data_4MS5 # _model_server_result.job_id OjFFoe76LwKJeuKuHk0pIQ _model_server_result.datetime_utc '2025-03-03 00:43:53' _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 4ms5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":102}' # _entry.id 4MS5 # _exptl.entry_id 4MS5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 783.713 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "(11,12-difluorodipyrido[3,2-a:2',3'-c]phenazine-kappa~2~N~4~,N~5~)[bis(pyrazino[2,3-f]quinoxaline-kappa~2~N~1~,N~10~)]ruthenium(2+)" _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 4MS5 _cell.length_a 47.61 _cell.length_b 47.61 _cell.length_c 34.6 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4MS5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 17.3 # _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 A O6 DG 4 A DG 4 1_555 B BA BA . A BA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.057 ? hydrog 'DC-DG PAIR' hydrog1 A N4 DC 1 A DC 1 1_555 A O6 DG 10 A DG 10 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N3 DC 2 A DC 2 1_555 A N1 DG 9 A DG 9 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N4 DC 2 A DC 2 1_555 A O6 DG 9 A DG 9 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A O2 DC 2 A DC 2 1_555 A N2 DG 9 A DG 9 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N1 DG 3 A DG 3 1_555 A N3 DC 8 A DC 8 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N2 DG 3 A DG 3 1_555 A O2 DC 8 A DC 8 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A O6 DG 3 A DG 3 1_555 A N4 DC 8 A DC 8 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N1 DG 4 A DG 4 1_555 A N3 DC 7 A DC 7 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N2 DG 4 A DG 4 1_555 A O2 DC 7 A DC 7 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O6 DG 4 A DG 4 1_555 A N4 DC 7 A DC 7 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N1 DA 5 A DA 5 1_555 A N3 DT 6 A DT 6 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N6 DA 5 A DA 5 1_555 A O4 DT 6 A DT 6 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N3 DT 6 A DT 6 1_555 A N1 DA 5 A DA 5 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O4 DT 6 A DT 6 1_555 A N6 DA 5 A DA 5 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N3 DC 7 A DC 7 1_555 A N1 DG 4 A DG 4 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N4 DC 7 A DC 7 1_555 A O6 DG 4 A DG 4 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A O2 DC 7 A DC 7 1_555 A N2 DG 4 A DG 4 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N3 DC 8 A DC 8 1_555 A N1 DG 3 A DG 3 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N4 DC 8 A DC 8 1_555 A O6 DG 3 A DG 3 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O2 DC 8 A DC 8 1_555 A N2 DG 3 A DG 3 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N1 DG 9 A DG 9 1_555 A N3 DC 2 A DC 2 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N2 DG 9 A DG 9 1_555 A O2 DC 2 A DC 2 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O6 DG 9 A DG 9 1_555 A N4 DC 2 A DC 2 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog24 A O6 DG 10 A DG 10 1_555 A N4 DC 1 A DC 1 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C38 H20 F2 N12 Ru 2' _chem_comp.formula_weight 783.713 _chem_comp.id RKF _chem_comp.mon_nstd_flag . _chem_comp.name "(11,12-difluorodipyrido[3,2-a:2',3'-c]phenazine-kappa~2~N~4~,N~5~)[bis(pyrazino[2,3-f]quinoxaline-kappa~2~N~1~,N~10~)]ruthenium(2+)" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 F2 C17 RKF