data_5EMM # _model_server_result.job_id 1kAT_L09ELsE9UBE1u9Tsw _model_server_result.datetime_utc '2024-12-27 01:30:36' _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 5emm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":701}' # _entry.id 5EMM # _exptl.entry_id 5EMM _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 5EMM _cell.length_a 103.53 _cell.length_b 138.18 _cell.length_c 179.21 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EMM _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 -138.18 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 -138.18 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 2.05 _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 367 n n N HN1 SFG sing 368 n n N HN2 SFG sing 369 n n CA C SFG sing 370 n n CA CB SFG sing 371 n n CA HA SFG sing 372 n n C O SFG doub 373 n n C OXT SFG sing 374 n n OXT HXT SFG sing 375 n n CB CG SFG sing 376 n n CB HB1 SFG sing 377 n n CB HB2 SFG sing 378 n n CG CD SFG sing 379 n n CG HG1 SFG sing 380 n n CG HG2 SFG sing 381 n n CD NE SFG sing 382 n n CD C5' SFG sing 383 n n CD HD SFG sing 384 n n NE HNE1 SFG sing 385 n n NE HNE2 SFG sing 386 n n C5' C4' SFG sing 387 n n C5' "H5'1" SFG sing 388 n n C5' "H5'2" SFG sing 389 n n C4' O4' SFG sing 390 n n C4' C3' SFG sing 391 n n C4' H4' SFG sing 392 n n O4' C1' SFG sing 393 n n C3' O3' SFG sing 394 n n C3' C2' SFG sing 395 n n C3' H3' SFG sing 396 n n O3' HO3' SFG sing 397 n n C2' O2' SFG sing 398 n n C2' C1' SFG sing 399 n n C2' H2' SFG sing 400 n n O2' HO2' SFG sing 401 n n C1' N9 SFG sing 402 n n C1' H1' SFG sing 403 n n N9 C8 SFG sing 404 n y N9 C4 SFG sing 405 n y C8 N7 SFG doub 406 n y C8 H8 SFG sing 407 n n N7 C5 SFG sing 408 n y C5 C6 SFG sing 409 n y C5 C4 SFG doub 410 n y C6 N6 SFG sing 411 n n C6 N1 SFG doub 412 n y N6 HN61 SFG sing 413 n n N6 HN62 SFG sing 414 n n N1 C2 SFG sing 415 n y C2 N3 SFG doub 416 n y C2 H2 SFG sing 417 n n N3 C4 SFG sing 418 n y # _atom_sites.entry_id 5EMM _atom_sites.fract_transf_matrix[1][1] 0.009659 _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] 0.007237 _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] 0.00558 _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 5QL A 1 702 1 5QL 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 59 HOH HOH . G 6 HOH A 2 802 56 HOH HOH . G 6 HOH A 3 803 65 HOH HOH . G 6 HOH A 4 804 25 HOH HOH . G 6 HOH A 5 805 2 HOH HOH . G 6 HOH A 6 806 61 HOH HOH . G 6 HOH A 7 807 48 HOH HOH . G 6 HOH A 8 808 36 HOH HOH . G 6 HOH A 9 809 46 HOH HOH . G 6 HOH A 10 810 47 HOH HOH . G 6 HOH A 11 811 50 HOH HOH . G 6 HOH A 12 812 44 HOH HOH . G 6 HOH A 13 813 62 HOH HOH . G 6 HOH A 14 814 4 HOH HOH . G 6 HOH A 15 815 42 HOH HOH . G 6 HOH A 16 816 28 HOH HOH . G 6 HOH A 17 817 39 HOH HOH . G 6 HOH A 18 818 11 HOH HOH . G 6 HOH A 19 819 8 HOH HOH . G 6 HOH A 20 820 23 HOH HOH . G 6 HOH A 21 821 5 HOH HOH . G 6 HOH A 22 822 29 HOH HOH . G 6 HOH A 23 823 19 HOH HOH . G 6 HOH A 24 824 26 HOH HOH . G 6 HOH A 25 825 3 HOH HOH . G 6 HOH A 26 826 51 HOH HOH . G 6 HOH A 27 827 12 HOH HOH . G 6 HOH A 28 828 9 HOH HOH . G 6 HOH A 29 829 7 HOH HOH . G 6 HOH A 30 830 52 HOH HOH . G 6 HOH A 31 831 32 HOH HOH . G 6 HOH A 32 832 30 HOH HOH . G 6 HOH A 33 833 17 HOH HOH . G 6 HOH A 34 834 1 HOH HOH . G 6 HOH A 35 835 24 HOH HOH . G 6 HOH A 36 836 16 HOH HOH . G 6 HOH A 37 837 13 HOH HOH . G 6 HOH A 38 838 14 HOH HOH . G 6 HOH A 39 839 31 HOH HOH . G 6 HOH A 40 840 34 HOH HOH . G 6 HOH A 41 841 21 HOH HOH . G 6 HOH A 42 842 15 HOH HOH . G 6 HOH A 43 843 22 HOH HOH . G 6 HOH A 44 844 68 HOH HOH . G 6 HOH A 45 845 41 HOH HOH . G 6 HOH A 46 846 49 HOH HOH . G 6 HOH A 47 847 58 HOH HOH . G 6 HOH A 48 848 27 HOH HOH . G 6 HOH A 49 849 37 HOH HOH . G 6 HOH A 50 850 57 HOH HOH . G 6 HOH A 51 851 64 HOH HOH . G 6 HOH A 52 852 63 HOH HOH . G 6 HOH A 53 853 53 HOH HOH . G 6 HOH A 54 854 54 HOH HOH . G 6 HOH A 55 855 45 HOH HOH . H 6 HOH B 1 401 67 HOH HOH . H 6 HOH B 2 402 18 HOH HOH . H 6 HOH B 3 403 6 HOH HOH . H 6 HOH B 4 404 20 HOH HOH . H 6 HOH B 5 405 43 HOH HOH . H 6 HOH B 6 406 60 HOH HOH . H 6 HOH B 7 407 35 HOH HOH . H 6 HOH B 8 408 38 HOH HOH . H 6 HOH B 9 409 66 HOH HOH . H 6 HOH B 10 410 33 HOH HOH . H 6 HOH B 11 411 40 HOH HOH . H 6 HOH B 12 412 10 HOH HOH . H 6 HOH B 13 413 55 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 24.052 -36.359 -6.693 1 49.6 ? N SFG 701 A 1 HETATM 2 C CA SFG . . . C 3 24.424 -37.65 -6.129 1 47.85 ? CA SFG 701 A 1 HETATM 3 C C SFG . . . C 3 25.339 -38.334 -7.084 1 49.46 ? C SFG 701 A 1 HETATM 4 O O SFG . . . C 3 25.163 -38.143 -8.318 1 44.2 ? O SFG 701 A 1 HETATM 5 O OXT SFG . . . C 3 26.235 -39.066 -6.589 1 53.36 ? OXT SFG 701 A 1 HETATM 6 C CB SFG . . . C 3 23.227 -38.572 -5.891 1 46.89 ? CB SFG 701 A 1 HETATM 7 C CG SFG . . . C 3 22.144 -38.452 -6.955 1 45.47 ? CG SFG 701 A 1 HETATM 8 C CD SFG . . . C 3 21.105 -39.556 -6.77 1 44.36 ? CD SFG 701 A 1 HETATM 9 N NE SFG . . . C 3 20.992 -40.238 -8.036 1 47.23 ? NE SFG 701 A 1 HETATM 10 C C5' SFG . . . C 3 19.738 -38.983 -6.396 1 41.98 ? C5' SFG 701 A 1 HETATM 11 C C4' SFG . . . C 3 19.723 -38.288 -5.025 1 41.62 ? C4' SFG 701 A 1 HETATM 12 O O4' SFG . . . C 3 18.597 -37.413 -4.954 1 41.55 ? O4' SFG 701 A 1 HETATM 13 C C3' SFG . . . C 3 19.578 -39.212 -3.831 1 43.65 ? C3' SFG 701 A 1 HETATM 14 O O3' SFG . . . C 3 20.551 -38.847 -2.847 1 44.07 ? O3' SFG 701 A 1 HETATM 15 C C2' SFG . . . C 3 18.171 -38.956 -3.315 1 42.49 ? C2' SFG 701 A 1 HETATM 16 O O2' SFG . . . C 3 18.052 -39.181 -1.905 1 46.12 ? O2' SFG 701 A 1 HETATM 17 C C1' SFG . . . C 3 17.937 -37.515 -3.69 1 41.76 ? C1' SFG 701 A 1 HETATM 18 N N9 SFG . . . C 3 16.498 -37.196 -3.879 1 42.4 ? N9 SFG 701 A 1 HETATM 19 C C8 SFG . . . C 3 15.629 -37.941 -4.562 1 43.3 ? C8 SFG 701 A 1 HETATM 20 N N7 SFG . . . C 3 14.391 -37.383 -4.557 1 46.72 ? N7 SFG 701 A 1 HETATM 21 C C5 SFG . . . C 3 14.464 -36.24 -3.864 1 41.9 ? C5 SFG 701 A 1 HETATM 22 C C6 SFG . . . C 3 13.516 -35.173 -3.488 1 41.17 ? C6 SFG 701 A 1 HETATM 23 N N6 SFG . . . C 3 12.225 -35.234 -3.879 1 48 ? N6 SFG 701 A 1 HETATM 24 N N1 SFG . . . C 3 13.972 -34.147 -2.746 1 41.72 ? N1 SFG 701 A 1 HETATM 25 C C2 SFG . . . C 3 15.275 -34.082 -2.371 1 41.13 ? C2 SFG 701 A 1 HETATM 26 N N3 SFG . . . C 3 16.19 -35.025 -2.684 1 40.96 ? N3 SFG 701 A 1 HETATM 27 C C4 SFG . . . C 3 15.856 -36.112 -3.424 1 40.74 ? C4 SFG 701 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 27 #