data_5X9P # _model_server_result.job_id VUIK5U7Le4X-DAtwKhrqZA _model_server_result.datetime_utc '2024-10-28 02:37:12' _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 5x9p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":801}' # _entry.id 5X9P # _exptl.entry_id 5X9P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 391.766 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-[[4-chloranyl-2-nitro-5-[(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)amino]phenyl]amino]propanoic acid' _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 120 _cell.entry_id 5X9P _cell.length_a 66.55 _cell.length_b 66.55 _cell.length_c 153.09 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5X9P _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 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 ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C 1 1 A,B,C 2 1,2 # 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' 10_554 -y,-x,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 0 0 -25.515 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C16 H14 Cl N5 O5' _chem_comp.formula_weight 391.766 _chem_comp.id 80L _chem_comp.mon_nstd_flag . _chem_comp.name '3-[[4-chloranyl-2-nitro-5-[(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)amino]phenyl]amino]propanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-(4-chloro-2-nitro-5-((2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)amino)phenyl)-beta-alanine # 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 O23 C13 80L doub 1 n n C13 N17 80L sing 2 n n C13 N18 80L sing 3 n n N17 C6 80L sing 4 n n N18 C7 80L sing 5 n n C6 C7 80L doub 6 n y C6 C1 80L sing 7 n y C7 C3 80L sing 8 n y C1 C2 80L doub 9 n y C3 C8 80L doub 10 n y C2 C8 80L sing 11 n y C8 N19 80L sing 12 n n N19 C10 80L sing 13 n n O24 C14 80L doub 14 n n C10 C4 80L doub 15 n y C10 C12 80L sing 16 n y CL1 C12 80L sing 17 n n C14 O26 80L sing 18 n n C14 C15 80L sing 19 n n C4 C9 80L sing 20 n y C12 C5 80L doub 21 n y C15 C16 80L sing 22 n n C9 N20 80L sing 23 n n C9 C11 80L doub 24 n y C16 N20 80L sing 25 n n C5 C11 80L sing 26 n y C11 N21 80L sing 27 n n N21 O25 80L sing 28 n n N21 O22 80L doub 29 n n C4 H1 80L sing 30 n n C5 H2 80L sing 31 n n C15 H3 80L sing 32 n n C15 H4 80L sing 33 n n C1 H5 80L sing 34 n n C2 H6 80L sing 35 n n C3 H7 80L sing 36 n n C16 H8 80L sing 37 n n C16 H9 80L sing 38 n n N17 H10 80L sing 39 n n N18 H11 80L sing 40 n n N19 H12 80L sing 41 n n N20 H13 80L sing 42 n n O26 H14 80L sing 43 n n # _atom_sites.entry_id 5X9P _atom_sites.fract_transf_matrix[1][1] 0.015026 _atom_sites.fract_transf_matrix[1][2] 0.008675 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017351 _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] 0.006532 _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 80L A 1 801 801 80L LIG . C 3 HOH A 1 901 28 HOH HOH . C 3 HOH A 2 902 24 HOH HOH . C 3 HOH A 3 903 27 HOH HOH . C 3 HOH A 4 904 53 HOH HOH . C 3 HOH A 5 905 38 HOH HOH . C 3 HOH A 6 906 12 HOH HOH . C 3 HOH A 7 907 11 HOH HOH . C 3 HOH A 8 908 37 HOH HOH . C 3 HOH A 9 909 56 HOH HOH . C 3 HOH A 10 910 7 HOH HOH . C 3 HOH A 11 911 15 HOH HOH . C 3 HOH A 12 912 49 HOH HOH . C 3 HOH A 13 913 20 HOH HOH . C 3 HOH A 14 914 36 HOH HOH . C 3 HOH A 15 915 31 HOH HOH . C 3 HOH A 16 916 6 HOH HOH . C 3 HOH A 17 917 