data_8VK6 # _model_server_result.job_id TzRD4P5WxmRF19KAmsUcXw _model_server_result.datetime_utc '2025-06-20 14:44:20' _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 8vk6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 8VK6 # _exptl.entry_id 8VK6 _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 98.5 _cell.angle_gamma 90 _cell.entry_id 8VK6 _cell.length_a 76.686 _cell.length_b 65.537 _cell.length_c 80.962 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VK6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 470 A CYS 470 1_555 B FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc2 B FE HEM . A HEM 601 1_555 C N10 A1AB6 . A A1AB6 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? # _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 225 n n CHA C4D HEM doub 226 n n CHA HHA HEM sing 227 n n CHB C4A HEM sing 228 n n CHB C1B HEM doub 229 n n CHB HHB HEM sing 230 n n CHC C4B HEM sing 231 n n CHC C1C HEM doub 232 n n CHC HHC HEM sing 233 n n CHD C4C HEM doub 234 n n CHD C1D HEM sing 235 n n CHD HHD HEM sing 236 n n C1A C2A HEM doub 237 n y C1A NA HEM sing 238 n y C2A C3A HEM sing 239 n y C2A CAA HEM sing 240 n n C3A C4A HEM doub 241 n y C3A CMA HEM sing 242 n n C4A NA HEM sing 243 n y CMA HMA HEM sing 244 n n CMA HMAA HEM sing 245 n n CMA HMAB HEM sing 246 n n CAA CBA HEM sing 247 n n CAA HAA HEM sing 248 n n CAA HAAA HEM sing 249 n n CBA CGA HEM sing 250 n n CBA HBA HEM sing 251 n n CBA HBAA HEM sing 252 n n CGA O1A HEM doub 253 n n CGA O2A HEM sing 254 n n C1B C2B HEM sing 255 n n C1B NB HEM sing 256 n n C2B C3B HEM doub 257 n n C2B CMB HEM sing 258 n n C3B C4B HEM sing 259 n n C3B CAB HEM sing 260 n n C4B NB HEM doub 261 n n CMB HMB HEM sing 262 n n CMB HMBA HEM sing 263 n n CMB HMBB HEM sing 264 n n CAB CBB HEM doub 265 n n CAB HAB HEM sing 266 n n CBB HBB HEM sing 267 n n CBB HBBA HEM sing 268 n n C1C C2C HEM sing 269 n y C1C NC HEM sing 270 n y C2C C3C HEM doub 271 n y C2C CMC HEM sing 272 n n C3C C4C HEM sing 273 n y C3C CAC HEM sing 274 n n C4C NC HEM sing 275 n y CMC HMC HEM sing 276 n n CMC HMCA HEM sing 277 n n CMC HMCB HEM sing 278 n n CAC CBC HEM doub 279 n n CAC HAC HEM sing 280 n n CBC HBC HEM sing 281 n n CBC HBCA HEM sing 282 n n C1D C2D HEM sing 283 n n C1D ND HEM doub 284 n n C2D C3D HEM doub 285 n n C2D CMD HEM sing 286 n n C3D C4D HEM sing 287 n n C3D CAD HEM sing 288 n n C4D ND HEM sing 289 n n CMD HMD HEM sing 290 n n CMD HMDA HEM sing 291 n n CMD HMDB HEM sing 292 n n CAD CBD HEM sing 293 n n CAD HAD HEM sing 294 n n CAD HADA HEM sing 295 n n CBD CGD HEM sing 296 n n CBD HBD HEM sing 297 n n CBD HBDA HEM sing 298 n n CGD O1D HEM doub 299 n n CGD O2D HEM sing 300 n n O2A H2A HEM sing 301 n n O2D H2D HEM sing 302 n n FE NA HEM sing 303 n n FE NB HEM sing 304 n n FE NC HEM sing 305 n n FE ND HEM sing 306 n n # _atom_sites.entry_id 8VK6 _atom_sites.fract_transf_matrix[1][1] 0.01304 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001949 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015259 _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] 0.012489 _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 1 601 601 HEM HEM . C 3 A1AB6 A 1 602 701 A1AB6 C46 . D 4 1PE A 1 603 702 1PE 1PE . E 5 LMT A 1 604 703 LMT LMT . F 6 HOH A 1 701 102 HOH HOH . F 6 HOH A 2 702 171 HOH HOH . F 6 HOH A 3 703 41 HOH HOH . F 6 HOH A 4 704 78 HOH HOH . F 6 HOH A 5 705 161 HOH HOH . F 6 HOH A 6 706 76 HOH HOH . F 6 HOH A 7 707 64 HOH HOH . F 6 HOH A 8 708 9 HOH HOH . F 6 HOH A 9 709 165 HOH HOH . F 6 HOH A 10 710 133 HOH HOH . F 6 HOH A 11 711 124 HOH HOH . F 6 HOH A 12 712 153 HOH HOH . F 6 HOH A 13 713 73 HOH HOH . F 6 HOH A 14 714 170 HOH HOH . F 6 HOH A 15 715 119 HOH HOH . F 6 HOH A 16 716 36 HOH HOH . F 6 HOH A 17 717 55 HOH HOH . F 6 HOH A 18 718 82 HOH HOH . F 6 HOH A 19 719 54 HOH HOH . F 6 HOH A 20 720 169 HOH HOH . F 6 HOH A 21 721 6 HOH HOH . F 6 HOH A 22 722 45 HOH HOH . F 6 HOH A 23 723 24 HOH HOH . F 6 HOH A 24 724 91 HOH HOH . F 6 HOH A 25 725 33 HOH HOH . F 6 HOH A 26 726 141 HOH HOH . F 6 HOH A 27 727 10 HOH HOH . F 6 HOH A 28 728 66 HOH HOH . F 6 HOH A 29 729 29 HOH HOH . F 6 HOH A 30 730 51 HOH HOH . F 6 HOH A 31 731 107 HOH HOH . F 6 HOH A 32 732 2 HOH HOH . F 6 HOH A 33 733 90 HOH HOH . F 6 HOH A 34 734 18 HOH HOH . F 6 HOH A 35 735 21 HOH HOH . F 6 HOH A 36 736 74 HOH HOH . F 6 HOH A 37 737 31 HOH HOH . F 6 HOH A 38 738 28 HOH HOH . F 6 HOH A 39 739 70 HOH HOH . F 6 HOH A 40 740 39 HOH HOH . F 6 HOH A 41 741 57 HOH HOH . F 6 HOH A 42 742 98 HOH HOH . F 6 HOH A 43 743 30 HOH HOH . F 6 HOH A 44 744 86 HOH HOH . F 6 HOH A 45 745 47 HOH HOH . F 6 HOH A 46 746 53 HOH HOH . F 6 HOH A 47 747 14 HOH HOH . F 6 HOH A 48 748 38 HOH HOH . F 6 HOH A 49 749 158 HOH HOH . F 6 HOH A 50 750 65 HOH HOH . F 6 HOH A 51 751 8 HOH HOH . F 6 HOH A 52 752 112 HOH HOH . F 6 HOH A 53 753 26 HOH HOH . F 6 HOH A 54 754 4 HOH HOH . F 6 HOH A 55 755 7 HOH HOH . F 6 HOH A 56 756 40 HOH HOH . F 6 HOH A 57 757 134 HOH HOH . F 6 HOH A 58 758 75 HOH HOH . F 6 HOH A 59 759 130 HOH HOH . F 6 HOH A 60 760 46 HOH HOH . F 6 HOH A 61 761 59 HOH HOH . F 6 HOH A 62 762 77 HOH HOH . F 6 HOH A 63 763 13 HOH HOH . F 6 HOH A 64 764 1 HOH HOH . F 6 HOH A 65 765 50 HOH HOH . F 6 HOH A 66 766 160 HOH HOH . F 6 HOH A 67 767 35 HOH HOH . F 6 HOH A 68 768 58 HOH HOH . F 6 HOH A 69 769 108 HOH HOH . F 6 HOH A 70 770 117 HOH HOH . F 6 HOH A 71 771 96 HOH HOH . F 6 HOH A 72 772 23 HOH HOH . F 6 HOH A 73 773 125 HOH HOH . F 6 HOH A 74 774 137 HOH HOH . F 6 HOH A 75 775 68 HOH HOH . F 6 HOH A 76 776 67 HOH HOH . F 6 HOH A 77 777 15 HOH HOH . F 6 HOH A 78 778 19 HOH HOH . F 6 HOH A 79 779 44 HOH HOH . F 6 HOH A 80 780 11 HOH HOH . F 6 HOH A 81 781 3 HOH HOH . F 6 HOH A 82 782 92 HOH HOH . F 6 HOH A 83 783 27 HOH HOH . F 6 HOH A 84 784 37 HOH HOH . F 6 HOH A 85 785 61 HOH HOH . F 6 HOH A 86 786 5 HOH HOH . F 6 HOH A 87 787 89 HOH HOH . F 6 HOH A 88 788 48 HOH HOH . F 6 HOH A 89 789 63 HOH HOH . F 6 HOH A 90 790 71 HOH HOH . F 6 HOH A 91 791 140 HOH HOH . F 6 HOH A 92 792 43 HOH HOH . F 6 HOH A 93 793 147 HOH HOH . F 6 HOH A 94 794 32 HOH HOH . F 6 HOH A 95 795 87 HOH HOH . F 6 HOH A 96 796 16 HOH HOH . F 6 HOH A 97 797 42 HOH HOH . F 6 HOH A 98 798 95 HOH HOH . F 6 HOH A 99 799 93 HOH HOH . F 6 HOH A 100 800 22 HOH HOH . F 6 HOH A 101 801 103 HOH HOH . F 6 HOH A 102 802 20 HOH HOH . F 6 HOH A 103 803 106 HOH HOH . F 6 HOH A 104 804 105 HOH HOH . F 6 HOH A 105 805 84 HOH HOH . F 6 HOH A 106 806 12 HOH HOH . F 6 HOH A 107 807 69 HOH HOH . F 6 HOH A 108 808 85 HOH HOH . F 6 HOH A 109 809 88 HOH HOH . F 6 HOH A 110 810 80 HOH HOH . F 6 HOH A 111 811 49 HOH HOH . F 6 HOH A 112 812 34 HOH HOH . F 6 HOH A 113 813 156 HOH HOH . F 6 HOH A 114 814 60 HOH HOH . F 6 HOH A 115 815 114 HOH HOH . F 6 HOH A 116 816 17 HOH HOH . F 6 HOH A 117 817 110 HOH HOH . F 6 HOH A 118 818 113 HOH HOH . F 6 HOH A 119 819 115 HOH HOH . F 6 HOH A 120 820 101 HOH HOH . F 6 HOH A 121 821 94 HOH HOH . F 6 HOH A 122 822 97 HOH HOH . F 6 HOH A 123 823 100 HOH HOH . F 6 HOH A 124 824 111 HOH HOH . F 6 HOH A 125 825 162 HOH HOH . F 6 HOH A 126 826 81 HOH HOH . F 6 HOH A 127 827 148 HOH HOH . F 6 HOH A 128 828 62 HOH HOH . F 6 HOH A 129 829 79 HOH HOH . F 6 HOH A 130 830 25 HOH HOH . F 6 HOH A 131 831 72 HOH HOH . F 6 HOH A 132 832 131 HOH HOH . F 6 HOH A 133 833 99 HOH HOH . F 6 HOH A 134 834 104 HOH HOH . F 6 HOH A 135 835 109 HOH HOH . F 6 HOH A 136 836 150 HOH HOH . F 6 HOH A 137 837 168 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 26.415 7.995 18.434 1 29.58 ? CHA HEM 601 A 1 HETATM 2 C CHB HEM . . . B 2 25.945 11.09 22.11 1 26.6 ? CHB HEM 601 A 1 HETATM 3 C CHC HEM . . . B 2 28.589 14.421 19.908 1 26.24 ? CHC HEM 601 A 1 HETATM 4 C CHD HEM . . . B 2 28.932 11.404 16.131 1 26.15 ? CHD HEM 601 A 1 HETATM 5 C C1A HEM . . . B 2 26.045 8.543 19.63 1 29.67 ? C1A HEM 601 A 1 HETATM 6 C C2A HEM . . . B 2 25.252 7.887 20.648 1 27.95 ? C2A HEM 601 A 1 HETATM 7 C C3A HEM . . . B 2 25.133 8.755 21.669 1 31.45 ? C3A HEM 601 A 1 HETATM 8 C C4A HEM . . . B 2 25.843 9.968 21.321 1 27.04 ? C4A HEM 601 A 1 HETATM 9 C CMA HEM . . . B 2 24.363 8.515 22.992 1 31.71 ? CMA HEM 601 A 1 HETATM 10 C CAA HEM . . . B 2 24.651 6.462 20.57 1 28.75 ? CAA HEM 601 A 1 HETATM 11 C CBA HEM . . . B 2 23.367 6.494 19.718 1 31.09 ? CBA HEM 601 A 1 HETATM 12 C CGA HEM . . . B 2 22.565 5.214 19.786 1 31.28 ? CGA HEM 601 A 1 HETATM 13 O O1A HEM . . . B 2 21.463 5.164 19.158 1 35.01 ? O1A HEM 601 A 1 HETATM 14 O O2A HEM . . . B 2 22.995 4.239 20.455 1 29.22 ? O2A HEM 601 A 1 HETATM 15 C C1B HEM . . . B 2 26.646 12.243 21.9 1 24.66 ? C1B HEM 601 A 1 HETATM 16 C C2B HEM . . . B 2 26.838 13.344 22.843 1 27.88 ? C2B HEM 601 A 1 HETATM 17 C C3B HEM . . . B 2 27.567 14.287 22.192 1 27.75 ? C3B HEM 601 A 1 HETATM 18 C C4B HEM . . . B 2 27.858 13.786 20.865 1 25.44 ? C4B HEM 601 A 1 HETATM 19 C CMB HEM . . . B 2 26.262 13.331 24.281 1 27.63 ? CMB HEM 601 A 1 HETATM 20 C CAB HEM . . . B 2 28.127 15.662 22.605 1 32.26 ? CAB HEM 601 A 1 HETATM 21 C CBB HEM . . . B 2 28.154 16.071 23.866 1 33.15 ? CBB HEM 601 A 1 HETATM 22 C C1C HEM . . . B 2 28.946 13.877 18.712 1 26.54 ? C1C HEM 601 A 1 HETATM 23 C C2C HEM . . . B 2 29.813 14.5 17.752 1 29.37 ? C2C HEM 601 A 1 HETATM 24 C C3C HEM . . . B 2 29.901 13.667 16.696 1 31.05 ? C3C HEM 601 A 1 HETATM 25 C C4C HEM . . . B 2 29.097 12.488 16.974 1 29.07 ? C4C HEM 601 A 1 HETATM 26 C CMC HEM . . . B 2 30.468 15.885 17.979 1 27.74 ? CMC HEM 601 A 1 HETATM 27 C CAC HEM . . . B 2 30.717 13.833 15.391 1 30.61 ? CAC HEM 601 A 1 HETATM 28 C CBC HEM . . . B 2 31.753 14.666 15.258 1 36.72 ? CBC HEM 601 A 1 HETATM 29 C C1D HEM . . . B 2 28.337 10.194 16.421 1 29.58 ? C1D HEM 601 A 1 HETATM 30 C C2D HEM . . . B 2 28.386 8.968 15.627 1 27.48 ? C2D HEM 601 A 1 HETATM 31 C C3D HEM . . . B 2 27.683 8.012 16.271 1 28.25 ? C3D HEM 601 A 1 HETATM 32 C C4D HEM . . . B 2 27.195 8.606 17.504 1 28.49 ? C4D HEM 601 A 1 HETATM 33 C CMD HEM . . . B 2 29.111 8.818 14.267 1 28.16 ? CMD HEM 601 A 1 HETATM 34 C CAD HEM . . . B 2 27.448 6.538 15.839 1 28.28 ? CAD HEM 601 A 1 HETATM 35 C CBD HEM . . . B 2 25.975 6.248 15.547 1 31.79 ? CBD HEM 601 A 1 HETATM 36 C CGD HEM . . . B 2 25.732 4.764 15.396 1 31.68 ? CGD HEM 601 A 1 HETATM 37 O O1D HEM . . . B 2 26.715 4.001 15.498 1 31.37 ? O1D HEM 601 A 1 HETATM 38 O O2D HEM . . . B 2 24.559 4.339 15.179 1 31.35 ? O2D HEM 601 A 1 HETATM 39 N NA HEM . . . B 2 26.383 9.819 20.058 1 26.24 ? NA HEM 601 A 1 HETATM 40 N NB HEM . . . B 2 27.268 12.578 20.734 1 24.09 ? NB HEM 601 A 1 HETATM 41 N NC HEM . . . B 2 28.526 12.651 18.23 1 30.3 ? NC HEM 601 A 1 HETATM 42 N ND HEM . . . B 2 27.619 9.917 17.559 1 27.14 ? ND HEM 601 A 1 HETATM 43 FE FE HEM . . . B 2 27.472 11.231 19.189 1 29.01 ? FE HEM 601 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #