data_8VWK # _model_server_result.job_id aqkHRie_7HxSBl0BGKbwdw _model_server_result.datetime_utc '2025-07-08 06:38:16' _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 8vwk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 8VWK # _exptl.entry_id 8VWK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 3 _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 8VWK _cell.length_a 88.722 _cell.length_b 88.722 _cell.length_c 117.975 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VWK _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 397 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 376 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id FE _struct_conn.ptnr2_label_comp_id HEM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id HEM _struct_conn.ptnr2_auth_seq_id 502 _struct_conn.ptnr2_symmetry 1_555 _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 2.351 _struct_conn.pdbx_value_order ? # _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 142 n n CHA C4D HEM doub 143 n n CHA HHA HEM sing 144 n n CHB C4A HEM sing 145 n n CHB C1B HEM doub 146 n n CHB HHB HEM sing 147 n n CHC C4B HEM sing 148 n n CHC C1C HEM doub 149 n n CHC HHC HEM sing 150 n n CHD C4C HEM doub 151 n n CHD C1D HEM sing 152 n n CHD HHD HEM sing 153 n n C1A C2A HEM doub 154 n y C1A NA HEM sing 155 n y C2A C3A HEM sing 156 n y C2A CAA HEM sing 157 n n C3A C4A HEM doub 158 n y C3A CMA HEM sing 159 n n C4A NA HEM sing 160 n y CMA HMA HEM sing 161 n n CMA HMAA HEM sing 162 n n CMA HMAB HEM sing 163 n n CAA CBA HEM sing 164 n n CAA HAA HEM sing 165 n n CAA HAAA HEM sing 166 n n CBA CGA HEM sing 167 n n CBA HBA HEM sing 168 n n CBA HBAA HEM sing 169 n n CGA O1A HEM doub 170 n n CGA O2A HEM sing 171 n n C1B C2B HEM sing 172 n n C1B NB HEM sing 173 n n C2B C3B HEM doub 174 n n C2B CMB HEM sing 175 n n C3B C4B HEM sing 176 n n C3B CAB HEM sing 177 n n C4B NB HEM doub 178 n n CMB HMB HEM sing 179 n n CMB HMBA HEM sing 180 n n CMB HMBB HEM sing 181 n n CAB CBB HEM doub 182 n n CAB HAB HEM sing 183 n n CBB HBB HEM sing 184 n n CBB HBBA HEM sing 185 n n C1C C2C HEM sing 186 n y C1C NC HEM sing 187 n y C2C C3C HEM doub 188 n y C2C CMC HEM sing 189 n n C3C C4C HEM sing 190 n y C3C CAC HEM sing 191 n n C4C NC HEM sing 192 n y CMC HMC HEM sing 193 n n CMC HMCA HEM sing 194 n n CMC HMCB HEM sing 195 n n CAC CBC HEM doub 196 n n CAC HAC HEM sing 197 n n CBC HBC HEM sing 198 n n CBC HBCA HEM sing 199 n n C1D C2D HEM sing 200 n n C1D ND HEM doub 201 n n C2D C3D HEM doub 202 n n C2D CMD HEM sing 203 n n C3D C4D HEM sing 204 n n C3D CAD HEM sing 205 n n C4D ND HEM sing 206 n n CMD HMD HEM sing 207 n n CMD HMDA HEM sing 208 n n CMD HMDB HEM sing 209 n n CAD CBD HEM sing 210 n n CAD HAD HEM sing 211 n n CAD HADA HEM sing 212 n n CBD CGD HEM sing 213 n n CBD HBD HEM sing 214 n n CBD HBDA HEM sing 215 n n CGD O1D HEM doub 216 n n CGD O2D HEM sing 217 n n O2A H2A HEM sing 218 n n O2D H2D HEM sing 219 n n FE NA HEM sing 220 n n FE NB HEM sing 221 n n FE NC HEM sing 222 n n FE ND HEM sing 223 n n # _atom_sites.entry_id 8VWK _atom_sites.fract_transf_matrix[1][1] 0.011271 _atom_sites.fract_transf_matrix[1][2] 0.006507 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013015 _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] 0.008476 _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 MYR A 1 501 1 MYR MYR . C 3 HEM A 1 502 1 HEM HEM . D 4 GOL A 1 503 1 GOL GOL . E 4 GOL A 1 504 2 GOL GOL . F 4 GOL A 1 505 3 GOL GOL . G 4 GOL A 1 506 4 GOL GOL . H 4 GOL A 1 507 5 GOL GOL . I 5 PEG A 1 508 1 PEG PEG . J 6 HOH A 1 601 1 HOH HOH . J 6 HOH A 2 602 46 HOH HOH . J 6 HOH A 3 603 123 HOH HOH . J 6 HOH A 4 604 81 HOH HOH . J 6 HOH A 5 605 49 HOH HOH . J 6 HOH A 6 606 29 HOH HOH . J 6 HOH A 7 607 52 HOH HOH . J 6 HOH A 8 608 93 HOH HOH . J 6 HOH A 9 609 127 HOH HOH . J 6 HOH A 10 610 45 HOH HOH . J 6 HOH A 11 611 18 HOH HOH . J 6 HOH A 12 612 138 HOH HOH . J 6 HOH A 13 613 69 HOH HOH . J 6 HOH A 14 614 34 HOH HOH . J 6 HOH A 15 615 53 HOH HOH . J 6 HOH A 16 616 133 HOH HOH . J 6 HOH A 17 617 74 HOH HOH . J 6 HOH A 18 618 15 HOH HOH . J 6 HOH A 19 619 7 HOH HOH . J 6 HOH A 20 620 11 HOH HOH . J 6 HOH A 21 621 20 HOH HOH . J 6 HOH A 22 622 5 HOH HOH . J 6 HOH A 23 623 77 HOH HOH . J 6 HOH A 24 624 19 HOH HOH . J 6 HOH A 25 625 70 HOH HOH . J 6 HOH A 26 626 33 HOH HOH . J 6 HOH A 27 627 73 HOH HOH . J 6 HOH A 28 628 57 HOH HOH . J 6 HOH A 29 629 30 HOH HOH . J 6 HOH A 30 630 94 HOH HOH . J 6 HOH A 31 631 4 HOH HOH . J 6 HOH A 32 632 92 HOH HOH . J 6 HOH A 33 633 23 HOH HOH . J 6 HOH A 34 634 63 HOH HOH . J 6 HOH A 35 635 6 HOH HOH . J 6 HOH A 36 636 124 HOH HOH . J 6 HOH A 37 637 8 HOH HOH . J 6 HOH A 38 638 43 HOH HOH . J 6 HOH A 39 639 98 HOH HOH . J 6 HOH A 40 640 24 HOH HOH . J 6 HOH A 41 641 66 HOH HOH . J 6 HOH A 42 642 38 HOH HOH . J 6 HOH A 43 643 36 HOH HOH . J 6 HOH A 44 644 67 HOH HOH . J 6 HOH A 45 645 47 HOH HOH . J 6 HOH A 46 646 40 HOH HOH . J 6 HOH A 47 647 72 HOH HOH . J 6 HOH A 48 648 14 HOH HOH . J 6 HOH A 49 649 75 HOH HOH . J 6 HOH A 50 650 54 HOH HOH . J 6 HOH A 51 651 141 HOH HOH . J 6 HOH A 52 652 35 HOH HOH . J 6 HOH A 53 653 10 HOH HOH . J 6 HOH A 54 654 68 HOH HOH . J 6 HOH A 55 655 102 HOH HOH . J 6 HOH A 56 656 39 HOH HOH . J 6 HOH A 57 657 132 HOH HOH . J 6 HOH A 58 658 21 HOH HOH . J 6 HOH A 59 659 51 HOH HOH . J 6 HOH A 60 660 61 HOH HOH . J 6 HOH A 61 661 60 HOH HOH . J 6 HOH A 62 662 103 HOH HOH . J 6 HOH A 63 663 79 HOH HOH . J 6 HOH A 64 664 13 HOH HOH . J 6 HOH A 65 665 27 HOH HOH . J 6 HOH A 66 666 41 HOH HOH . J 6 HOH A 67 667 71 HOH HOH . J 6 HOH A 68 668 137 HOH HOH . J 6 HOH A 69 669 16 HOH HOH . J 6 HOH A 70 670 55 HOH HOH . J 6 HOH A 71 671 91 HOH HOH . J 6 HOH A 72 672 76 HOH HOH . J 6 HOH A 73 673 42 HOH HOH . J 6 HOH A 74 674 58 HOH HOH . J 6 HOH A 75 675 26 HOH HOH . J 6 HOH A 76 676 22 HOH HOH . J 6 HOH A 77 677 48 HOH HOH . J 6 HOH A 78 678 50 HOH HOH . J 6 HOH A 79 679 31 HOH HOH . J 6 HOH A 80 680 86 HOH HOH . J 6 HOH A 81 681 116 HOH HOH . J 6 HOH A 82 682 105 HOH HOH . J 6 HOH A 83 683 109 HOH HOH . J 6 HOH A 84 684 125 HOH HOH . J 6 HOH A 85 685 90 HOH HOH . J 6 HOH A 86 686 2 HOH HOH . J 6 HOH A 87 687 130 HOH HOH . J 6 HOH A 88 688 89 HOH HOH . J 6 HOH A 89 689 87 HOH HOH . J 6 HOH A 90 690 118 HOH HOH . J 6 HOH A 91 691 120 HOH HOH . J 6 HOH A 92 692 25 HOH HOH . J 6 HOH A 93 693 88 HOH HOH . J 6 HOH A 94 694 56 HOH HOH . J 6 HOH A 95 695 44 HOH HOH . J 6 HOH A 96 696 32 HOH HOH . J 6 HOH A 97 697 9 HOH HOH . J 6 HOH A 98 698 106 HOH HOH . J 6 HOH A 99 699 97 HOH HOH . J 6 HOH A 100 700 101 HOH HOH . J 6 HOH A 101 701 122 HOH HOH . J 6 HOH A 102 702 108 HOH HOH . J 6 HOH A 103 703 128 HOH HOH . J 6 HOH A 104 704 111 HOH HOH . J 6 HOH A 105 705 3 HOH HOH . J 6 HOH A 106 706 107 HOH HOH . J 6 HOH A 107 707 114 HOH HOH . J 6 HOH A 108 708 115 HOH HOH . J 6 HOH A 109 709 17 HOH HOH . J 6 HOH A 110 710 104 HOH HOH . J 6 HOH A 111 711 117 HOH HOH . J 6 HOH A 112 712 37 HOH HOH . J 6 HOH A 113 713 80 HOH HOH . J 6 HOH A 114 714 126 HOH HOH . J 6 HOH A 115 715 12 HOH HOH . J 6 HOH A 116 716 113 HOH HOH . J 6 HOH A 117 717 95 HOH HOH . J 6 HOH A 118 718 129 HOH HOH . J 6 HOH A 119 719 140 HOH HOH . J 6 HOH A 120 720 134 HOH HOH . J 6 HOH A 121 721 112 HOH HOH . J 6 HOH A 122 722 131 HOH HOH . J 6 HOH A 123 723 62 HOH HOH . J 6 HOH A 124 724 121 HOH HOH . J 6 HOH A 125 725 100 HOH HOH . J 6 HOH A 126 726 59 HOH HOH . J 6 HOH A 127 727 136 HOH HOH . J 6 HOH A 128 728 78 HOH HOH . J 6 HOH A 129 729 65 HOH HOH . J 6 HOH A 130 730 83 HOH HOH . J 6 HOH A 131 731 99 HOH HOH . J 6 HOH A 132 732 119 HOH HOH . J 6 HOH A 133 733 110 HOH HOH . J 6 HOH A 134 734 64 HOH HOH . J 6 HOH A 135 735 96 HOH HOH . J 6 HOH A 136 736 139 HOH HOH . J 6 HOH A 137 737 84 HOH HOH . J 6 HOH A 138 738 82 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 . . . C 3 -1.913 24.6 -14.795 1 51.06 ? CHA HEM 502 A 1 HETATM 2 C CHB HEM . . . C 3 0.328 28.662 -16.179 1 48.72 ? CHB HEM 502 A 1 HETATM 3 C CHC HEM . . . C 3 -3.556 31.211 -14.818 1 47.56 ? CHC HEM 502 A 1 HETATM 4 C CHD HEM . . . C 3 -5.563 27.219 -12.969 1 48.64 ? CHD HEM 502 A 1 HETATM 5 C C1A HEM . . . C 3 -1 25.471 -15.334 1 51.24 ? C1A HEM 502 A 1 HETATM 6 C C2A HEM . . . C 3 0.218 25.086 -16.006 1 49.61 ? C2A HEM 502 A 1 HETATM 7 C C3A HEM . . . C 3 0.844 26.202 -16.387 1 48.6 ? C3A HEM 502 A 1 HETATM 8 C C4A HEM . . . C 3 0.037 27.334 -15.973 1 48.72 ? C4A HEM 502 A 1 HETATM 9 C CMA HEM . . . C 3 2.19 26.278 -17.141 1 49.12 ? CMA HEM 502 A 1 HETATM 10 C CAA HEM . . . C 3 0.696 23.63 -16.203 1 51.24 ? CAA HEM 502 A 1 HETATM 11 C CBA HEM . . . C 3 0.397 23.108 -17.608 1 52.58 ? CBA HEM 502 A 1 HETATM 12 C CGA HEM . . . C 3 0.75 21.641 -17.648 1 55.9 ? CGA HEM 502 A 1 HETATM 13 O O1A HEM . . . C 3 0.932 21.095 -18.765 1 55.76 ? O1A HEM 502 A 1 HETATM 14 O O2A HEM . . . C 3 0.859 21.019 -16.558 1 54.56 ? O2A HEM 502 A 1 HETATM 15 C C1B HEM . . . C 3 -0.481 29.715 -15.812 1 49.09 ? C1B HEM 502 A 1 HETATM 16 C C2B HEM . . . C 3 -0.089 31.106 -15.711 1 48.95 ? C2B HEM 502 A 1 HETATM 17 C C3B HEM . . . C 3 -1.17 31.813 -15.328 1 49.95 ? C3B HEM 502 A 1 HETATM 18 C C4B HEM . . . C 3 -2.271 30.883 -15.179 1 48.22 ? C4B HEM 502 A 1 HETATM 19 C CMB HEM . . . C 3 1.341 31.604 -16.006 1 47.07 ? CMB HEM 502 A 1 HETATM 20 C CAB HEM . . . C 3 -1.336 33.331 -15.061 1 47.47 ? CAB HEM 502 A 1 HETATM 21 C CBB HEM . . . C 3 -0.364 34.238 -15.171 1 51.94 ? CBB HEM 502 A 1 HETATM 22 C C1C HEM . . . C 3 -4.476 30.349 -14.274 1 48.48 ? C1C HEM 502 A 1 HETATM 23 C C2C HEM . . . C 3 -5.833 30.676 -13.894 1 47.02 ? C2C HEM 502 A 1 HETATM 24 C C3C HEM . . . C 3 -6.397 29.568 -13.37 1 47.12 ? C3C HEM 502 A 1 HETATM 25 C C4C HEM . . . C 3 -5.402 28.513 -13.409 1 49.67 ? C4C HEM 502 A 1 HETATM 26 C CMC HEM . . . C 3 -6.445 32.079 -14.094 1 46.33 ? CMC HEM 502 A 1 HETATM 27 C CAC HEM . . . C 3 -7.831 29.345 -12.822 1 47.16 ? CAC HEM 502 A 1 HETATM 28 C CBC HEM . . . C 3 -8.826 30.235 -12.901 1 49.38 ? CBC HEM 502 A 1 HETATM 29 C C1D HEM . . . C 3 -4.718 26.17 -13.258 1 50.68 ? C1D HEM 502 A 1 HETATM 30 C C2D HEM . . . C 3 -4.85 24.806 -12.783 1 50.44 ? C2D HEM 502 A 1 HETATM 31 C C3D HEM . . . C 3 -3.842 24.09 -13.285 1 52.67 ? C3D HEM 502 A 1 HETATM 32 C C4D HEM . . . C 3 -3.039 24.968 -14.104 1 50.64 ? C4D HEM 502 A 1 HETATM 33 C CMD HEM . . . C 3 -5.961 24.283 -11.853 1 51.43 ? CMD HEM 502 A 1 HETATM 34 C CAD HEM . . . C 3 -3.571 22.585 -13.072 1 52.11 ? CAD HEM 502 A 1 HETATM 35 C CBD HEM . . . C 3 -4.287 21.849 -14.206 1 52.99 ? CBD HEM 502 A 1 HETATM 36 C CGD HEM . . . C 3 -3.843 20.411 -14.307 1 58.03 ? CGD HEM 502 A 1 HETATM 37 O O1D HEM . . . C 3 -2.805 20.049 -13.694 1 57.08 ? O1D HEM 502 A 1 HETATM 38 O O2D HEM . . . C 3 -4.528 19.626 -15.013 1 57.68 ? O2D HEM 502 A 1 HETATM 39 N NA HEM . . . C 3 -1.089 26.851 -15.337 1 47.91 ? NA HEM 502 A 1 HETATM 40 N NB HEM . . . C 3 -1.82 29.618 -15.487 1 51.12 ? NB HEM 502 A 1 HETATM 41 N NC HEM . . . C 3 -4.244 29.023 -13.964 1 49.3 ? NC HEM 502 A 1 HETATM 42 N ND HEM . . . C 3 -3.596 26.23 -14.064 1 50.22 ? ND HEM 502 A 1 HETATM 43 FE FE HEM . . . C 3 -2.789 27.915 -14.905 1 45.25 ? FE HEM 502 A 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 46 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 43 #