I 8 HOH B 3 2003 2003 HOH HOH . J 8 HOH C 1 2001 2001 HOH HOH . J 8 HOH C 2 2002 2002 HOH HOH . J 8 HOH C 3 2003 2003 HOH HOH . K 8 HOH D 1 2001 2001 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id G _atom_site.label_entity_id 7 _atom_site.Cartn_x 56.783 _atom_site.Cartn_y 206.535 _atom_site.Cartn_z 111.014 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 13.63 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 1243 _atom_site.auth_asym_id C _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 1 #