data_4M3V # _model_server_result.job_id OoFqLsIvCNx1QNf0vkd3xA _model_server_result.datetime_utc '2025-04-05 18:18:49' _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 4m3v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":102}' # _entry.id 4M3V # _exptl.entry_id 4M3V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 775.785 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "(11,12-dimethyldipyrido[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 2 _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 4M3V _cell.length_a 52.22 _cell.length_b 52.22 _cell.length_c 34.52 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4M3V _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,E _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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N 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 D BA BA . A BA 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? metalc ? metalc2 A O4 DT 5 A DT 5 1_555 D BA BA . A BA 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? hydrog WATSON-CRICK hydrog1 A N3 DT 1 A DT 1 1_555 A N1 DA 10 A DA 10 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A O4 DT 1 A DT 1 1_555 A N6 DA 10 A DA 10 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N3 DC 2 A DC 2 1_555 A N1 DG 9 A DG 9 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N4 DC 2 A DC 2 1_555 A O6 DG 9 A DG 9 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O2 DC 2 A DC 2 1_555 A N2 DG 9 A DG 9 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 DG 3 A DG 3 1_555 A N3 DC 8 A DC 8 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N2 DG 3 A DG 3 1_555 A O2 DC 8 A DC 8 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O6 DG 3 A DG 3 1_555 A N4 DC 8 A DC 8 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 DG 4 A DG 4 1_555 A N3 DC 7 A DC 7 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N2 DG 4 A DG 4 1_555 A O2 DC 7 A DC 7 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O6 DG 4 A DG 4 1_555 A N4 DC 7 A DC 7 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N3 DT 5 A DT 5 1_555 A N1 DA 6 A DA 6 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O4 DT 5 A DT 5 1_555 A N6 DA 6 A DA 6 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N1 DA 6 A DA 6 1_555 A N3 DT 5 A DT 5 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N6 DA 6 A DA 6 1_555 A O4 DT 5 A DT 5 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 DC 7 A DC 7 1_555 A N1 DG 4 A DG 4 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N4 DC 7 A DC 7 1_555 A O6 DG 4 A DG 4 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O2 DC 7 A DC 7 1_555 A N2 DG 4 A DG 4 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N3 DC 8 A DC 8 1_555 A N1 DG 3 A DG 3 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N4 DC 8 A DC 8 1_555 A O6 DG 3 A DG 3 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O2 DC 8 A DC 8 1_555 A N2 DG 3 A DG 3 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N1 DG 9 A DG 9 1_555 A N3 DC 2 A DC 2 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N2 DG 9 A DG 9 1_555 A O2 DC 2 A DC 2 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O6 DG 9 A DG 9 1_555 A N4 DC 2 A DC 2 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N1 DA 10 A DA 10 1_555 A N3 DT 1 A DT 1 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N6 DA 10 A DA 10 1_555 A O4 DT 1 A DT 1 7_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C40 H26 N12 Ru 2' _chem_comp.formula_weight 775.785 _chem_comp.id RML _chem_comp.mon_nstd_flag . _chem_comp.name "(11,12-dimethyldipyrido[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 Lambda-[Ru(1,4,5,8-tetraazaphenanthrene)2(11,12-dimethyl-dipyridophenazine)]2+ # 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 C23 C24 RML doub 152 n y C23 C22 RML sing 153 n y C24 C25 RML sing 154 n y N6 C22 RML doub 155 n y N6 C21 RML sing 156 n y C22 C19 RML sing 157 n y C25 N7 RML doub 158 n y C25 C26 RML sing 159 n y N7 C27 RML sing 160 n y C21 C20 RML doub 161 n y C19 C26 RML sing 162 n y C19 N5 RML doub 163 n y C26 N8 RML doub 164 n y C27 C28 RML doub 165 n y C20 N5 RML sing 166 n y N5 RU RML sing 167 n n N8 C28 RML sing 168 n y N8 RU RML sing 169 n n C38 C37 RML doub 170 n y C38 N12 RML sing 171 n y C37 N11 RML sing 172 n y C12 N1 RML doub 173 n y C12 C11 RML sing 174 n y N12 RU RML sing 175 n n N12 C36 RML doub 176 n y RU N1 RML sing 177 n n RU N2 RML sing 178 n n RU N9 RML sing 179 n n N1 C10 RML sing 180 n y C11 C9 RML doub 181 n y N11 C35 RML doub 182 n y C36 C35 RML sing 183 n y C36 C29 RML sing 184 n y C9 C8 RML sing 185 n y C10 C8 RML doub 186 n y C10 C1 RML sing 187 n y C35 C34 RML sing 188 n y N2 C2 RML doub 189 n y N2 C1 RML sing 190 n y C2 C3 RML sing 191 n y C8 C7 RML sing 192 n y C1 C5 RML doub 193 n y N9 C29 RML doub 194 n y N9 C30 RML sing 195 n y C29 C32 RML sing 196 n y C34 C33 RML doub 197 n y C3 C4 RML doub 198 n y C7 N4 RML doub 199 n y C7 C6 RML sing 200 n y C30 C31 RML doub 201 n y C5 C4 RML sing 202 n y C5 C6 RML sing 203 n y N4 C13 RML sing 204 n y C6 N3 RML doub 205 n y C32 C33 RML sing 206 n y C32 N10 RML doub 207 n y C31 N10 RML sing 208 n y C13 C14 RML doub 209 n y C13 C15 RML sing 210 n y N3 C15 RML sing 211 n y C14 C18 RML sing 212 n y C15 C16 RML doub 213 n y C18 C52 RML sing 214 n n C18 C17 RML doub 215 n y C16 C17 RML sing 216 n y C17 C53 RML sing 217 n n C53 H1 RML sing 218 n n C53 H2 RML sing 219 n n C53 H3 RML sing 220 n n C52 H4 RML sing 221 n n C52 H5 RML sing 222 n n C52 H6 RML sing 223 n n C14 H7 RML sing 224 n n C16 H8 RML sing 225 n n C4 H9 RML sing 226 n n C3 H10 RML sing 227 n n C2 H11 RML sing 228 n n C12 H12 RML sing 229 n n C11 H13 RML sing 230 n n C9 H14 RML sing 231 n n C28 H15 RML sing 232 n n C27 H16 RML sing 233 n n C24 H17 RML sing 234 n n C23 H18 RML sing 235 n n C20 H19 RML sing 236 n n C21 H20 RML sing 237 n n C38 H21 RML sing 238 n n C37 H22 RML sing 239 n n C30 H23 RML sing 240 n n C31 H24 RML sing 241 n n C34 H25 RML sing 242 n n C33 H26 RML sing 243 n n # _atom_sites.entry_id 4M3V _atom_sites.fract_transf_matrix[1][1] 0.01915 _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] 0.01915 _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] 0.028969 _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 RML A 1 101 11 RML RML . C 2 RML A 1 102 12 RML RML . D 3 BA A 1 103 13 BA BA . E 4 HOH A 1 201 2 HOH HOH . E 4 HOH A 2 202 3 HOH HOH . E 4 HOH A 3 203 7 HOH HOH . E 4 HOH A 4 204 9 HOH HOH . E 4 HOH A 5 205 12 HOH HOH . E 4 HOH A 6 206 13 HOH HOH . E 4 HOH A 7 207 14 HOH HOH . E 4 HOH A 8 208 15 HOH HOH . E 4 HOH A 9 209 18 HOH HOH . E 4 HOH A 10 210 19 HOH HOH . E 4 HOH A 11 211 23 HOH HOH . E 4 HOH A 12 212 24 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 C53 RML . . . C 2 35.842 35.801 -1.073 0.5 40.05 ? C53 RML 102 A 1 HETATM 2 C C17 RML . . . C 2 36.686 37.022 -1.414 0.5 38.89 ? C17 RML 102 A 1 HETATM 3 C C18 RML . . . C 2 36.51 37.773 -2.532 0.5 36.82 ? C18 RML 102 A 1 HETATM 4 C C52 RML . . . C 2 35.456 37.487 -3.591 0.5 35.85 ? C52 RML 102 A 1 HETATM 5 C C14 RML . . . C 2 37.321 38.86 -2.716 0.5 36.58 ? C14 RML 102 A 1 HETATM 6 C C16 RML . . . C 2 37.688 37.392 -0.495 0.5 38.07 ? C16 RML 102 A 1 HETATM 7 C C15 RML . . . C 2 38.523 38.502 -0.65 0.5 37.57 ? C15 RML 102 A 1 HETATM 8 N N3 RML . . . C 2 39.457 38.805 0.26 0.5 34.6 ? N3 RML 102 A 1 HETATM 9 C C13 RML . . . C 2 38.3 39.223 -1.798 0.5 37.63 ? C13 RML 102 A 1 HETATM 10 N N4 RML . . . C 2 39.06 40.279 -2.009 0.5 37.72 ? N4 RML 102 A 1 HETATM 11 C C7 RML . . . C 2 40.024 40.593 -1.08 0.5 36.64 ? C7 RML 102 A 1 HETATM 12 C C6 RML . . . C 2 40.254 39.875 0.072 0.5 38.46 ? C6 RML 102 A 1 HETATM 13 C C5 RML . . . C 2 41.293 40.292 0.957 0.5 37.9 ? C5 RML 102 A 1 HETATM 14 C C4 RML . . . C 2 41.535 39.588 2.13 0.5 39.48 ? C4 RML 102 A 1 HETATM 15 C C3 RML . . . C 2 42.543 40.039 2.963 0.5 40.63 ? C3 RML 102 A 1 HETATM 16 C C2 RML . . . C 2 43.324 41.175 2.644 0.5 43.86 ? C2 RML 102 A 1 HETATM 17 C C8 RML . . . C 2 40.816 41.679 -1.331 0.5 40.78 ? C8 RML 102 A 1 HETATM 18 C C10 RML . . . C 2 41.867 42.122 -0.44 0.5 42.04 ? C10 RML 102 A 1 HETATM 19 C C1 RML . . . C 2 42.117 41.426 0.724 0.5 43.56 ? C1 RML 102 A 1 HETATM 20 N N2 RML . . . C 2 43.132 41.975 1.539 0.5 47.23 ? N2 RML 102 A 1 HETATM 21 N N1 RML . . . C 2 42.651 43.209 -0.596 0.5 41.84 ? N1 RML 102 A 1 HETATM 22 C C12 RML . . . C 2 42.26 43.76 -1.818 0.5 46.87 ? C12 RML 102 A 1 HETATM 23 C C11 RML . . . C 2 41.301 43.394 -2.71 0.5 43.87 ? C11 RML 102 A 1 HETATM 24 C C9 RML . . . C 2 40.513 42.311 -2.5 0.5 40.99 ? C9 RML 102 A 1 HETATM 25 RU RU RML . . . C 2 44.023 43.386 0.702 0.5 48.79 ? RU RML 102 A 1 HETATM 26 N N8 RML . . . C 2 45.042 44.874 -0.256 1 75.47 ? N8 RML 102 A 1 HETATM 27 C C28 RML . . . C 2 45.21 46.269 -0.581 1 220.45 ? C28 RML 102 A 1 HETATM 28 C C27 RML . . . C 2 46.226 46.96 -1.343 1 99.29 ? C27 RML 102 A 1 HETATM 29 N N7 RML . . . C 2 47.223 46.347 -1.967 1 95.08 ? N7 RML 102 A 1 HETATM 30 C C26 RML . . . C 2 46.172 44.349 -1.024 1 100.5 ? C26 RML 102 A 1 HETATM 31 C C25 RML . . . C 2 47.165 45.017 -1.781 0.5 92.76 ? C25 RML 102 A 1 HETATM 32 C C24 RML . . . C 2 48.171 44.356 -2.408 0.5 88.04 ? C24 RML 102 A 1 HETATM 33 C C23 RML . . . C 2 48.269 42.981 -2.318 0.5 87.81 ? C23 RML 102 A 1 HETATM 34 C C22 RML . . . C 2 47.345 42.228 -1.568 0.5 83.98 ? C22 RML 102 A 1 HETATM 35 N N6 RML . . . C 2 47.465 40.835 -1.523 0.5 80.04 ? N6 RML 102 A 1 HETATM 36 C C19 RML . . . C 2 46.291 42.908 -0.918 0.5 83.35 ? C19 RML 102 A 1 HETATM 37 N N5 RML . . . C 2 45.183 42.294 -0.257 0.5 65.97 ? N5 RML 102 A 1 HETATM 38 C C20 RML . . . C 2 45.478 40.939 -0.127 0.5 67.49 ? C20 RML 102 A 1 HETATM 39 C C21 RML . . . C 2 46.515 40.245 -0.781 0.5 70.24 ? C21 RML 102 A 1 HETATM 40 N N12 RML . . . C 2 45.463 43.509 2.052 1 67.28 ? N12 RML 102 A 1 HETATM 41 C C38 RML . . . C 2 46.761 42.98 2.163 1 65.13 ? C38 RML 102 A 1 HETATM 42 C C37 RML . . . C 2 47.644 43.228 3.214 1 62.67 ? C37 RML 102 A 1 HETATM 43 N N11 RML . . . C 2 47.289 43.987 4.238 1 67.88 ? N11 RML 102 A 1 HETATM 44 C C36 RML . . . C 2 45.145 44.286 3.145 1 64.09 ? C36 RML 102 A 1 HETATM 45 C C29 RML . . . C 2 43.802 44.844 3.043 1 62.58 ? C29 RML 102 A 1 HETATM 46 N N9 RML . . . C 2 42.913 44.5 1.865 1 62.48 ? N9 RML 102 A 1 HETATM 47 C C30 RML . . . C 2 41.709 45.234 2.126 1 62.18 ? C30 RML 102 A 1 HETATM 48 C C31 RML . . . C 2 41.487 46.005 3.31 1 63.11 ? C31 RML 102 A 1 HETATM 49 C C35 RML . . . C 2 46.035 44.529 4.225 1 65.02 ? C35 RML 102 A 1 HETATM 50 C C34 RML . . . C 2 45.648 45.343 5.306 1 65.8 ? C34 RML 102 A 1 HETATM 51 C C33 RML . . . C 2 44.401 45.871 5.233 1 60.97 ? C33 RML 102 A 1 HETATM 52 C C32 RML . . . C 2 43.527 45.618 4.161 1 57.27 ? C32 RML 102 A 1 HETATM 53 N N10 RML . . . C 2 42.387 46.204 4.292 1 62.93 ? N10 RML 102 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 224 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 53 #