data_4ZFB # _model_server_result.job_id A2RDB7XJTiQ4PKHbHJ845A _model_server_result.datetime_utc '2024-11-13 00:06:20' _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 4zfb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4ZFB # _exptl.entry_id 4ZFB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 2 _entity.src_method nat _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 4ZFB _cell.length_a 55.679 _cell.length_b 55.679 _cell.length_c 707.577 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZFB _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # _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,H,I _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 N THR 2 A THR 1 1_555 E NI NI . A NI 504 10_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc2 A OG1 THR 2 A THR 1 1_555 E NI NI . A NI 504 10_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc3 A NE2 HIS 139 A HIS 138 1_555 F NI NI . A NI 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc4 A OD1 ASP 215 A ASP 214 1_555 G NI NI . A NI 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? metalc ? metalc5 A OD1 ASP 232 A ASP 231 1_555 H NI NI . A NI 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.751 ? metalc ? metalc6 A NE2 HIS 237 A HIS 236 1_555 H NI NI . A NI 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? metalc ? metalc7 A NE2 HIS 286 A HIS 285 1_555 G NI NI . A NI 506 1_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc8 A OD2 ASP 339 A ASP 338 1_555 E NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc9 A OE2 GLU 349 A GLU 348 1_555 E NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc10 A SG CYS 401 A CYS 400 1_555 B FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? metalc ? metalc11 A NE2 HIS 427 A HIS 426 1_555 F NI NI . A NI 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? # _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 138 n n CHA C4D HEM doub 139 n n CHA HHA HEM sing 140 n n CHB C4A HEM sing 141 n n CHB C1B HEM doub 142 n n CHB HHB HEM sing 143 n n CHC C4B HEM sing 144 n n CHC C1C HEM doub 145 n n CHC HHC HEM sing 146 n n CHD C4C HEM doub 147 n n CHD C1D HEM sing 148 n n CHD HHD HEM sing 149 n n C1A C2A HEM doub 150 n y C1A NA HEM sing 151 n y C2A C3A HEM sing 152 n y C2A CAA HEM sing 153 n n C3A C4A HEM doub 154 n y C3A CMA HEM sing 155 n n C4A NA HEM sing 156 n y CMA HMA HEM sing 157 n n CMA HMAA HEM sing 158 n n CMA HMAB HEM sing 159 n n CAA CBA HEM sing 160 n n CAA HAA HEM sing 161 n n CAA HAAA HEM sing 162 n n CBA CGA HEM sing 163 n n CBA HBA HEM sing 164 n n CBA HBAA HEM sing 165 n n CGA O1A HEM doub 166 n n CGA O2A HEM sing 167 n n C1B C2B HEM sing 168 n n C1B NB HEM sing 169 n n C2B C3B HEM doub 170 n n C2B CMB HEM sing 171 n n C3B C4B HEM sing 172 n n C3B CAB HEM sing 173 n n C4B NB HEM doub 174 n n CMB HMB HEM sing 175 n n CMB HMBA HEM sing 176 n n CMB HMBB HEM sing 177 n n CAB CBB HEM doub 178 n n CAB HAB HEM sing 179 n n CBB HBB HEM sing 180 n n CBB HBBA HEM sing 181 n n C1C C2C HEM sing 182 n y C1C NC HEM sing 183 n y C2C C3C HEM doub 184 n y C2C CMC HEM sing 185 n n C3C C4C HEM sing 186 n y C3C CAC HEM sing 187 n n C4C NC HEM sing 188 n y CMC HMC HEM sing 189 n n CMC HMCA HEM sing 190 n n CMC HMCB HEM sing 191 n n CAC CBC HEM doub 192 n n CAC HAC HEM sing 193 n n CBC HBC HEM sing 194 n n CBC HBCA HEM sing 195 n n C1D C2D HEM sing 196 n n C1D ND HEM doub 197 n n C2D C3D HEM doub 198 n n C2D CMD HEM sing 199 n n C3D C4D HEM sing 200 n n C3D CAD HEM sing 201 n n C4D ND HEM sing 202 n n CMD HMD HEM sing 203 n n CMD HMDA HEM sing 204 n n CMD HMDB HEM sing 205 n n CAD CBD HEM sing 206 n n CAD HAD HEM sing 207 n n CAD HADA HEM sing 208 n n CBD CGD HEM sing 209 n n CBD HBD HEM sing 210 n n CBD HBDA HEM sing 211 n n CGD O1D HEM doub 212 n n CGD O2D HEM sing 213 n n O2A H2A HEM sing 214 n n O2D H2D HEM sing 215 n n FE NA HEM sing 216 n n FE NB HEM sing 217 n n FE NC HEM sing 218 n n FE ND HEM sing 219 n n # _atom_sites.entry_id 4ZFB _atom_sites.fract_transf_matrix[1][1] 0.01796 _atom_sites.fract_transf_matrix[1][2] 0.010369 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020738 _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] 0.001413 _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 PLM A 1 502 501 PLM PLM . D 4 EDO A 1 503 502 EDO EDO . E 5 NI A 1 504 601 NI NI . F 5 NI A 1 505 602 NI NI . G 5 NI A 1 506 603 NI NI . H 5 NI A 1 507 604 NI NI . I 6 HOH A 1 601 732 HOH HOH . I 6 HOH A 2 602 704 HOH HOH . I 6 HOH A 3 603 721 HOH HOH . I 6 HOH A 4 604 702 HOH HOH . I 6 HOH A 5 605 736 HOH HOH . I 6 HOH A 6 606 714 HOH HOH . I 6 HOH A 7 607 716 HOH HOH . I 6 HOH A 8 608 745 HOH HOH . I 6 HOH A 9 609 701 HOH HOH . I 6 HOH A 10 610 737 HOH HOH . I 6 HOH A 11 611 750 HOH HOH . I 6 HOH A 12 612 746 HOH HOH . I 6 HOH A 13 613 734 HOH HOH . I 6 HOH A 14 614 727 HOH HOH . I 6 HOH A 15 615 707 HOH HOH . I 6 HOH A 16 616 744 HOH HOH . I 6 HOH A 17 617 725 HOH HOH . I 6 HOH A 18 618 724 HOH HOH . I 6 HOH A 19 619 742 HOH HOH . I 6 HOH A 20 620 715 HOH HOH . I 6 HOH A 21 621 713 HOH HOH . I 6 HOH A 22 622 731 HOH HOH . I 6 HOH A 23 623 747 HOH HOH . I 6 HOH A 24 624 717 HOH HOH . I 6 HOH A 25 625 728 HOH HOH . I 6 HOH A 26 626 719 HOH HOH . I 6 HOH A 27 627 733 HOH HOH . I 6 HOH A 28 628 749 HOH HOH . I 6 HOH A 29 629 740 HOH HOH . I 6 HOH A 30 630 703 HOH HOH . I 6 HOH A 31 631 723 HOH HOH . I 6 HOH A 32 632 739 HOH HOH . I 6 HOH A 33 633 711 HOH HOH . I 6 HOH A 34 634 708 HOH HOH . I 6 HOH A 35 635 709 HOH HOH . I 6 HOH A 36 636 726 HOH HOH . I 6 HOH A 37 637 712 HOH HOH . I 6 HOH A 38 638 751 HOH HOH . I 6 HOH A 39 639 706 HOH HOH . I 6 HOH A 40 640 741 HOH HOH . I 6 HOH A 41 641 718 HOH HOH . I 6 HOH A 42 642 753 HOH HOH . I 6 HOH A 43 643 722 HOH HOH . I 6 HOH A 44 644 752 HOH HOH . I 6 HOH A 45 645 720 HOH HOH . I 6 HOH A 46 646 730 HOH HOH . I 6 HOH A 47 647 705 HOH HOH . I 6 HOH A 48 648 710 HOH HOH . I 6 HOH A 49 649 756 HOH HOH . I 6 HOH A 50 650 743 HOH HOH . I 6 HOH A 51 651 729 HOH HOH . I 6 HOH A 52 652 748 HOH HOH . I 6 HOH A 53 653 735 HOH HOH . I 6 HOH A 54 654 754 HOH HOH . I 6 HOH A 55 655 738 HOH HOH . I 6 HOH A 56 656 755 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 9.136 0.085 31.074 1 41.44 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . B 2 8.753 -4.239 28.904 1 40.64 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . B 2 6.559 -2.152 25.113 1 36.79 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . B 2 7.671 2.216 26.909 1 40.57 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . B 2 9.217 -1.276 30.852 1 41.86 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . B 2 9.736 -2.286 31.759 1 42 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . B 2 9.634 -3.477 31.164 1 41.33 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . B 2 9.04 -3.274 29.852 1 43.55 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . B 2 10.079 -4.818 31.792 1 37.85 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . B 2 10.321 -2.049 33.168 1 40.45 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . B 2 11.764 -1.579 33.03 1 39.5 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . B 2 12.387 -1.538 34.397 1 39.87 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . B 2 13.629 -1.358 34.495 1 38.38 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . B 2 11.632 -1.7 35.39 1 42.07 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . B 2 8.083 -4.058 27.704 1 39.21 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . B 2 7.639 -5.11 26.804 1 41.23 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . B 2 7.033 -4.54 25.745 1 39.44 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . B 2 7.072 -3.107 25.957 1 36.76 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . B 2 7.871 -6.613 27.079 1 40.4 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . B 2 6.37 -5.19 24.499 1 40.2 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . B 2 6.164 -6.503 24.339 1 37.08 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . B 2 6.636 -0.793 25.311 1 37.77 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . B 2 5.973 0.201 24.498 1 38.12 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . B 2 6.274 1.417 24.984 1 41.15 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . B 2 7.139 1.216 26.129 1 40.65 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . B 2 5.089 -0.17 23.288 1 37.36 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . B 2 5.83 2.822 24.498 1 41.81 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . B 2 4.989 3.056 23.484 1 39.94 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . B 2 8.149 2.076 28.191 1 40.02 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . B 2 8.533 3.165 29.06 1 40.5 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . B 2 8.994 2.485 30.362 1 39 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . B 2 8.834 1.065 30.144 1 41.62 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . B 2 8.491 4.675 28.724 1 38.23 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . B 2 9.51 3.144 31.66 1 42.61 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . B 2 8.433 4.066 32.227 1 42.72 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . B 2 8.74 4.443 33.655 1 42.33 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . B 2 8.312 5.544 34.09 1 42.04 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . B 2 9.414 3.65 34.36 1 44.04 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . B 2 8.802 -1.921 29.704 1 42.14 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . B 2 7.717 -2.847 27.151 1 39.6 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . B 2 7.341 -0.141 26.3 1 39.33 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . B 2 8.338 0.87 28.858 1 40.72 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . B 2 8.088 -0.983 27.984 1 44.32 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 43 #