sing 152 n n F1 C18 RKF sing 153 n n C17 C18 RKF doub 154 n y C17 C16 RKF sing 155 n y C18 C14 RKF sing 156 n y C16 C15 RKF doub 157 n y C14 C13 RKF doub 158 n y C15 C13 RKF sing 159 n y C15 N3 RKF sing 160 n y C13 N4 RKF sing 161 n y N10 C31 RKF doub 162 n y N10 C32 RKF sing 163 n y N3 C6 RKF doub 164 n y C31 C30 RKF sing 165 n y N4 C7 RKF doub 166 n y C33 C32 RKF doub 167 n y C33 C34 RKF sing 168 n y C6 C7 RKF sing 169 n y C6 C5 RKF sing 170 n y C32 C29 RKF sing 171 n y C7 C8 RKF sing 172 n y C30 N9 RKF doub 173 n y C4 C5 RKF doub 174 n y C4 C3 RKF sing 175 n y C5 C1 RKF sing 176 n y C34 C35 RKF doub 177 n y C3 C2 RKF doub 178 n y C8 C9 RKF doub 179 n y C8 C10 RKF sing 180 n y C29 N9 RKF sing 181 n y C29 C36 RKF doub 182 n y N9 RU RKF sing 183 n n C9 C11 RKF sing 184 n y C1 C10 RKF sing 185 n y C1 N2 RKF doub 186 n y C10 N1 RKF doub 187 n y C2 N2 RKF sing 188 n y N2 RU RKF sing 189 n n C35 C36 RKF sing 190 n y C35 N11 RKF sing 191 n y C36 N12 RKF sing 192 n y C11 C12 RKF doub 193 n y N1 C12 RKF sing 194 n y N1 RU RKF sing 195 n n RU N12 RKF sing 196 n n RU N8 RKF sing 197 n n RU N5 RKF sing 198 n n N11 C37 RKF doub 199 n y N12 C38 RKF doub 200 n y C28 N8 RKF doub 201 n y C28 C27 RKF sing 202 n y N8 C26 RKF sing 203 n y C37 C38 RKF sing 204 n y C27 N7 RKF doub 205 n y N5 C20 RKF doub 206 n y N5 C19 RKF sing 207 n y C20 C21 RKF sing 208 n y C26 C19 RKF doub 209 n y C26 C25 RKF sing 210 n y C19 C22 RKF sing 211 n y N7 C25 RKF sing 212 n y C25 C24 RKF doub 213 n y C21 N6 RKF doub 214 n y C22 N6 RKF sing 215 n y C22 C23 RKF doub 216 n y C24 C23 RKF sing 217 n y C14 H1 RKF sing 218 n n C9 H2 RKF sing 219 n n C11 H3 RKF sing 220 n n C12 H4 RKF sing 221 n n C16 H5 RKF sing 222 n n C4 H6 RKF sing 223 n n C3 H7 RKF sing 224 n n C2 H8 RKF sing 225 n n C38 H9 RKF sing 226 n n C20 H10 RKF sing 227 n n C21 H11 RKF sing 228 n n C23 H12 RKF sing 229 n n C24 H13 RKF sing 230 n n C27 H14 RKF sing 231 n n C28 H15 RKF sing 232 n n C30 H16 RKF sing 233 n n C31 H17 RKF sing 234 n n C33 H18 RKF sing 235 n n C34 H19 RKF sing 236 n n C37 H20 RKF sing 237 n n # _atom_sites.entry_id 4MS5 _atom_sites.fract_transf_matrix[1][1] 0.021004 _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] 0.021004 _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] 0.028902 _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 BA A 1 101 102 BA BA . C 3 RKF A 1 102 11 RKF RKF . D 4 HOH A 1 201 1 HOH HOH . D 4 HOH A 2 202 3 HOH HOH . D 4 HOH A 3 203 4 HOH HOH . D 4 HOH A 4 204 5 HOH HOH . D 4 HOH A 5 205 6 HOH HOH . D 4 HOH A 6 206 7 HOH HOH . D 4 HOH A 7 207 11 HOH HOH . D 4 HOH A 8 208 13 HOH HOH . D 4 HOH A 9 209 14 HOH HOH . D 4 HOH A 10 210 15 HOH HOH . D 4 HOH A 11 211 16 HOH HOH . D 4 HOH A 12 212 17 HOH HOH . D 4 HOH A 13 213 19 HOH HOH . D 4 HOH A 14 214 20 HOH HOH . D 4 HOH A 15 215 21 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 F F2 RKF . . . C 3 7.005 -19.883 -7.081 1 41.18 ? F2 RKF 102 A 1 HETATM 2 C C17 RKF . . . C 3 6.31 -19.101 -6.248 1 37.63 ? C17 RKF 102 A 1 HETATM 3 C C18 RKF . . . C 3 6.883 -17.9 -5.983 1 36.83 ? C18 RKF 102 A 1 HETATM 4 F F1 RKF . . . C 3 8.072 -17.679 -6.566 1 38.83 ? F1 RKF 102 A 1 HETATM 5 C C14 RKF . . . C 3 6.24 -16.992 -5.146 1 34.47 ? C14 RKF 102 A 1 HETATM 6 C C13 RKF . . . C 3 5.004 -17.33 -4.575 1 31.63 ? C13 RKF 102 A 1 HETATM 7 N N4 RKF . . . C 3 4.396 -16.459 -3.742 1 28.9 ? N4 RKF 102 A 1 HETATM 8 C C7 RKF . . . C 3 3.195 -16.749 -3.196 1 29.12 ? C7 RKF 102 A 1 HETATM 9 C C8 RKF . . . C 3 2.578 -15.808 -2.365 1 28.02 ? C8 RKF 102 A 1 HETATM 10 C C9 RKF . . . C 3 3.131 -14.557 -2.099 1 27.98 ? C9 RKF 102 A 1 HETATM 11 C C11 RKF . . . C 3 2.429 -13.69 -1.275 1 27.13 ? C11 RKF 102 A 1 HETATM 12 C C12 RKF . . . C 3 1.189 -14.067 -0.733 1 30.63 ? C12 RKF 102 A 1 HETATM 13 C C10 RKF . . . C 3 1.343 -16.099 -1.792 1 28.92 ? C10 RKF 102 A 1 HETATM 14 N N1 RKF . . . C 3 0.675 -15.282 -0.947 1 27.44 ? N1 RKF 102 A 1 HETATM 15 C C16 RKF . . . C 3 5.076 -19.457 -5.689 1 36.21 ? C16 RKF 102 A 1 HETATM 16 C C15 RKF . . . C 3 4.412 -18.559 -4.842 1 31.88 ? C15 RKF 102 A 1 HETATM 17 N N3 RKF . . . C 3 3.218 -18.88 -4.275 1 30.25 ? N3 RKF 102 A 1 HETATM 18 C C6 RKF . . . C 3 2.589 -17.984 -3.463 1 29.3 ? C6 RKF 102 A 1 HETATM 19 C C5 RKF . . . C 3 1.357 -18.27 -2.879 1 28 ? C5 RKF 102 A 1 HETATM 20 C C1 RKF . . . C 3 0.765 -17.314 -2.052 1 29.25 ? C1 RKF 102 A 1 HETATM 21 C C4 RKF . . . C 3 0.69 -19.47 -3.079 1 26.74 ? C4 RKF 102 A 1 HETATM 22 C C3 RKF . . . C 3 -0.53 -19.667 -2.458 1 26.35 ? C3 RKF 102 A 1 HETATM 23 C C2 RKF . . . C 3 -1.061 -18.656 -1.663 1 31.02 ? C2 RKF 102 A 1 HETATM 24 N N2 RKF . . . C 3 -0.421 -17.466 -1.479 1 28.64 ? N2 RKF 102 A 1 HETATM 25 RU RU RKF . . . C 3 -0.952 -15.957 -0.598 1 31.76 ? RU RKF 102 A 1 HETATM 26 N N12 RKF . . . C 3 -2.579 -16.632 -0.31 1 26.65 ? N12 RKF 102 A 1 HETATM 27 C C36 RKF . . . C 3 -3.372 -16.308 -1.335 1 28.21 ? C36 RKF 102 A 1 HETATM 28 C C38 RKF . . . C 3 -3.116 -17.398 0.625 1 31.91 ? C38 RKF 102 A 1 HETATM 29 N N5 RKF . . . C 3 -0.36 -16.612 1 1 29.94 ? N5 RKF 102 A 1 HETATM 30 C C20 RKF . . . C 3 0.23 -17.763 1.342 1 36.31 ? C20 RKF 102 A 1 HETATM 31 C C21 RKF . . . C 3 0.611 -18.01 2.681 1 33.02 ? C21 RKF 102 A 1 HETATM 32 N N6 RKF . . . C 3 0.402 -17.128 3.671 1 30.99 ? N6 RKF 102 A 1 HETATM 33 C C19 RKF . . . C 3 -0.573 -15.763 2.006 1 31.27 ? C19 RKF 102 A 1 HETATM 34 C C22 RKF . . . C 3 -0.218 -15.981 3.342 1 31.16 ? C22 RKF 102 A 1 HETATM 35 C C23 RKF . . . C 3 -0.504 -15.004 4.289 1 29.62 ? C23 RKF 102 A 1 HETATM 36 C C24 RKF . . . C 3 -1.114 -13.817 3.896 1 27.82 ? C24 RKF 102 A 1 HETATM 37 C C25 RKF . . . C 3 -1.468 -13.63 2.574 1 28.81 ? C25 RKF 102 A 1 HETATM 38 N N7 RKF . . . C 3 -2.058 -12.509 2.146 1 29.76 ? N7 RKF 102 A 1 HETATM 39 C C27 RKF . . . C 3 -2.331 -12.331 0.858 1 25.74 ? C27 RKF 102 A 1 HETATM 40 C C28 RKF . . . C 3 -2.033 -13.329 -0.059 1 30.62 ? C28 RKF 102 A 1 HETATM 41 C C26 RKF . . . C 3 -1.181 -14.593 1.623 1 31.49 ? C26 RKF 102 A 1 HETATM 42 N N8 RKF . . . C 3 -1.455 -14.472 0.309 1 27.49 ? N8 RKF 102 A 1 HETATM 43 N N9 RKF . . . C 3 -1.564 -15.292 -2.158 1 26.55 ? N9 RKF 102 A 1 HETATM 44 C C29 RKF . . . C 3 -2.838 -15.546 -2.327 1 27.27 ? C29 RKF 102 A 1 HETATM 45 C C30 RKF . . . C 3 -1.006 -14.546 -3.106 1 29.83 ? C30 RKF 102 A 1 HETATM 46 C C31 RKF . . . C 3 -1.747 -14.112 -4.214 1 27.71 ? C31 RKF 102 A 1 HETATM 47 N N10 RKF . . . C 3 -3.041 -14.411 -4.363 1 28.08 ? N10 RKF 102 A 1 HETATM 48 C C32 RKF . . . C 3 -3.579 -15.136 -3.41 1 26.04 ? C32 RKF 102 A 1 HETATM 49 C C33 RKF . . . C 3 -4.876 -15.474 -3.518 1 26.41 ? C33 RKF 102 A 1 HETATM 50 C C34 RKF . . . C 3 -5.437 -16.237 -2.519 1 26.64 ? C34 RKF 102 A 1 HETATM 51 C C35 RKF . . . C 3 -4.698 -16.66 -1.439 1 26.86 ? C35 RKF 102 A 1 HETATM 52 N N11 RKF . . . C 3 -5.24 -17.419 -0.492 1 26.53 ? N11 RKF 102 A 1 HETATM 53 C C37 RKF . . . C 3 -4.466 -17.783 0.531 1 28.03 ? C37 RKF 102 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 53 #