data_5K7K # _model_server_result.job_id kOm4gCeCJL6_6dlS1EW6GA _model_server_result.datetime_utc '2024-12-02 14:04:52' _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 5k7k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5K7K # _exptl.entry_id 5K7K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _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 5K7K _cell.length_a 91.69 _cell.length_b 91.69 _cell.length_c 169.88 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K7K _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _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 # 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 SG CYS 418 A CYS 435 1_555 B FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc2 B FE HEM . A HEM 501 1_555 C N28 6RJ . A 6RJ 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? # _chem_comp.formula 'C34 H32 Fe N4 O4' _chem_comp.formula_weight 616.487 _chem_comp.id HEM _chem_comp.mon_nstd_flag . _chem_comp.name 'PROTOPORPHYRIN IX CONTAINING FE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms HEME # 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 CHA C1A HEM sing 174 n n CHA C4D HEM doub 175 n n CHA HHA HEM sing 176 n n CHB C4A HEM sing 177 n n CHB C1B HEM doub 178 n n CHB HHB HEM sing 179 n n CHC C4B HEM sing 180 n n CHC C1C HEM doub 181 n n CHC HHC HEM sing 182 n n CHD C4C HEM doub 183 n n CHD C1D HEM sing 184 n n CHD HHD HEM sing 185 n n C1A C2A HEM doub 186 n y C1A NA HEM sing 187 n y C2A C3A HEM sing 188 n y C2A CAA HEM sing 189 n n C3A C4A HEM doub 190 n y C3A CMA HEM sing 191 n n C4A NA HEM sing 192 n y CMA HMA HEM sing 193 n n CMA HMAA HEM sing 194 n n CMA HMAB HEM sing 195 n n CAA CBA HEM sing 196 n n CAA HAA HEM sing 197 n n CAA HAAA HEM sing 198 n n CBA CGA HEM sing 199 n n CBA HBA HEM sing 200 n n CBA HBAA HEM sing 201 n n CGA O1A HEM doub 202 n n CGA O2A HEM sing 203 n n C1B C2B HEM sing 204 n n C1B NB HEM sing 205 n n C2B C3B HEM doub 206 n n C2B CMB HEM sing 207 n n C3B C4B HEM sing 208 n n C3B CAB HEM sing 209 n n C4B NB HEM doub 210 n n CMB HMB HEM sing 211 n n CMB HMBA HEM sing 212 n n CMB HMBB HEM sing 213 n n CAB CBB HEM doub 214 n n CAB HAB HEM sing 215 n n CBB HBB HEM sing 216 n n CBB HBBA HEM sing 217 n n C1C C2C HEM sing 218 n y C1C NC HEM sing 219 n y C2C C3C HEM doub 220 n y C2C CMC HEM sing 221 n n C3C C4C HEM sing 222 n y C3C CAC HEM sing 223 n n C4C NC HEM sing 224 n y CMC HMC HEM sing 225 n n CMC HMCA HEM sing 226 n n CMC HMCB HEM sing 227 n n CAC CBC HEM doub 228 n n CAC HAC HEM sing 229 n n CBC HBC HEM sing 230 n n CBC HBCA HEM sing 231 n n C1D C2D HEM sing 232 n n C1D ND HEM doub 233 n n C2D C3D HEM doub 234 n n C2D CMD HEM sing 235 n n C3D C4D HEM sing 236 n n C3D CAD HEM sing 237 n n C4D ND HEM sing 238 n n CMD HMD HEM sing 239 n n CMD HMDA HEM sing 240 n n CMD HMDB HEM sing 241 n n CAD CBD HEM sing 242 n n CAD HAD HEM sing 243 n n CAD HADA HEM sing 244 n n CBD CGD HEM sing 245 n n CBD HBD HEM sing 246 n n CBD HBDA HEM sing 247 n n CGD O1D HEM doub 248 n n CGD O2D HEM sing 249 n n O2A H2A HEM sing 250 n n O2D H2D HEM sing 251 n n FE NA HEM sing 252 n n FE NB HEM sing 253 n n FE NC HEM sing 254 n n FE ND HEM sing 255 n n # _atom_sites.entry_id 5K7K _atom_sites.fract_transf_matrix[1][1] 0.010906 _atom_sites.fract_transf_matrix[1][2] 0.006297 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012594 _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] 0.005887 _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 HEM A 1 501 500 HEM HEM . C 3 6RJ A 1 502 4000 6RJ PFE . D 4 HOH A 1 601 15 HOH HOH . D 4 HOH A 2 602 12 HOH HOH . D 4 HOH A 3 603 17 HOH HOH . D 4 HOH A 4 604 13 HOH HOH . D 4 HOH A 5 605 3 HOH HOH . D 4 HOH A 6 606 83 HOH HOH . D 4 HOH A 7 607 24 HOH HOH . D 4 HOH A 8 608 9 HOH HOH . D 4 HOH A 9 609 16 HOH HOH . D 4 HOH A 10 610 41 HOH HOH . D 4 HOH A 11 611 43 HOH HOH . D 4 HOH A 12 612 57 HOH HOH . D 4 HOH A 13 613 44 HOH HOH . D 4 HOH A 14 614 22 HOH HOH . D 4 HOH A 15 615 6 HOH HOH . D 4 HOH A 16 616 7 HOH HOH . D 4 HOH A 17 617 37 HOH HOH . D 4 HOH A 18 618 10 HOH HOH . D 4 HOH A 19 619 2 HOH HOH . D 4 HOH A 20 620 8 HOH HOH . D 4 HOH A 21 621 66 HOH HOH . D 4 HOH A 22 622 4 HOH HOH . D 4 HOH A 23 623 42 HOH HOH . D 4 HOH A 24 624 55 