data_5EMJ # _model_server_result.job_id p-CAzaqj6qhLie2I8T8Xvg _model_server_result.datetime_utc '2024-11-22 13:28:03' _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 5emj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":701}' # _entry.id 5EMJ # _exptl.entry_id 5EMJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 381.387 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SINEFUNGIN _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 5EMJ _cell.length_a 104.24 _cell.length_b 138.83 _cell.length_c 179.34 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EMJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -138.83 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_545 x,-y-1,-z 1 0 0 0 -1 0 0 0 -1 0 -138.83 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 216 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 208 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 255 _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 247 _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 2.033 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C15 H23 N7 O5' _chem_comp.formula_weight 381.387 _chem_comp.id SFG _chem_comp.mon_nstd_flag . _chem_comp.name SINEFUNGIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ADENOSYL-ORNITHINE # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N CA SFG sing 365 n n N HN1 SFG sing 366 n n N HN2 SFG sing 367 n n CA C SFG sing 368 n n CA CB SFG sing 369 n n CA HA SFG sing 370 n n C O SFG doub 371 n n C OXT SFG sing 372 n n OXT HXT SFG sing 373 n n CB CG SFG sing 374 n n CB HB1 SFG sing 375 n n CB HB2 SFG sing 376 n n CG CD SFG sing 377 n n CG HG1 SFG sing 378 n n CG HG2 SFG sing 379 n n CD NE SFG sing 380 n n CD C5' SFG sing 381 n n CD HD SFG sing 382 n n NE HNE1 SFG sing 383 n n NE HNE2 SFG sing 384 n n C5' C4' SFG sing 385 n n C5' "H5'1" SFG sing 386 n n C5' "H5'2" SFG sing 387 n n C4' O4' SFG sing 388 n n C4' C3' SFG sing 389 n n C4' H4' SFG sing 390 n n O4' C1' SFG sing 391 n n C3' O3' SFG sing 392 n n C3' C2' SFG sing 393 n n C3' H3' SFG sing 394 n n O3' HO3' SFG sing 395 n n C2' O2' SFG sing 396 n n C2' C1' SFG sing 397 n n C2' H2' SFG sing 398 n n O2' HO2' SFG sing 399 n n C1' N9 SFG sing 400 n n C1' H1' SFG sing 401 n n N9 C8 SFG sing 402 n y N9 C4 SFG sing 403 n y C8 N7 SFG doub 404 n y C8 H8 SFG sing 405 n n N7 C5 SFG sing 406 n y C5 C6 SFG sing 407 n y C5 C4 SFG doub 408 n y C6 N6 SFG sing 409 n n C6 N1 SFG doub 410 n y N6 HN61 SFG sing 411 n n N6 HN62 SFG sing 412 n n N1 C2 SFG sing 413 n y C2 N3 SFG doub 414 n y C2 H2 SFG sing 415 n n N3 C4 SFG sing 416 n y # _atom_sites.entry_id 5EMJ _atom_sites.fract_transf_matrix[1][1] 0.009593 _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] 0.007203 _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] 0.005576 _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 C 3 SFG A 1 701 1 SFG SFG . D 4 5QJ A 1 702 1 5QJ EPZ . E 5 GOL A 1 703 1 GOL GOL . F 5 GOL A 1 704 2 GOL GOL . G 5 GOL A 1 705 3 GOL GOL . H 5 GOL B 1 401 4 GOL GOL . I 6 HOH A 1 801 184 HOH HOH . I 6 HOH A 2 802 104 HOH HOH . I 6 HOH A 3 803 122 HOH HOH . I 6 HOH A 4 804 120 HOH HOH . I 6 HOH A 5 805 95 HOH HOH . I 6 HOH A 6 806 185 HOH HOH . I 6 HOH A 7 807 118 HOH HOH . I 6 HOH A 8 808 117 HOH HOH . I 6 HOH A 9 809 127 HOH HOH . I 6 HOH A 10 810 51 HOH HOH . I 6 HOH A 11 811 80 HOH HOH . I 6 HOH A 12 812 129 HOH HOH . I 6 HOH A 13 813 147 HOH HOH . I 6 HOH A 14 814 41 HOH HOH . I 6 HOH A 15 815 91 HOH HOH . I 6 HOH A 16 816 85 HOH HOH . I 6 HOH A 17 817 200 HOH HOH . I 6 HOH A 18 818 7 HOH HOH . I 6 HOH A 19 819 150 HOH HOH . I 6 HOH A 20 820 136 HOH HOH . I 6 HOH A 21 821 79 HOH HOH . I 6 HOH A 22 822 196 HOH HOH . I 6 HOH A 23 823 16 HOH HOH . I 6 HOH A 24 824 140 HOH HOH . I 6 HOH A 25 825 1 HOH HOH . I 6 HOH A 26 826 19 HOH HOH . I 6 HOH A 27 827 40 HOH HOH . I 6 HOH A 28 828 153 HOH HOH . I 6 HOH A 29 829 13 HOH HOH . I 6 HOH A 30 830 84 HOH HOH . I 6 HOH A 31 831 31 HOH HOH . I 6 HOH A 32 832 160 HOH HOH . I 6 HOH A 33 833 2 HOH HOH . I 6 HOH A 34 834 37 HOH HOH . I 6 HOH A 35 835 29 HOH HOH . I 6 HOH A 36 836 141 HOH HOH . I 6 HOH A 37 837 183 HOH HOH . I 6 HOH A 38 838 108 HOH HOH . I 6 HOH A 39 839 3 HOH HOH . I 6 HOH A 40 840 56 HOH HOH . I 6 HOH A 41 841 4 HOH HOH . I 6 HOH A 42 842 106 HOH HOH . I 6 HOH A 43 843 12 HOH HOH . I 6 HOH A 44 844 191 HOH HOH . I 6 HOH A 45 845 52 HOH HOH . I 6 HOH A 46 846 9 HOH HOH . I 6 HOH A 47 847 93 HOH HOH . I 6 HOH A 48 848 15 HOH HOH . I 6 HOH A 49 849 49 HOH HOH . I 6 HOH A 50 850 135 HOH HOH . I 6 HOH A 51 851 61 HOH HOH . I 6 HOH A 52 852 27 HOH HOH . I 6 HOH A 53 853 123 HOH HOH . I 6 HOH A 54 854 11 HOH HOH . I 6 HOH A 55 855 47 HOH HOH . I 6 HOH A 56 856 62 HOH HOH . I 6 HOH A 57 857 22 HOH HOH . I 6 HOH A 58 858 68 HOH HOH . I 6 HOH A 59 859 5 HOH HOH . I 6 HOH A 60 860 139 HOH HOH . I 6 HOH A 61 861 99 HOH HOH . I 6 HOH A 62 862 50 HOH HOH . I 6 HOH A 63 863 53 HOH HOH . I 6 HOH A 64 864 177 HOH HOH . I 6 HOH A 65 865 54 HOH HOH . I 6 HOH A 66 866 145 HOH HOH . I 6 HOH A 67 867 6 HOH HOH . I 6 HOH A 68 868 186 HOH HOH . I 6 HOH A 69 869 38 HOH HOH . I 6 HOH A 70 870 63 HOH HOH . I 6 HOH A 71 871 161 HOH HOH . I 6 HOH A 72 872 25 HOH HOH . I 6 HOH A 73 873 39 HOH HOH . I 6 HOH A 74 874 82 HOH HOH . I 6 HOH A 75 875 67 HOH HOH . I 6 HOH A 76 876 128 HOH HOH . I 6 HOH A 77 877 42 HOH HOH . I 6 HOH A 78 878 81 HOH HOH . I 6 HOH A 79 879 143 HOH HOH . I 6 HOH A 80 880 64 HOH HOH . I 6 HOH A 81 881 90 HOH HOH . I 6 HOH A 82 882 165 HOH HOH . I 6 HOH A 83 883 45 HOH HOH . I 6 HOH A 84 884 69 HOH HOH . I 6 HOH A 85 885 182 HOH HOH . I 6 HOH A 86 886 192 HOH HOH . I 6 HOH A 87 887 83 HOH HOH . I 6 HOH A 88 888 33 HOH HOH . I 6 HOH A 89 889 176 HOH HOH . I 6 HOH A 90 890 17 HOH HOH . I 6 HOH A 91 891 195 HOH HOH . I 6 HOH A 92 892 114 HOH HOH . I 6 HOH A 93 893 131 HOH HOH . I 6 HOH A 94 894 26 HOH HOH . I 6 HOH A 95 895 138 HOH HOH . I 6 HOH A 96 896 18 HOH HOH . I 6 HOH A 97 897 152 HOH HOH . I 6 HOH A 98 898 30 HOH HOH . I 6 HOH A 99 899 166 HOH HOH . I 6 HOH A 100 900 34 HOH HOH . I 6 HOH A 101 901 78 HOH HOH . I 6 HOH A 102 902 151 HOH HOH . I 6 HOH A 103 903 162 HOH HOH . I 6 HOH A 104 904 154 HOH HOH . I 6 HOH A 105 905 48 HOH HOH . I 6 HOH A 106 906 72 HOH HOH . I 6 HOH A 107 907 199 HOH HOH . I 6 HOH A 108 908 116 HOH HOH . I 6 HOH A 109 909 105 HOH HOH . I 6 HOH A 110 910 170 HOH HOH . I 6 HOH A 111 911 36 HOH HOH . I 6 HOH A 112 912 171 HOH HOH . I 6 HOH A 113 913 44 HOH HOH . I 6 HOH A 114 914 32 HOH HOH . I 6 HOH A 115 915 121 HOH HOH . I 6 HOH A 116 916 20 HOH HOH . I 6 HOH A 117 917 14 HOH HOH . I 6 HOH A 118 918 75 HOH HOH . I 6 HOH A 119 919 146 HOH HOH . I 6 HOH A 120 920 65 HOH HOH . I 6 HOH A 121 921 124 HOH HOH . I 6 HOH A 122 922 86 HOH HOH . I 6 HOH A 123 923 100 HOH HOH . I 6 HOH A 124 924 43 HOH HOH . I 6 HOH A 125 925 155 HOH HOH . I 6 HOH A 126 926 187 HOH HOH . I 6 HOH A 127 927 59 HOH HOH . I 6 HOH A 128 928 70 HOH HOH . I 6 HOH A 129 929 94 HOH HOH . I 6 HOH A 130 930 142 HOH HOH . I 6 HOH A 131 931 92 HOH HOH . I 6 HOH A 132 932 159 HOH HOH . I 6 HOH A 133 933 133 HOH HOH . I 6 HOH A 134 934 101 HOH HOH . I 6 HOH A 135 935 97 HOH HOH . I 6 HOH A 136 936 96 HOH HOH . I 6 HOH A 137 937 201 HOH HOH . I 6 HOH A 138 938 119 HOH HOH . I 6 HOH A 139 939 189 HOH HOH . I 6 HOH A 140 940 126 HOH HOH . I 6 HOH A 141 941 181 HOH HOH . I 6 HOH A 142 942 169 HOH HOH . I 6 HOH A 143 943 125 HOH HOH . I 6 HOH A 144 944 203 HOH HOH . I 6 HOH A 145 945 98 HOH HOH . I 6 HOH A 146 946 115 HOH HOH . I 6 HOH A 147 947 89 HOH HOH . I 6 HOH A 148 948 157 HOH HOH . I 6 HOH A 149 949 88 HOH HOH . I 6 HOH A 150 950 190 HOH HOH . I 6 HOH A 151 951 130 HOH HOH . I 6 HOH A 152 952 149 HOH HOH . I 6 HOH A 153 953 107 HOH HOH . I 6 HOH A 154 954 188 HOH HOH . I 6 HOH A 155 955 134 HOH HOH . I 6 HOH A 156 956 137 HOH HOH . I 6 HOH A 157 957 148 HOH HOH . I 6 HOH A 158 958 173 HOH HOH . I 6 HOH A 159 959 156 HOH HOH . I 6 HOH A 160 960 87 HOH HOH . I 6 HOH A 161 961 202 HOH HOH . I 6 HOH A 162 962 144 HOH HOH . I 6 HOH A 163 963 158 HOH HOH . J 6 HOH B 1 501 198 HOH HOH . J 6 HOH B 2 502 8 HOH HOH . J 6 HOH B 3 503 109 HOH HOH . J 6 HOH B 4 504 74 HOH HOH . J 6 HOH B 5 505 110 HOH HOH . J 6 HOH B 6 506 180 HOH HOH . J 6 HOH B 7 507 71 HOH HOH . J 6 HOH B 8 508 35 HOH HOH . J 6 HOH B 9 509 111 HOH HOH . J 6 HOH B 10 510 58 HOH HOH . J 6 HOH B 11 511 168 HOH HOH . J 6 HOH B 12 512 77 HOH HOH . J 6 HOH B 13 513 163 HOH HOH . J 6 HOH B 14 514 24 HOH HOH . J 6 HOH B 15 515 60 HOH HOH . J 6 HOH B 16 516 57 HOH HOH . J 6 HOH B 17 517 21 HOH HOH . J 6 HOH B 18 518 76 HOH HOH . J 6 HOH B 19 519 164 HOH HOH . J 6 HOH B 20 520 193 HOH HOH . J 6 HOH B 21 521 46 HOH HOH . J 6 HOH B 22 522 194 HOH HOH . J 6 HOH B 23 523 73 HOH HOH . J 6 HOH B 24 524 66 HOH HOH . J 6 HOH B 25 525 113 HOH HOH . J 6 HOH B 26 526 174 HOH HOH . J 6 HOH B 27 527 172 HOH HOH . J 6 HOH B 28 528 197 HOH HOH . J 6 HOH B 29 529 132 HOH HOH . J 6 HOH B 30 530 23 HOH HOH . J 6 HOH B 31 531 55 HOH HOH . J 6 HOH B 32 532 10 HOH HOH . J 6 HOH B 33 533 167 HOH HOH . J 6 HOH B 34 534 102 HOH HOH . J 6 HOH B 35 535 28 HOH HOH . J 6 HOH B 36 536 112 HOH HOH . J 6 HOH B 37 537 179 HOH HOH . J 6 HOH B 38 538 178 HOH HOH . J 6 HOH B 39 539 175 HOH HOH . J 6 HOH B 40 540 103 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N SFG . . . C 3 23.592 -36.68 -6.826 1 39.84 ? N SFG 701 A 1 HETATM 2 C CA SFG . . . C 3 24.204 -37.855 -6.207 1 39.54 ? CA SFG 701 A 1 HETATM 3 C C SFG . . . C 3 25.171 -38.524 -7.133 1 36.24 ? C SFG 701 A 1 HETATM 4 O O SFG . . . C 3 25.119 -38.337 -8.382 1 33.34 ? O SFG 701 A 1 HETATM 5 O OXT SFG . . . C 3 25.947 -39.317 -6.578 1 33.61 ? OXT SFG 701 A 1 HETATM 6 C CB SFG . . . C 3 23.149 -38.923 -5.855 1 39.51 ? CB SFG 701 A 1 HETATM 7 C CG SFG . . . C 3 22.125 -39.057 -6.979 1 42.8 ? CG SFG 701 A 1 HETATM 8 C CD SFG . . . C 3 20.923 -39.955 -6.657 1 43.46 ? CD SFG 701 A 1 HETATM 9 N NE SFG . . . C 3 20.605 -40.669 -7.882 1 41.98 ? NE SFG 701 A 1 HETATM 10 C C5' SFG . . . C 3 19.679 -39.151 -6.291 1 39.94 ? C5' SFG 701 A 1 HETATM 11 C C4' SFG . . . C 3 19.659 -38.508 -4.904 1 38.97 ? C4' SFG 701 A 1 HETATM 12 O O4' SFG . . . C 3 18.46 -37.729 -4.847 1 40.92 ? O4' SFG 701 A 1 HETATM 13 C C3' SFG . . . C 3 19.502 -39.514 -3.784 1 38.27 ? C3' SFG 701 A 1 HETATM 14 O O3' SFG . . . C 3 20.491 -39.258 -2.8 1 34.99 ? O3' SFG 701 A 1 HETATM 15 C C2' SFG . . . C 3 18.084 -39.3 -3.232 1 34.38 ? C2' SFG 701 A 1 HETATM 16 O O2' SFG . . . C 3 17.984 -39.522 -1.827 1 34.9 ? O2' SFG 701 A 1 HETATM 17 C C1' SFG . . . C 3 17.806 -37.874 -3.57 1 34.53 ? C1' SFG 701 A 1 HETATM 18 N N9 SFG . . . C 3 16.381 -37.533 -3.804 1 34.77 ? N9 SFG 701 A 1 HETATM 19 C C8 SFG . . . C 3 15.508 -38.235 -4.551 1 35.38 ? C8 SFG 701 A 1 HETATM 20 N N7 SFG . . . C 3 14.291 -37.625 -4.596 1 36.86 ? N7 SFG 701 A 1 HETATM 21 C C5 SFG . . . C 3 14.374 -36.501 -3.864 1 34.92 ? C5 SFG 701 A 1 HETATM 22 C C6 SFG . . . C 3 13.466 -35.4 -3.514 1 34.55 ? C6 SFG 701 A 1 HETATM 23 N N6 SFG . . . C 3 12.176 -35.371 -3.943 1 42.39 ? N6 SFG 701 A 1 HETATM 24 N N1 SFG . . . C 3 13.958 -34.423 -2.725 1 37.1 ? N1 SFG 701 A 1 HETATM 25 C C2 SFG . . . C 3 15.254 -34.413 -2.296 1 34.45 ? C2 SFG 701 A 1 HETATM 26 N N3 SFG . . . C 3 16.119 -35.394 -2.585 1 32.75 ? N3 SFG 701 A 1 HETATM 27 C C4 SFG . . . C 3 15.761 -36.438 -3.359 1 32.47 ? C4 SFG 701 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #