data_8RKP # _model_server_result.job_id GaymcqIDJ-AYy_6PBITBzQ _model_server_result.datetime_utc '2025-01-25 13:29:19' _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 8rkp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":205}' # _entry.id 8RKP # _exptl.entry_id 8RKP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _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 8RKP _cell.length_a 83.671 _cell.length_b 83.671 _cell.length_c 88.247 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RKP _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62 2 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,F,G _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' 4_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 -41.8355 72.461212 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id F _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 covale ? covale1 A SG CYS 123 A CYS 124 1_555 F CAB HEC . A HEC 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.806 ? covale ? covale2 A SG CYS 126 A CYS 127 1_555 F CAC HEC . A HEC 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.767 ? metalc ? metalc1 B N NO . A NO 201 1_555 F FE HEC . A HEC 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc2 B O NO . A NO 201 1_555 F FE HEC . A HEC 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? # _chem_comp.formula 'C34 H34 Fe N4 O4' _chem_comp.formula_weight 618.503 _chem_comp.id HEC _chem_comp.mon_nstd_flag . _chem_comp.name 'HEME C' _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 FE NA HEC sing 149 n n FE NB HEC sing 150 n n FE NC HEC sing 151 n n FE ND HEC sing 152 n n CHA C1A HEC doub 153 n n CHA C4D HEC sing 154 n n CHA HHA HEC sing 155 n n CHB C4A HEC doub 156 n n CHB C1B HEC sing 157 n n CHB HHB HEC sing 158 n n CHC C4B HEC doub 159 n n CHC C1C HEC sing 160 n n CHC HHC HEC sing 161 n n CHD C4C HEC doub 162 n n CHD C1D HEC sing 163 n n CHD HHD HEC sing 164 n n NA C1A HEC sing 165 n y NA C4A HEC sing 166 n y C1A C2A HEC sing 167 n y C2A C3A HEC doub 168 n y C2A CAA HEC sing 169 n n C3A C4A HEC sing 170 n y C3A CMA HEC sing 171 n n CMA HMA1 HEC sing 172 n n CMA HMA2 HEC sing 173 n n CMA HMA3 HEC sing 174 n n CAA CBA HEC sing 175 n n CAA HAA1 HEC sing 176 n n CAA HAA2 HEC sing 177 n n CBA CGA HEC sing 178 n n CBA HBA1 HEC sing 179 n n CBA HBA2 HEC sing 180 n n CGA O1A HEC doub 181 n n CGA O2A HEC sing 182 n n O2A H2A HEC sing 183 n n NB C1B HEC sing 184 n y NB C4B HEC sing 185 n y C1B C2B HEC doub 186 n y C2B C3B HEC sing 187 n y C2B CMB HEC sing 188 n n C3B C4B HEC sing 189 n y C3B CAB HEC doub 190 e n CMB HMB1 HEC sing 191 n n CMB HMB2 HEC sing 192 n n CMB HMB3 HEC sing 193 n n CAB CBB HEC sing 194 n n CAB HAB HEC sing 195 n n CBB HBB1 HEC sing 196 n n CBB HBB2 HEC sing 197 n n CBB HBB3 HEC sing 198 n n NC C1C HEC sing 199 n y NC C4C HEC sing 200 n y C1C C2C HEC doub 201 n y C2C C3C HEC sing 202 n y C2C CMC HEC sing 203 n n C3C C4C HEC sing 204 n y C3C CAC HEC doub 205 e n CMC HMC1 HEC sing 206 n n CMC HMC2 HEC sing 207 n n CMC HMC3 HEC sing 208 n n CAC CBC HEC sing 209 n n CAC HAC HEC sing 210 n n CBC HBC1 HEC sing 211 n n CBC HBC2 HEC sing 212 n n CBC HBC3 HEC sing 213 n n ND