data_5EMK # _model_server_result.job_id '_PbhKG2HSNTJlypnvL3p7Q' _model_server_result.datetime_utc '2024-12-26 18:41:54' _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 5emk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":701}' # _entry.id 5EMK # _exptl.entry_id 5EMK _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 5EMK _cell.length_a 102.79 _cell.length_b 137.75 _cell.length_c 178.52 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EMK _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 _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 -137.75 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 -137.75 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 2.065 _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 360 n n N HN1 SFG sing 361 n n N HN2 SFG sing 362 n n CA C SFG sing 363 n n CA CB SFG sing 364 n n CA HA SFG sing 365 n n C O SFG doub 366 n n C OXT SFG sing 367 n n OXT HXT SFG sing 368 n n CB CG SFG sing 369 n n CB HB1 SFG sing 370 n n CB HB2 SFG sing 371 n n CG CD SFG sing 372 n n CG HG1 SFG sing 373 n n CG HG2 SFG sing 374 n n CD NE SFG sing 375 n n CD C5' SFG sing 376 n n CD HD SFG sing 377 n n NE HNE1 SFG sing 378 n n NE HNE2 SFG sing 379 n n C5' C4' SFG sing 380 n n C5' "H5'1" SFG sing 381 n n C5' "H5'2" SFG sing 382 n n C4' O4' SFG sing 383 n n C4' C3' SFG sing 384 n n C4' H4' SFG sing 385 n n O4' C1' SFG sing 386 n n C3' O3' SFG sing 387 n n C3' C2' SFG sing 388 n n C3' H3' SFG sing 389 n n O3' HO3' SFG sing 390 n n C2' O2' SFG sing 391 n n C2' C1' SFG sing 392 n n C2' H2' SFG sing 393 n n O2' HO2' SFG sing 394 n n C1' N9 SFG sing 395 n n C1' H1' SFG sing 396 n n N9 C8 SFG sing 397 n y N9 C4 SFG sing 398 n y C8 N7 SFG doub 399 n y C8 H8 SFG sing 400 n n N7 C5 SFG sing 401 n y C5 C6 SFG sing 402 n y C5 C4 SFG doub 403 n y C6 N6 SFG sing 404 n n C6 N1 SFG doub 405 n y N6 HN61 SFG sing 406 n n N6 HN62 SFG sing 407 n n N1 C2 SFG sing 408 n y C2 N3 SFG doub 409 n y C2 H2 SFG sing 410 n n N3 C4 SFG sing 411 n y # _atom_sites.entry_id 5EMK _atom_sites.fract_transf_matrix[1][1] 0.009729 _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] 0.00726 _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] 0.005602 _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 5QH A 1 702 1 5QH EPZ . E 5 GOL A 1 703 1 GOL GOL . F 5 GOL A 1 704 2 GOL GOL . G 6 HOH A 1 801 51 HOH HOH . G 6 HOH A 2 802 40 HOH HOH . G 6 HOH A 3 803 30 HOH HOH . G 6 HOH A 4 804 14 HOH HOH . G 6 HOH A 5 805 26 HOH HOH . G 6 HOH A 6 806 1 HOH HOH . G 6 HOH A 7 807 52 HOH HOH . G 6 HOH A 8 808 71 HOH HOH . G 6 HOH A 9 809 12 HOH HOH . G 6 HOH A 10 810 29 HOH HOH . G 6 HOH A 11 811 7 HOH HOH . G 6 HOH A 12 812 61 HOH HOH . G 6 HOH A 13 813 3 HOH HOH . G 6 HOH A 14 814 65 HOH HOH . G 6 HOH A 15 815 70 HOH HOH . G 6 HOH A 16 816 15 HOH HOH . G 6 HOH A 17 817 44 HOH HOH . G 6 HOH A 18 818 24 HOH HOH . G 6 HOH A 19 819 69 HOH HOH . G 6 HOH A 20 820 63 HOH HOH . G 6 HOH A 21 821 36 HOH HOH . G 6 HOH A 22 822 46 HOH HOH . G 6 HOH A 23 823 4 HOH HOH . G 6 HOH A 24 824 32 HOH HOH . G 6 HOH A 25 825 21 HOH HOH . G 6 HOH A 26 826 13 HOH HOH . G 6 HOH A 27 827 6 HOH HOH . G 6 HOH A 28 828 55 HOH HOH . G 6 HOH A 29 829 76 HOH HOH . G 6 HOH A 30 830 35 HOH HOH . G 6 HOH A 31 831 38 HOH HOH . G 6 HOH A 32 832 19 HOH HOH . G 6 HOH A 33 833 53 HOH HOH . G 6 HOH A 34 834 16 HOH HOH . G 6 HOH A 35 835 64 HOH HOH . G 6 HOH A 36 836 22 HOH HOH . G 6 HOH A 37 837 28 HOH HOH . G 6 HOH A 38 838 25 HOH HOH . G 6 HOH A 39 839 50 HOH HOH . G 6 HOH A 40 840 39 HOH HOH . G 6 HOH A 41 841 48 HOH HOH . G 6 HOH A 42 842 8 HOH HOH . G 6 HOH A 43 843 43 HOH HOH . G 6 HOH A 44 844 23 HOH HOH . G 6 HOH A 45 845 68 HOH HOH . G 6 HOH A 46 846 5 HOH HOH . G 6 HOH A 47 847 10 HOH HOH . G 6 HOH A 48 848 58 HOH HOH . G 6 HOH A 49 849 77 HOH HOH . G 6 HOH A 50 850 56 HOH HOH . G 6 HOH A 51 851 18 HOH HOH . G 6 HOH A 52 852 37 HOH HOH . G 6 HOH A 53 853 67 HOH HOH . G 6 HOH A 54 854 54 HOH HOH . G 6 HOH A 55 855 42 HOH HOH . G 6 HOH A 56 856 9 HOH HOH . G 6 HOH A 57 857 57 HOH HOH . G 6 HOH A 58 858 45 HOH HOH . G 6 HOH A 59 859 31 HOH HOH . G 6 HOH A 60 860 66 HOH HOH . G 6 HOH A 61 861 47 HOH HOH . G 6 HOH A 62 862 72 HOH HOH . G 6 HOH A 63 863 49 HOH HOH . G 6 HOH A 64 864 62 HOH HOH . G 6 HOH A 65 865 78 HOH HOH . H 6 HOH B 1 401 73 HOH HOH . H 6 HOH B 2 402 41 HOH HOH . H 6 HOH B 3 403 60 HOH HOH . H 6 HOH B 4 404 11 HOH HOH . H 6 HOH B 5 405 59 HOH HOH . H 6 HOH B 6 406 34 HOH HOH . H 6 HOH B 7 407 17 HOH HOH . H 6 HOH B 8 408 2 HOH HOH . H 6 HOH B 9 409 27 HOH HOH . H 6 HOH B 10 410 20 HOH HOH . H 6 HOH B 11 411 33 HOH HOH . H 6 HOH B 12 412 75 HOH HOH . H 6 HOH B 13 413 74 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 24.041 -36.027 -6.698 1 41.55 ? N SFG 701 A 1 HETATM 2 C CA SFG . . . C 3 24.228 -37.348 -6.129 1 44.31 ? CA SFG 701 A 1 HETATM 3 C C SFG . . . C 3 25.161 -38.118 -7.003 1 44.18 ? C SFG 701 A 1 HETATM 4 O O SFG . . . C 3 25.065 -37.987 -8.249 1 38.83 ? O SFG 701 A 1 HETATM 5 O OXT SFG . . . C 3 26.003 -38.839 -6.415 1 51.09 ? OXT SFG 701 A 1 HETATM 6 C CB SFG . . . C 3 22.924 -38.136 -5.898 1 45.77 ? CB SFG 701 A 1 HETATM 7 C CG SFG . . . C 3 22.03 -38.395 -7.109 1 44.59 ? CG SFG 701 A 1 HETATM 8 C CD SFG . . . C 3 20.941 -39.399 -6.722 1 47.73 ? CD SFG 701 A 1 HETATM 9 N NE SFG . . . C 3 20.765 -40.32 -7.817 1 57.6 ? NE SFG 701 A 1 HETATM 10 C C5' SFG . . . C 3 19.595 -38.73 -6.434 1 40.04 ? C5' SFG 701 A 1 HETATM 11 C C4' SFG . . . C 3 19.565 -38.06 -5.052 1 41.06 ? C4' SFG 701 A 1 HETATM 12 O O4' SFG . . . C 3 18.415 -37.23 -4.945 1 43.76 ? O4' SFG 701 A 1 HETATM 13 C C3' SFG . . . C 3 19.484 -38.981 -3.84 1 44.06 ? C3' SFG 701 A 1 HETATM 14 O O3' SFG . . . C 3 20.502 -38.635 -2.887 1 40.3 ? O3' SFG 701 A 1 HETATM 15 C C2' SFG . . . C 3 18.096 -38.717 -3.257 1 44.39 ? C2' SFG 701 A 1 HETATM 16 O O2' SFG . . . C 3 18.004 -38.963 -1.845 1 47.58 ? O2' SFG 701 A 1 HETATM 17 C C1' SFG . . . C 3 17.865 -37.282 -3.633 1 42.86 ? C1' SFG 701 A 1 HETATM 18 N N9 SFG . . . C 3 16.454 -36.929 -3.812 1 43.53 ? N9 SFG 701 A 1 HETATM 19 C C8 SFG . . . C 3 15.551 -37.591 -4.556 1 45.89 ? C8 SFG 701 A 1 HETATM 20 N N7 SFG . . . C 3 14.319 -36.995 -4.524 1 43.48 ? N7 SFG 701 A 1 HETATM 21 C C5 SFG . . . C 3 14.448 -35.902 -3.76 1 42.93 ? C5 SFG 701 A 1 HETATM 22 C C6 SFG . . . C 3 13.543 -34.83 -3.329 1 42.99 ? C6 SFG 701 A 1 HETATM 23 N N6 SFG . . . C 3 12.258 -34.813 -3.744 1 51.42 ? N6 SFG 701 A 1 HETATM 24 N N1 SFG . . . C 3 14.044 -33.878 -2.522 1 46.39 ? N1 SFG 701 A 1 HETATM 25 C C2 SFG . . . C 3 15.359 -33.878 -2.156 1 47.31 ? C2 SFG 701 A 1 HETATM 26 N N3 SFG . . . C 3 16.254 -34.827 -2.51 1 42.99 ? N3 SFG 701 A 1 HETATM 27 C C4 SFG . . . C 3 15.859 -35.85 -3.304 1 43.43 ? C4 SFG 701 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 376 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #