data_4X8Y # _model_server_result.job_id XczP6bMN3XSYWHrBFpndIA _model_server_result.datetime_utc '2024-12-27 02:11:14' _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 4x8y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 4X8Y # _exptl.entry_id 4X8Y _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 2 _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 4X8Y _cell.length_a 167.23 _cell.length_b 167.23 _cell.length_c 63.46 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4X8Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1,2 B,D,F 2 1,3 # 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' 5_556 -x+1/2,y,-z+7/4 -1 0 0 0 1 0 0 0 -1 83.615 0 111.055 3 'crystal symmetry operation' 16_556 -y+1/2,-x+1/2,-z+3/2 0 -1 0 -1 0 0 0 0 -1 83.615 83.615 95.19 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N 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 disulf ? disulf1 A SG CYS 66 A CYS 129 1_555 A SG CYS 66 A CYS 129 5_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? disulf ? disulf2 B SG CYS 66 B CYS 129 1_555 B SG CYS 66 B CYS 129 16_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc1 A OH TYR 50 A TYR 113 1_555 C FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc2 B OH TYR 50 B TYR 113 1_555 D FE HEM . B HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? # _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 129 n n CHA C4D HEM doub 130 n n CHA HHA HEM sing 131 n n CHB C4A HEM sing 132 n n CHB C1B HEM doub 133 n n CHB HHB HEM sing 134 n n CHC C4B HEM sing 135 n n CHC C1C HEM doub 136 n n CHC HHC HEM sing 137 n n CHD C4C HEM doub 138 n n CHD C1D HEM sing 139 n n CHD HHD HEM sing 140 n n C1A C2A HEM doub 141 n y C1A NA HEM sing 142 n y C2A C3A HEM sing 143 n y C2A CAA HEM sing 144 n n C3A C4A HEM doub 145 n y C3A CMA HEM sing 146 n n C4A NA HEM sing 147 n y CMA HMA HEM sing 148 n n CMA HMAA HEM sing 149 n n CMA HMAB HEM sing 150 n n CAA CBA HEM sing 151 n n CAA HAA HEM sing 152 n n CAA HAAA HEM sing 153 n n CBA CGA HEM sing 154 n n CBA HBA HEM sing 155 n n CBA HBAA HEM sing 156 n n CGA O1A HEM doub 157 n n CGA O2A HEM sing 158 n n C1B C2B HEM sing 159 n n C1B NB HEM sing 160 n n C2B C3B HEM doub 161 n n C2B CMB HEM sing 162 n n C3B C4B HEM sing 163 n n C3B CAB HEM sing 164 n n C4B NB HEM doub 165 n n CMB HMB HEM sing 166 n n CMB HMBA HEM sing 167 n n CMB HMBB HEM sing 168 n n CAB CBB HEM doub 169 n n CAB HAB HEM sing 170 n n CBB HBB HEM sing 171 n n CBB HBBA HEM sing 172 n n C1C C2C HEM sing 173 n y C1C NC HEM sing 174 n y C2C C3C HEM doub 175 n y C2C CMC HEM sing 176 n n C3C C4C HEM sing 177 n y C3C CAC HEM sing 178 n n C4C NC HEM sing 179 n y CMC HMC HEM sing 180 n n CMC HMCA HEM sing 181 n n CMC HMCB HEM sing 182 n n CAC CBC HEM doub 183 n n CAC HAC HEM sing 184 n n CBC HBC HEM sing 185 n n CBC HBCA HEM sing 186 n n C1D C2D HEM sing 187 n n C1D ND HEM doub 188 n n C2D C3D HEM doub 189 n n C2D CMD HEM sing 190 n n C3D C4D HEM sing 191 n n C3D CAD HEM sing 192 n n C4D ND HEM sing 193 n n CMD HMD HEM sing 194 n n CMD HMDA HEM sing 195 n n CMD HMDB HEM sing 196 n n CAD CBD HEM sing 197 n n CAD HAD HEM sing 198 n n CAD HADA HEM sing 199 n n CBD CGD HEM sing 200 n n CBD HBD HEM sing 201 n n CBD HBDA HEM sing 202 n n CGD O1D HEM doub 203 n n CGD O2D HEM sing 204 n n O2A H2A HEM sing 205 n n O2D H2D HEM sing 206 n n FE NA HEM sing 207 n n FE NB HEM sing 208 n n FE NC HEM sing 209 n n FE ND HEM sing 210 n n # _atom_sites.entry_id 4X8Y _atom_sites.fract_transf_matrix[1][1] 0.00598 _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] 0.00598 _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] 0.015758 _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 C 2 HEM A 1 500 500 HEM HEM . D 2 HEM B 1 500 500 HEM HEM . E 3 HOH A 1 601 623 HOH HOH . E 3 HOH A 2 602 635 HOH HOH . E 3 HOH A 3 603 633 HOH HOH . E 3 HOH A 4 604 661 HOH HOH . E 3 HOH A 5 605 615 HOH HOH . E 3 HOH A 6 606 608 HOH HOH . E 3 HOH A 7 607 642 HOH HOH . E 3 HOH A 8 608 680 HOH HOH . E 3 HOH A 9 609 609 HOH HOH . E 3 HOH A 10 610 614 HOH HOH . E 3 HOH A 11 611 622 HOH HOH . E 3 HOH A 12 612 629 HOH HOH . E 3 HOH A 13 613 647 HOH HOH . E 3 HOH A 14 614 669 HOH HOH . E 3 HOH A 15 615 616 HOH HOH . E 3 HOH A 16 616 675 HOH HOH . E 3 HOH A 17 617 619 HOH HOH . E 3 HOH A 18 618 621 HOH HOH . E 3 HOH A 19 619 678 HOH HOH . E 3 HOH A 20 620 630 HOH HOH . E 3 HOH A 21 621 628 HOH HOH . E 3 HOH A 22 622 641 HOH HOH . E 3 HOH A 23 623 617 HOH HOH . E 3 HOH A 24 624 634 HOH HOH . E 3 HOH A 25 625 640 HOH HOH . E 3 HOH A 26 626 681 HOH HOH . E 3 HOH A 27 627 668 HOH HOH . E 3 HOH A 28 628 654 HOH HOH . E 3 HOH A 29 629 601 HOH HOH . E 3 HOH A 30 630 602 HOH HOH . E 3 HOH A 31 631 603 HOH HOH . E 3 HOH A 32 632 604 HOH HOH . E 3 HOH A 33 633 605 HOH HOH . E 3 HOH A 34 634 606 HOH HOH . E 3 HOH A 35 635 607 HOH HOH . E 3 HOH A 36 636 610 HOH HOH . E 3 HOH A 37 637 611 HOH HOH . E 3 HOH A 38 638 612 HOH HOH . E 3 HOH A 39 639 613 HOH HOH . E 3 HOH A 40 640 618 HOH HOH . E 3 HOH A 41 641 620 HOH HOH . E 3 HOH A 42 642 624 HOH HOH . E 3 HOH A 43 643 625 HOH HOH . E 3 HOH A 44 644 626 HOH HOH . E 3 HOH A 45 645 627 HOH HOH . E 3 HOH A 46 646 631 HOH HOH . E 3 HOH A 47 647 632 HOH HOH . E 3 HOH A 48 648 636 HOH HOH . E 3 HOH A 49 649 637 HOH HOH . E 3 HOH A 50 650 638 HOH HOH . E 3 HOH A 51 651 639 HOH HOH . E 3 HOH A 52 652 643 HOH HOH . E 3 HOH A 53 653 644 HOH HOH . E 3 HOH A 54 654 645 HOH HOH . E 3 HOH A 55 655 646 HOH HOH . E 3 HOH A 56 656 648 HOH HOH . E 3 HOH A 57 657 649 HOH HOH . E 3 HOH A 58 658 650 HOH HOH . E 3 HOH A 59 659 651 HOH HOH . E 3 HOH A 60 660 652 HOH HOH . E 3 HOH A 61 661 653 HOH HOH . E 3 HOH A 62 662 655 HOH HOH . E 3 HOH A 63 663 656 HOH HOH . E 3 HOH A 64 664 657 HOH HOH . E 3 HOH A 65 665 658 HOH HOH . E 3 HOH A 66 666 659 HOH HOH . E 3 HOH A 67 667 660 HOH HOH . E 3 HOH A 68 668 662 HOH HOH . E 3 HOH A 69 669 663 HOH HOH . E 3 HOH A 70 670 664 HOH HOH . E 3 HOH A 71 671 665 HOH HOH . E 3 HOH A 72 672 666 HOH HOH . E 3 HOH A 73 673 667 HOH HOH . E 3 HOH A 74 674 670 HOH HOH . E 3 HOH A 75 675 671 HOH HOH . E 3 HOH A 76 676 672 HOH HOH . E 3 HOH A 77 677 673 HOH HOH . E 3 HOH A 78 678 674 HOH HOH . E 3 HOH A 79 679 676 HOH HOH . E 3 HOH A 80 680 677 HOH HOH . E 3 HOH A 81 681 679 HOH HOH . E 3 HOH A 82 682 682 HOH HOH . E 3 HOH A 83 683 683 HOH HOH . E 3 HOH A 84 684 608 HOH HOH . F 3 HOH B 1 601 617 HOH HOH . F 3 HOH B 2 602 626 HOH HOH . F 3 HOH B 3 603 623 HOH HOH . F 3 HOH B 4 604 620 HOH HOH . F 3 HOH B 5 605 601 HOH HOH . F 3 HOH B 6 606 602 HOH HOH . F 3 HOH B 7 607 603 HOH HOH . F 3 HOH B 8 608 604 HOH HOH . F 3 HOH B 9 609 605 HOH HOH . F 3 HOH B 10 610 606 HOH HOH . F 3 HOH B 11 611 607 HOH HOH . F 3 HOH B 12 612 609 HOH HOH . F 3 HOH B 13 613 610 HOH HOH . F 3 HOH B 14 614 611 HOH HOH . F 3 HOH B 15 615 612 HOH HOH . F 3 HOH B 16 616 613 HOH HOH . F 3 HOH B 17 617 614 HOH HOH . F 3 HOH B 18 618 615 HOH HOH . F 3 HOH B 19 619 616 HOH HOH . F 3 HOH B 20 620 618 HOH HOH . F 3 HOH B 21 621 619 HOH HOH . F 3 HOH B 22 622 621 HOH HOH . F 3 HOH B 23 623 622 HOH HOH . F 3 HOH B 24 624 624 HOH HOH . F 3 HOH B 25 625 625 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 . . . D 2 76.536 -2.408 51.582 1 46.06 ? CHA HEM 500 B 1 HETATM 2 C CHB HEM . . . D 2 80.612 -0.045 50.4 1 53.1 ? CHB HEM 500 B 1 HETATM 3 C CHC HEM . . . D 2 77.991 3.971 49.672 1 47.71 ? CHC HEM 500 B 1 HETATM 4 C CHD HEM . . . D 2 73.883 1.488 50.329 1 46.23 ? CHD HEM 500 B 1 HETATM 5 C C1A HEM . . . D 2 77.855 -2.113 51.343 1 47.96 ? C1A HEM 500 B 1 HETATM 6 C C2A HEM . . . D 2 78.954 -3.038 51.504 1 50.26 ? C2A HEM 500 B 1 HETATM 7 C C3A HEM . . . D 2 80.081 -2.39 51.177 1 51.38 ? C3A HEM 500 B 1 HETATM 8 C C4A HEM . . . D 2 79.734 -1.032 50.8 1 50.59 ? C4A HEM 500 B 1 HETATM 9 C CMA HEM . . . D 2 81.511 -2.973 51.198 1 48.95 ? CMA HEM 500 B 1 HETATM 10 C CAA HEM . . . D 2 78.813 -4.509 51.97 1 52.59 ? CAA HEM 500 B 1 HETATM 11 C CBA HEM . . . D 2 78.884 -4.603 53.492 1 55.55 ? CBA HEM 500 B 1 HETATM 12 C CGA HEM . . . D 2 78.653 -6.021 53.966 1 61.15 ? CGA HEM 500 B 1 HETATM 13 O O1A HEM . . . D 2 78.08 -6.846 53.204 1 60.74 ? O1A HEM 500 B 1 HETATM 14 O O2A HEM . . . D 2 79.037 -6.333 55.121 1 63.25 ? O2A HEM 500 B 1 HETATM 15 C C1B HEM . . . D 2 80.272 1.249 50.068 1 51.58 ? C1B HEM 500 B 1 HETATM 16 C C2B HEM . . . D 2 81.17 2.285 49.582 1 51.77 ? C2B HEM 500 B 1 HETATM 17 C C3B HEM . . . D 2 80.435 3.402 49.388 1 51.88 ? C3B HEM 500 B 1 HETATM 18 C C4B HEM . . . D 2 79.056 3.093 49.739 1 50.17 ? C4B HEM 500 B 1 HETATM 19 C CMB HEM . . . D 2 82.691 2.067 49.362 1 52.82 ? CMB HEM 500 B 1 HETATM 20 C CAB HEM . . . D 2 80.845 4.808 48.878 1 67.71 ? CAB HEM 500 B 1 HETATM 21 C CBB HEM . . . D 2 82.054 5.121 48.401 1 73.05 ? CBB HEM 500 B 1 HETATM 22 C C1C HEM . . . D 2 76.653 3.636 49.693 1 50.85 ? C1C HEM 500 B 1 HETATM 23 C C2C HEM . . . D 2 75.532 4.466 49.267 1 54 ? C2C HEM 500 B 1 HETATM 24 C C3C HEM . . . D 2 74.406 3.748 49.449 1 48.85 ? C3C HEM 500 B 1 HETATM 25 C C4C HEM . . . D 2 74.783 2.471 50 1 47.6 ? C4C HEM 500 B 1 HETATM 26 C CMC HEM . . . D 2 75.647 5.899 48.696 1 50.54 ? CMC HEM 500 B 1 HETATM 27 C CAC HEM . . . D 2 72.912 4.08 49.195 1 61.26 ? CAC HEM 500 B 1 HETATM 28 C CBC HEM . . . D 2 72.424 5.292 48.922 1 70.87 ? CBC HEM 500 B 1 HETATM 29 C C1D HEM . . . D 2 74.198 0.227 50.769 1 45.82 ? C1D HEM 500 B 1 HETATM 30 C C2D HEM . . . D 2 73.233 -0.761 51.174 1 44.41 ? C2D HEM 500 B 1 HETATM 31 C C3D HEM . . . D 2 74.068 -1.982 51.565 1 47.71 ? C3D HEM 500 B 1 HETATM 32 C C4D HEM . . . D 2 75.446 -1.602 51.353 1 47.61 ? C4D HEM 500 B 1 HETATM 33 C CMD HEM . . . D 2 71.701 -0.597 51.202 1 49.21 ? CMD HEM 500 B 1 HETATM 34 C CAD HEM . . . D 2 73.56 -3.335 52.078 1 47.11 ? CAD HEM 500 B 1 HETATM 35 C CBD HEM . . . D 2 73.757 -3.349 53.589 1 48.58 ? CBD HEM 500 B 1 HETATM 36 C CGD HEM . . . D 2 73.126 -4.606 54.118 1 48.7 ? CGD HEM 500 B 1 HETATM 37 O O1D HEM . . . D 2 73.727 -5.697 53.946 1 51.05 ? O1D HEM 500 B 1 HETATM 38 O O2D HEM . . . D 2 72.019 -4.512 54.706 1 45.22 ? O2D HEM 500 B 1 HETATM 39 N NA HEM . . . D 2 78.363 -0.9 50.915 1 49.65 ? NA HEM 500 B 1 HETATM 40 N NB HEM . . . D 2 79.003 1.778 50.147 1 52.36 ? NB HEM 500 B 1 HETATM 41 N NC HEM . . . D 2 76.152 2.423 50.14 1 48.29 ? NC HEM 500 B 1 HETATM 42 N ND HEM . . . D 2 75.472 -0.303 50.887 1 48.75 ? ND HEM 500 B 1 HETATM 43 FE FE HEM . . . D 2 77.242 0.772 50.671 1 48.91 ? FE HEM 500 B 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 43 #