C1D HEC sing 214 n y ND C4D HEC sing 215 n y C1D C2D HEC doub 216 n y C2D C3D HEC sing 217 n y C2D CMD HEC sing 218 n n C3D C4D HEC doub 219 n y C3D CAD HEC sing 220 n n CMD HMD1 HEC sing 221 n n CMD HMD2 HEC sing 222 n n CMD HMD3 HEC sing 223 n n CAD CBD HEC sing 224 n n CAD HAD1 HEC sing 225 n n CAD HAD2 HEC sing 226 n n CBD CGD HEC sing 227 n n CBD HBD1 HEC sing 228 n n CBD HBD2 HEC sing 229 n n CGD O1D HEC doub 230 n n CGD O2D HEC sing 231 n n O2D H2D HEC sing 232 n n # _atom_sites.entry_id 8RKP _atom_sites.fract_transf_matrix[1][1] 0.011952 _atom_sites.fract_transf_matrix[1][2] 0.0069 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0138 _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] 0.011332 _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 NO A 1 201 202 NO NO . C 3 ASC A 1 202 203 ASC ASC . D 3 ASC A 1 203 205 ASC ASC . E 3 ASC A 1 204 206 ASC ASC . F 4 HEC A 1 205 207 HEC HEC . G 5 HOH A 1 301 59 HOH HOH . G 5 HOH A 2 302 62 HOH HOH . G 5 HOH A 3 303 31 HOH HOH . G 5 HOH A 4 304 75 HOH HOH . G 5 HOH A 5 305 6 HOH HOH . G 5 HOH A 6 306 30 HOH HOH . G 5 HOH A 7 307 20 HOH HOH . G 5 HOH A 8 308 43 HOH HOH . G 5 HOH A 9 309 35 HOH HOH . G 5 HOH A 10 310 71 HOH HOH . G 5 HOH A 11 311 36 HOH HOH . G 5 HOH A 12 312 17 HOH HOH . G 5 HOH A 13 313 23 HOH HOH . G 5 HOH A 14 314 1 HOH HOH . G 5 HOH A 15 315 4 HOH HOH . G 5 HOH A 16 316 3 HOH HOH . G 5 HOH A 17 317 47 HOH HOH . G 5 HOH A 18 318 21 HOH HOH . G 5 HOH A 19 319 12 HOH HOH . G 5 HOH A 20 320 66 HOH HOH . G 5 HOH A 21 321 46 HOH HOH . G 5 HOH A 22 322 29 HOH HOH . G 5 HOH A 23 323 14 HOH HOH . G 5 HOH A 24 324 9 HOH HOH . G 5 HOH A 25 325 33 HOH HOH . G 5 HOH A 26 326 55 HOH HOH . G 5 HOH A 27 327 5 HOH HOH . G 5 HOH A 28 328 7 HOH HOH . G 5 HOH A 29 329 8 HOH HOH . G 5 HOH A 30 330 15 HOH HOH . G 5 HOH A 31 331 61 HOH HOH . G 5 HOH A 32 332 24 HOH HOH . G 5 HOH A 33 333 13 HOH HOH . G 5 HOH A 34 334 10 HOH HOH . G 5 HOH A 35 335 39 HOH HOH . G 5 HOH A 36 336 54 HOH HOH . G 5 HOH A 37 337 52 HOH HOH . G 5 HOH A 38 338 48 HOH HOH . G 5 HOH A 39 339 26 HOH HOH . G 5 HOH A 40 340 19 HOH HOH . G 5 HOH A 41 341 58 HOH HOH . G 5 HOH A 42 342 40 HOH HOH . G 5 HOH A 43 343 2 HOH HOH . G 5 HOH A 44 344 27 HOH HOH . G 5 HOH A 45 345 60 HOH HOH . G 5 HOH A 46 346 44 HOH HOH . G 5 HOH A 47 347 11 HOH HOH . G 5 HOH A 48 348 49 HOH HOH . G 5 HOH A 49 349 18 HOH HOH . G 5 HOH A 50 350 42 HOH HOH . G 5 HOH A 51 351 22 HOH HOH . G 5 HOH A 52 352 32 HOH HOH . G 5 HOH A 53 353 68 HOH HOH . G 5 HOH A 54 354 53 HOH HOH . G 5 HOH A 55 355 67 HOH HOH . G 5 HOH A 56 356 25 HOH HOH . G 5 HOH A 57 357 65 HOH HOH . G 5 HOH A 58 358 50 HOH HOH . G 5 HOH A 59 359 51 HOH HOH . G 5 HOH A 60 360 41 HOH HOH . G 5 HOH A 61 361 64 HOH HOH . G 5 HOH A 62 362 72 HOH HOH . G 5 HOH A 63 363 63 HOH HOH . G 5 HOH A 64 364 38 HOH HOH . G 5 HOH A 65 365 56 HOH HOH . G 5 HOH A 66 366 57 HOH HOH . G 5 HOH A 67 367 28 HOH HOH . G 5 HOH A 68 368 73 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 FE FE HEC . . . F 4 -31.044 30.661 -2.617 1 25.01 ? FE HEC 205 A 1 HETATM 2 C CHA HEC . . . F 4 -29.647 30.852 0.531 1 23.42 ? CHA HEC 205 A 1 HETATM 3 C CHB HEC . . . F 4 -31.039 34.088 -2.787 1 23.68 ? CHB HEC 205 A 1 HETATM 4 C CHC HEC . . . F 4 -31.584 30.423 -5.944 1 24.8 ? CHC HEC 205 A 1 HETATM 5 C CHD HEC . . . F 4 -31.184 27.188 -2.303 1 26.03 ? CHD HEC 205 A 1 HETATM 6 N NA HEC . . . F 4 -30.427 32.2 -1.326 1 23.33 ? NA HEC 205 A 1 HETATM 7 C C1A HEC . . . F 4 -29.897 32.108 -0.1 1 23.38 ? C1A HEC 205 A 1 HETATM 8 C C2A HEC . . . F 4 -29.639 33.378 0.523 1 24.05 ? C2A HEC 205 A 1 HETATM 9 C C3A HEC . . . F 4 -30.064 34.347 -0.474 1 23.01 ? C3A HEC 205 A 1 HETATM 10 C C4A HEC . . . F 4 -30.546 33.495 -1.549 1 25.68 ? C4A HEC 205 A 1 HETATM 11 C CMA HEC . . . F 4 -30.048 35.843 -0.431 1 26.3 ? CMA HEC 205 A 1 HETATM 12 C CAA HEC . . . F 4 -29.022 33.735 1.878 1 25.87 ? CAA HEC 205 A 1 HETATM 13 C CBA HEC . . . F 4 -27.535 33.605 1.658 1 27.69 ? CBA HEC 205 A 1 HETATM 14 C CGA HEC . . . F 4 -26.732 33.948 2.941 1 34.22 ? CGA HEC 205 A 1 HETATM 15 O O1A HEC . . . F 4 -25.969 34.919 2.958 1 38.66 ? O1A HEC 205 A 1 HETATM 16 O O2A HEC . . . F 4 -26.825 33.242 3.94 1 36.28 ? O2A HEC 205 A 1 HETATM 17 N NB HEC . . . F 4 -31.25 32.049 -4.093 1 25.27 ? NB HEC 205 A 1 HETATM 18 C C1B HEC . . . F 4 -31.277 33.362 -3.996 1 26.57 ? C1B HEC 205 A 1 HETATM 19 C C2B HEC . . . F 4 -31.525 34.079 -5.28 1 27.24 ? C2B HEC 205 A 1 HETATM 20 C C3B HEC . . . F 4 -31.672 32.989 -6.214 1 24.93 ? C3B HEC 205 A 1 HETATM 21 C C4B HEC . . . F 4 -31.474 31.78 -5.396 1 24.79 ? C4B HEC 205 A 1 HETATM 22 C CMB HEC . . . F 4 -31.61 35.539 -5.463 1 28.8 ? CMB HEC 205 A 1 HETATM 23 C CAB HEC . . . F 4 -32.015 33.091 -7.662 1 24.28 ? CAB HEC 205 A 1 HETATM 24 C CBB HEC . . . F 4 -31.221 34.099 -8.405 1 24.73 ? CBB HEC 205 A 1 HETATM 25 N NC HEC . . . F 4 -31.318 29.072 -3.908 1 27.54 ? NC HEC 205 A 1 HETATM 26 C C1C HEC . . . F 4 -31.51 29.166 -5.239 1 28.06 ? C1C HEC 205 A 1 HETATM 27 C C2C HEC . . . F 4 -31.788 27.861 -5.905 1 30.12 ? C2C HEC 205 A 1 HETATM 28 C C3C HEC . . . F 4 -31.635 26.901 -4.804 1 30.29 ? C3C HEC 205 A 1 HETATM 29 C C4C HEC . . . F 4 -31.41 27.758 -3.617 1 28.05 ? C4C HEC 205 A 1 HETATM 30 C CMC HEC . . . F 4 -32.111 27.703 -7.373 1 30.91 ? CMC HEC 205 A 1 HETATM 31 C CAC HEC . . . F 4 -31.932 25.429 -4.773 1 32.99 ? CAC HEC 205 A 1 HETATM 32 C CBC HEC . . . F 4 -31.502 24.686 -5.998 1 33.37 ? CBC HEC 205 A 1 HETATM 33 N ND HEC . . . F 4 -30.536 29.305 -1.183 1 25.83 ? ND HEC 205 A 1 HETATM 34 C C1D HEC . . . F 4 -30.664 27.962 -1.206 1 28.54 ? C1D HEC 205 A 1 HETATM 35 C C2D HEC . . . F 4 -30.14 27.248 -0.055 1 25.01 ? C2D HEC 205 A 1 HETATM 36 C C3D HEC . . . F 4 -29.721 28.326 0.803 1 27.98 ? C3D HEC 205 A 1 HETATM 37 C C4D HEC . . . F 4 -29.979 29.548 0.018 1 24 ? C4D HEC 205 A 1 HETATM 38 C CMD HEC . . . F 4 -30.215 25.78 0.18 1 26.6 ? CMD HEC 205 A 1 HETATM 39 C CAD HEC . . . F 4 -29.074 28.173 2.147 1 25.75 ? CAD HEC 205 A 1 HETATM 40 C CBD HEC . . . F 4 -27.558 28.212 1.946 1 24.31 ? CBD HEC 205 A 1 HETATM 41 C CGD HEC . . . F 4 -26.867 27.981 3.264 1 22.34 ? CGD HEC 205 A 1 HETATM 42 O O1D HEC . . . F 4 -27.226 28.677 4.245 1 23.71 ? O1D HEC 205 A 1 HETATM 43 O O2D HEC . . . F 4 -25.972 27.161 3.331 1 24.41 ? O2D HEC 205 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 43 #