HOH HOH . D 4 HOH A 25 625 62 HOH HOH . D 4 HOH A 26 626 31 HOH HOH . D 4 HOH A 27 627 65 HOH HOH . D 4 HOH A 28 628 11 HOH HOH . D 4 HOH A 29 629 18 HOH HOH . D 4 HOH A 30 630 92 HOH HOH . D 4 HOH A 31 631 23 HOH HOH . D 4 HOH A 32 632 47 HOH HOH . D 4 HOH A 33 633 1 HOH HOH . D 4 HOH A 34 634 54 HOH HOH . D 4 HOH A 35 635 35 HOH HOH . D 4 HOH A 36 636 20 HOH HOH . D 4 HOH A 37 637 81 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 CHA HEM . . . B 2 17.253 -33.517 3.893 1 30.89 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . B 2 19.317 -37.981 3.184 1 29.89 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . B 2 19.31 -36.98 -1.788 1 28.34 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . B 2 17.335 -32.53 -1 1 26.24 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . B 2 17.808 -34.768 4.132 1 29.15 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . B 2 18.063 -35.534 5.415 1 33.3 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . B 2 18.564 -36.726 5.116 1 32.38 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . B 2 18.666 -36.846 3.67 1 29.3 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . B 2 19.043 -37.855 6.092 1 33.61 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . B 2 17.734 -34.904 6.81 1 36.34 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . B 2 16.248 -34.878 7.133 1 37.78 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . B 2 16.109 -34.521 8.595 1 40.98 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . B 2 15.732 -35.288 9.531 1 42.79 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . B 2 16.39 -33.36 8.891 1 38.8 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . B 2 19.554 -38.078 1.774 1 28.88 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . B 2 20.085 -39.204 1.059 1 30.6 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . B 2 20.028 -38.858 -0.262 1 30.93 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . B 2 19.515 -37.571 -0.502 1 29.84 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . B 2 20.621 -40.602 1.783 1 31.75 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . B 2 20.479 -39.666 -1.53 1 37.67 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . B 2 21.065 -40.814 -1.329 1 38.69 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . B 2 18.714 -35.698 -1.891 1 30.08 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . B 2 18.435 -35.165 -3.111 1 29.65 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . B 2 17.903 -33.9 -2.94 1 29.22 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . B 2 17.889 -33.684 -1.586 1 27.15 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . B 2 18.717 -36.018 -4.37 1 32.71 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . B 2 17.236 -32.763 -3.779 1 34.87 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . B 2 16.341 -32.749 -4.66 1 39.83 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . B 2 17.282 -32.661 0.413 1 31.24 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . B 2 16.796 -31.522 1.06 1 33.6 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . B 2 16.723 -31.812 2.464 1 31.78 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . B 2 17.194 -33.098 2.551 1 30.58 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . B 2 16.241 -30.16 0.546 1 34.16 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . B 2 16.157 -30.757 3.506 1 31.96 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . B 2 14.783 -31.272 3.977 1 37.78 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . B 2 14.244 -30.312 5.025 1 41.85 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . B 2 13.008 -30.061 5.211 1 41.51 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . B 2 15.166 -29.763 5.68 1 40.59 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . B 2 18.235 -35.589 3.086 1 28.22 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . B 2 19.207 -36.998 0.766 1 27.7 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . B 2 18.394 -34.842 -0.92 1 28.41 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . B 2 17.584 -33.765 1.319 1 29.23 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . B 2 18.357 -35.322 1.072 1 31.99 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #