data_5DQN # _model_server_result.job_id CZ7CBcfpdokHoFl5kGmhGQ _model_server_result.datetime_utc '2024-11-15 18:20:14' _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 5dqn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5DQN # _exptl.entry_id 5DQN _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 90 _cell.entry_id 5DQN _cell.length_a 108.821 _cell.length_b 108.821 _cell.length_c 118.809 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DQN _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41' # _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,E,F,G _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 360 A CYS 360 1_555 B FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc2 B FE HEM . A HEM 501 1_555 F OH2 1PE . A 1PE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? # _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 186 n n CHA C4D HEM doub 187 n n CHA HHA HEM sing 188 n n CHB C4A HEM sing 189 n n CHB C1B HEM doub 190 n n CHB HHB HEM sing 191 n n CHC C4B HEM sing 192 n n CHC C1C HEM doub 193 n n CHC HHC HEM sing 194 n n CHD C4C HEM doub 195 n n CHD C1D HEM sing 196 n n CHD HHD HEM sing 197 n n C1A C2A HEM doub 198 n y C1A NA HEM sing 199 n y C2A C3A HEM sing 200 n y C2A CAA HEM sing 201 n n C3A C4A HEM doub 202 n y C3A CMA HEM sing 203 n n C4A NA HEM sing 204 n y CMA HMA HEM sing 205 n n CMA HMAA HEM sing 206 n n CMA HMAB HEM sing 207 n n CAA CBA HEM sing 208 n n CAA HAA HEM sing 209 n n CAA HAAA HEM sing 210 n n CBA CGA HEM sing 211 n n CBA HBA HEM sing 212 n n CBA HBAA HEM sing 213 n n CGA O1A HEM doub 214 n n CGA O2A HEM sing 215 n n C1B C2B HEM sing 216 n n C1B NB HEM sing 217 n n C2B C3B HEM doub 218 n n C2B CMB HEM sing 219 n n C3B C4B HEM sing 220 n n C3B CAB HEM sing 221 n n C4B NB HEM doub 222 n n CMB HMB HEM sing 223 n n CMB HMBA HEM sing 224 n n CMB HMBB HEM sing 225 n n CAB CBB HEM doub 226 n n CAB HAB HEM sing 227 n n CBB HBB HEM sing 228 n n CBB HBBA HEM sing 229 n n C1C C2C HEM sing 230 n y C1C NC HEM sing 231 n y C2C C3C HEM doub 232 n y C2C CMC HEM sing 233 n n C3C C4C HEM sing 234 n y C3C CAC HEM sing 235 n n C4C NC HEM sing 236 n y CMC HMC HEM sing 237 n n CMC HMCA HEM sing 238 n n CMC HMCB HEM sing 239 n n CAC CBC HEM doub 240 n n CAC HAC HEM sing 241 n n CBC HBC HEM sing 242 n n CBC HBCA HEM sing 243 n n C1D C2D HEM sing 244 n n C1D ND HEM doub 245 n n C2D C3D HEM doub 246 n n C2D CMD HEM sing 247 n n C3D C4D HEM sing 248 n n C3D CAD HEM sing 249 n n C4D ND HEM sing 250 n n CMD HMD HEM sing 251 n n CMD HMDA HEM sing 252 n n CMD HMDB HEM sing 253 n n CAD CBD HEM sing 254 n n CAD HAD HEM sing 255 n n CAD HADA HEM sing 256 n n CBD CGD HEM sing 257 n n CBD HBD HEM sing 258 n n CBD HBDA HEM sing 259 n n CGD O1D HEM doub 260 n n CGD O2D HEM sing 261 n n O2A H2A HEM sing 262 n n O2D H2D HEM sing 263 n n FE NA HEM sing 264 n n FE NB HEM sing 265 n n FE NC HEM sing 266 n n FE ND HEM sing 267 n n # _atom_sites.entry_id 5DQN _atom_sites.fract_transf_matrix[1][1] 0.009189 _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] 0.009189 _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] 0.008417 _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 1418 HEM HEM . C 3 PO4 A 1 502 601 PO4 PO4 . D 3 PO4 A 1 503 602 PO4 PO4 . E 4 CIT A 1 504 701 CIT CIT . F 5 1PE A 1 505 502 1PE P6E . G 6 HOH A 1 601 42 HOH HOH . G 6 HOH A 2 602 48 HOH HOH . G 6 HOH A 3 603 18 HOH HOH . G 6 HOH A 4 604 39 HOH HOH . G 6 HOH A 5 605 36 HOH HOH . G 6 HOH A 6 606 19 HOH HOH . G 6 HOH A 7 607 1 HOH HOH . G 6 HOH A 8 608 76 HOH HOH . G 6 HOH A 9 609 23 HOH HOH . G 6 HOH A 10 610 5 HOH HOH . G 6 HOH A 11 611 75 HOH HOH . G 6 HOH A 12 612 30 HOH HOH . G 6 HOH A 13 613 29 HOH HOH . G 6 HOH A 14 614 46 HOH HOH . G 6 HOH A 15 615 63 HOH HOH . G 6 HOH A 16 616 49 HOH HOH . G 6 HOH A 17 617 2 HOH HOH . G 6 HOH A 18 618 66 HOH HOH . G 6 HOH A 19 619 86 HOH HOH . G 6 HOH A 20 620 34 HOH HOH . G 6 HOH A 21 621 47 HOH HOH . G 6 HOH A 22 622 7 HOH HOH . G 6 HOH A 23 623 52 HOH HOH . G 6 HOH A 24 624 8 HOH HOH . G 6 HOH A 25 625 57 HOH HOH . G 6 HOH A 26 626 83 HOH HOH . G 6 HOH A 27 627 10 HOH HOH . G 6 HOH A 28 628 13 HOH HOH . G 6 HOH A 29 629 16 HOH HOH . G 6 HOH A 30 630 41 HOH HOH . G 6 HOH A 31 631 22 HOH HOH . G 6 HOH A 32 632 69 HOH HOH . G 6 HOH A 33 633 77 HOH HOH . G 6 HOH A 34 634 6 HOH HOH . G 6 HOH A 35 635 44 HOH HOH . G 6 HOH A 36 636 28 HOH HOH . G 6 HOH A 37 637 87 HOH HOH . G 6 HOH A 38 638 24 HOH HOH . G 6 HOH A 39 639 14 HOH HOH . G 6 HOH A 40 640 59 HOH HOH . G 6 HOH A 41 641 65 HOH HOH . G 6 HOH A 42 642 43 HOH HOH . G 6 HOH A 43 643 21 HOH HOH . G 6 HOH A 44 644 4 HOH HOH . G 6 HOH A 45 645 71 HOH HOH . G 6 HOH A 46 646 68 HOH HOH . G 6 HOH A 47 647 9 HOH HOH . G 6 HOH A 48 648 70 HOH HOH . G 6 HOH A 49 649 64 HOH HOH . G 6 HOH A 50 650 58 HOH HOH . G 6 HOH A 51 651 11 HOH HOH . G 6 HOH A 52 652 60 HOH HOH . G 6 HOH A 53 653 40 HOH HOH . G 6 HOH A 54 654 3 HOH HOH . G 6 HOH A 55 655 37 HOH HOH . G 6 HOH A 56 656 50 HOH HOH . G 6 HOH A 57 657 56 HOH HOH . G 6 HOH A 58 658 12 HOH HOH . G 6 HOH A 59 659 61 HOH HOH . G 6 HOH A 60 660 17 HOH HOH . G 6 HOH A 61 661 54 HOH HOH . G 6 HOH A 62 662 74 HOH HOH . G 6 HOH A 63 663 20 HOH HOH . G 6 HOH A 64 664 62 HOH HOH . G 6 HOH A 65 665 79 HOH HOH . G 6 HOH A 66 666 51 HOH HOH . G 6 HOH A 67 667 15 HOH HOH . G 6 HOH A 68 668 35 HOH HOH . G 6 HOH A 69 669 38 HOH HOH . G 6 HOH A 70 670 32 HOH HOH . G 6 HOH A 71 671 31 HOH HOH . G 6 HOH A 72 672 27 HOH HOH . G 6 HOH A 73 673 45 HOH HOH . G 6 HOH A 74 674 84 HOH HOH . G 6 HOH A 75 675 53 HOH HOH . G 6 HOH A 76 676 25 HOH HOH . G 6 HOH A 77 677 26 HOH HOH . G 6 HOH A 78 678 55 HOH HOH . G 6 HOH A 79 679 85 HOH HOH . G 6 HOH A 80 680 72 HOH HOH . G 6 HOH A 81 681 73 HOH HOH . G 6 HOH A 82 682 89 HOH HOH . G 6 HOH A 83 683 88 HOH HOH . G 6 HOH A 84 684 67 HOH HOH . G 6 HOH A 85 685 81 HOH HOH . G 6 HOH A 86 686 33 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 18.526 -9.682 -7.252 1 39.09 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . B 2 21.439 -10.49 -3.449 1 42.04 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . B 2 22.819 -5.856 -3.461 1 42.28 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . B 2 19.485 -4.893 -6.837 1 37.84 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . B 2 19.243 -10.333 -6.272 1 43.26 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . B 2 19.314 -11.775 -6.051 1 41.78 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . B 2 20.121 -11.969 -4.997 1 39.1 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . B 2 20.592 -10.683 -4.521 1 43.71 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . B 2 20.516 -13.318 -4.361 1 40.05 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . B 2 18.615 -12.899 -6.872 1 31.74 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . A . B 2 19.594 -13.674 -7.742 0.47 36.46 ? CBA HEM 501 A 1 HETATM 12 C CBA HEM . B . B 2 17.109 -12.965 -6.706 0.53 46.68 ? CBA HEM 501 A 1 HETATM 13 C CGA HEM . A . B 2 18.849 -14.745 -8.495 0.47 36.84 ? CGA HEM 501 A 1 HETATM 14 C CGA HEM . B . B 2 16.565 -14.286 -7.205 0.53 46.63 ? CGA HEM 501 A 1 HETATM 15 O O1A HEM . A . B 2 17.605 -14.842 -8.337 0.47 46.15 ? O1A HEM 501 A 1 HETATM 16 O O1A HEM . B . B 2 17.301 -15.017 -7.918 0.53 46.26 ? O1A HEM 501 A 1 HETATM 17 O O2A HEM . A . B 2 19.499 -15.51 -9.25 0.47 34.48 ? O2A HEM 501 A 1 HETATM 18 O O2A HEM . B . B 2 15.39 -14.616 -6.893 0.53 33.06 ? O2A HEM 501 A 1 HETATM 19 C C1B HEM . . . B 2 22.097 -9.325 -3.135 1 40.03 ? C1B HEM 501 A 1 HETATM 20 C C2B HEM . . . B 2 23.127 -9.166 -2.129 1 40.38 ? C2B HEM 501 A 1 HETATM 21 C C3B HEM . . . B 2 23.499 -7.873 -2.124 1 47.48 ? C3B HEM 501 A 1 HETATM 22 C C4B HEM . . . B 2 22.727 -7.192 -3.143 1 41.07 ? C4B HEM 501 A 1 HETATM 23 C CMB HEM . . . B 2 23.639 -10.319 -1.232 1 47.02 ? CMB HEM 501 A 1 HETATM 24 C CAB HEM . . . B 2 24.57 -7.147 -1.263 1 46.1 ? CAB HEM 501 A 1 HETATM 25 C CBB HEM . . . B 2 25.552 -7.77 -0.6 1 36.25 ? CBB HEM 501 A 1 HETATM 26 C C1C HEM . . . B 2 22.032 -5.187 -4.37 1 42.7 ? C1C HEM 501 A 1 HETATM 27 C C2C HEM . . . B 2 22.099 -3.772 -4.676 1 44.94 ? C2C HEM 501 A 1 HETATM 28 C C3C HEM . . . B 2 21.179 -3.515 -5.623 1 43.66 ? C3C HEM 501 A 1 HETATM 29 C C4C HEM . . . B 2 20.501 -4.756 -5.922 1 39.93 ? C4C HEM 501 A 1 HETATM 30 C CMC HEM . . . B 2 23.098 -2.796 -4.009 1 44.26 ? CMC HEM 501 A 1 HETATM 31 C CAC HEM . . . B 2 20.791 -2.182 -6.315 1 46.87 ? CAC HEM 501 A 1 HETATM 32 C CBC HEM . . . B 2 21.136 -0.971 -5.864 1 45.8 ? CBC HEM 501 A 1 HETATM 33 C C1D HEM . . . B 2 18.895 -6.068 -7.24 1 44.24 ? C1D HEM 501 A 1 HETATM 34 C C2D HEM . . . B 2 17.804 -6.146 -8.176 1 43.98 ? C2D HEM 501 A 1 HETATM 35 C C3D HEM . . . B 2 17.498 -7.643 -8.314 1 42.49 ? C3D HEM 501 A 1 HETATM 36 C C4D HEM . . . B 2 18.439 -8.316 -7.44 1 41.73 ? C4D HEM 501 A 1 HETATM 37 C CMD HEM . . . B 2 17.108 -4.964 -8.881 1 40.8 ? CMD HEM 501 A 1 HETATM 38 C CAD HEM . . . B 2 16.412 -8.286 -9.198 1 37.66 ? CAD HEM 501 A 1 HETATM 39 C CBD HEM . . . B 2 17.039 -8.708 -10.525 1 44.44 ? CBD HEM 501 A 1 HETATM 40 C CGD HEM . . . B 2 16.064 -9.546 -11.319 1 48.47 ? CGD HEM 501 A 1 HETATM 41 O O1D HEM . . . B 2 15.14 -10.15 -10.703 1 44.85 ? O1D HEM 501 A 1 HETATM 42 O O2D HEM . . . B 2 16.221 -9.621 -12.57 1 45.01 ? O2D HEM 501 A 1 HETATM 43 N NA HEM . . . B 2 20.038 -9.706 -5.322 1 38.69 ? NA HEM 501 A 1 HETATM 44 N NB HEM . . . B 2 21.88 -8.103 -3.733 1 44.11 ? NB HEM 501 A 1 HETATM 45 N NC HEM . . . B 2 21.047 -5.758 -5.149 1 41.47 ? NC HEM 501 A 1 HETATM 46 N ND HEM . . . B 2 19.239 -7.354 -6.83 1 38.47 ? ND HEM 501 A 1 HETATM 47 FE FE HEM . . . B 2 20.689 -7.746 -5.359 1 45.26 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 47 #