1 HOH HOH . C 3 HOH A 18 918 29 HOH HOH . C 3 HOH A 19 919 9 HOH HOH . C 3 HOH A 20 920 23 HOH HOH . C 3 HOH A 21 921 21 HOH HOH . C 3 HOH A 22 922 40 HOH HOH . C 3 HOH A 23 923 30 HOH HOH . C 3 HOH A 24 924 25 HOH HOH . C 3 HOH A 25 925 16 HOH HOH . C 3 HOH A 26 926 42 HOH HOH . C 3 HOH A 27 927 3 HOH HOH . C 3 HOH A 28 928 44 HOH HOH . C 3 HOH A 29 929 34 HOH HOH . C 3 HOH A 30 930 13 HOH HOH . C 3 HOH A 31 931 8 HOH HOH . C 3 HOH A 32 932 5 HOH HOH . C 3 HOH A 33 933 41 HOH HOH . C 3 HOH A 34 934 54 HOH HOH . C 3 HOH A 35 935 18 HOH HOH . C 3 HOH A 36 936 2 HOH HOH . C 3 HOH A 37 937 26 HOH HOH . C 3 HOH A 38 938 19 HOH HOH . C 3 HOH A 39 939 4 HOH HOH . C 3 HOH A 40 940 22 HOH HOH . C 3 HOH A 41 941 46 HOH HOH . C 3 HOH A 42 942 17 HOH HOH . C 3 HOH A 43 943 45 HOH HOH . C 3 HOH A 44 944 47 HOH HOH . C 3 HOH A 45 945 55 HOH HOH . C 3 HOH A 46 946 33 HOH HOH . C 3 HOH A 47 947 10 HOH HOH . C 3 HOH A 48 948 35 HOH HOH . C 3 HOH A 49 949 14 HOH HOH . C 3 HOH A 50 950 32 HOH HOH . C 3 HOH A 51 951 52 HOH HOH . C 3 HOH A 52 952 39 HOH HOH . C 3 HOH A 53 953 48 HOH HOH . C 3 HOH A 54 954 51 HOH HOH . C 3 HOH A 55 955 43 HOH HOH . C 3 HOH A 56 956 50 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 C C4 80L . . . B 2 38.958 -7.3 -11.274 1 62.03 ? C4 80L 801 A 1 HETATM 2 C C5 80L . . . B 2 36.79 -8.238 -9.861 1 60.99 ? C5 80L 801 A 1 HETATM 3 C C6 80L . . . B 2 40.916 -7.391 -16.076 1 62.06 ? C6 80L 801 A 1 HETATM 4 C C7 80L . . . B 2 40.603 -8.697 -15.861 1 60.37 ? C7 80L 801 A 1 HETATM 5 C C8 80L . . . B 2 39.06 -8.08 -14.205 1 59.68 ? C8 80L 801 A 1 HETATM 6 C C10 80L . . . B 2 38.014 -8.102 -11.904 1 61.07 ? C10 80L 801 A 1 HETATM 7 C C13 80L . . . B 2 42.165 -8.658 -17.49 1 62.34 ? C13 80L 801 A 1 HETATM 8 C C15 80L . . . B 2 40.59 -4.394 -10.762 1 77.99 ? C15 80L 801 A 1 HETATM 9 C C1 80L . . . B 2 40.314 -6.38 -15.364 1 61.84 ? C1 80L 801 A 1 HETATM 10 C C2 80L . . . B 2 39.371 -6.744 -14.422 1 61.05 ? C2 80L 801 A 1 HETATM 11 C C3 80L . . . B 2 39.676 -9.074 -14.93 1 59.28 ? C3 80L 801 A 1 HETATM 12 C C9 80L . . . B 2 38.838 -6.943 -9.94 1 65.22 ? C9 80L 801 A 1 HETATM 13 C C11 80L . . . B 2 37.733 -7.431 -9.258 1 63 ? C11 80L 801 A 1 HETATM 14 C C12 80L . . . B 2 36.935 -8.57 -11.184 1 59.08 ? C12 80L 801 A 1 HETATM 15 C C14 80L . . . B 2 41.769 -4.122 -11.644 1 81.91 ? C14 80L 801 A 1 HETATM 16 C C16 80L . . . B 2 40.959 -5.585 -9.912 1 74.3 ? C16 80L 801 A 1 HETATM 17 N N17 80L . . . B 2 41.88 -7.366 -17.082 1 62.79 ? N17 80L 801 A 1 HETATM 18 N N18 80L . . . B 2 41.362 -9.471 -16.721 1 61.06 ? N18 80L 801 A 1 HETATM 19 N N19 80L . . . B 2 38.11 -8.456 -13.258 1 60.72 ? N19 80L 801 A 1 HETATM 20 N N20 80L . . . B 2 39.776 -6.117 -9.269 1 69.83 ? N20 80L 801 A 1 HETATM 21 N N21 80L . . . B 2 37.468 -7.107 -7.87 1 62.99 ? N21 80L 801 A 1 HETATM 22 O O22 80L . . . B 2 38.392 -6.753 -7.117 1 66.01 ? O22 80L 801 A 1 HETATM 23 O O23 80L . . . B 2 42.959 -9.023 -18.345 1 65.69 ? O23 80L 801 A 1 HETATM 24 O O24 80L . . . B 2 41.865 -4.458 -12.817 1 82.39 ? O24 80L 801 A 1 HETATM 25 O O25 80L . . . B 2 36.271 -7.13 -7.553 1 58.7 ? O25 80L 801 A 1 HETATM 26 O O26 80L . . . B 2 42.727 -3.457 -10.954 1 84.59 ? O26 80L 801 A 1 HETATM 27 CL CL1 80L . . . B 2 35.68 -9.563 -11.836 1 54.91 ? CL1 80L 801 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 27 #