data_8VX0 # _model_server_result.job_id 1lCSAYRs2zpYtBfTXfvBKg _model_server_result.datetime_utc '2024-12-03 20:32:25' _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 8vx0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":504}' # _entry.id 8VX0 # _exptl.entry_id 8VX0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 4 _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 8VX0 _cell.length_a 75.209 _cell.length_b 141.659 _cell.length_c 161.879 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VX0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 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 _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 4 _struct_asym.id E _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 417 A CYS 435 1_555 E FE HEM . A HEM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc2 E FE HEM . A HEM 504 1_555 G O HOH . A HOH 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? # _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 8VX0 _atom_sites.fract_transf_matrix[1][1] 0.013296 _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] 0.007059 _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] 0.006177 _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 LSN A 1 501 501 LSN lsn . C 2 LSN A 1 502 502 LSN lsn . D 3 K A 1 503 505 K K . E 4 HEM A 1 504 504 HEM HEM . F 5 PO4 A 1 505 1 PO4 PO4 . G 6 HOH A 1 601 8 HOH HOH . G 6 HOH A 2 602 655 HOH HOH . G 6 HOH A 3 603 612 HOH HOH . G 6 HOH A 4 604 111 HOH HOH . G 6 HOH A 5 605 641 HOH HOH . G 6 HOH A 6 606 43 HOH HOH . G 6 HOH A 7 607 602 HOH HOH . G 6 HOH A 8 608 610 HOH HOH . G 6 HOH A 9 609 614 HOH HOH . G 6 HOH A 10 610 643 HOH HOH . G 6 HOH A 11 611 14 HOH HOH . G 6 HOH A 12 612 616 HOH HOH . G 6 HOH A 13 613 81 HOH HOH . G 6 HOH A 14 614 45 HOH HOH . G 6 HOH A 15 615 606 HOH HOH . G 6 HOH A 16 616 622 HOH HOH . G 6 HOH A 17 617 604 HOH HOH . G 6 HOH A 18 618 601 HOH HOH . G 6 HOH A 19 619 31 HOH HOH . G 6 HOH A 20 620 665 HOH HOH . G 6 HOH A 21 621 672 HOH HOH . G 6 HOH A 22 622 12 HOH HOH . G 6 HOH A 23 623 22 HOH HOH . G 6 HOH A 24 624 650 HOH HOH . G 6 HOH A 25 625 652 HOH HOH . G 6 HOH A 26 626 16 HOH HOH . G 6 HOH A 27 627 657 HOH HOH . G 6 HOH A 28 628 638 HOH HOH . G 6 HOH A 29 629 61 HOH HOH . G 6 HOH A 30 630 671 HOH HOH . G 6 HOH A 31 631 87 HOH HOH . G 6 HOH A 32 632 129 HOH HOH . G 6 HOH A 33 633 613 HOH HOH . G 6 HOH A 34 634 104 HOH HOH . G 6 HOH A 35 635 656 HOH HOH . G 6 HOH A 36 636 25 HOH HOH . G 6 HOH A 37 637 669 HOH HOH . G 6 HOH A 38 638 626 HOH HOH . G 6 HOH A 39 639 629 HOH HOH . G 6 HOH A 40 640 658 HOH HOH . G 6 HOH A 41 641 635 HOH HOH . G 6 HOH A 42 642 679 HOH HOH . G 6 HOH A 43 643 664 HOH HOH . G 6 HOH A 44 644 608 HOH HOH . G 6 HOH A 45 645 100 HOH HOH . G 6 HOH A 46 646 649 HOH HOH . G 6 HOH A 47 647 640 HOH HOH . G 6 HOH A 48 648 660 HOH HOH . G 6 HOH A 49 649 692 HOH HOH . G 6 HOH A 50 650 673 HOH HOH . G 6 HOH A 51 651 96 HOH HOH . G 6 HOH A 52 652 695 HOH HOH . G 6 HOH A 53 653 644 HOH HOH . G 6 HOH A 54 654 677 HOH HOH . G 6 HOH A 55 655 630 HOH HOH . G 6 HOH A 56 656 627 HOH HOH . G 6 HOH A 57 657 636 HOH HOH . G 6 HOH A 58 658 44 HOH HOH . G 6 HOH A 59 659 80 HOH HOH . G 6 HOH A 60 660 691 HOH HOH . G 6 HOH A 61 661 647 HOH HOH . G 6 HOH A 62 662 105 HOH HOH . G 6 HOH A 63 663 62 HOH HOH . G 6 HOH A 64 664 674 HOH HOH . G 6 HOH A 65 665 662 HOH HOH . G 6 HOH A 66 666 623 HOH HOH . G 6 HOH A 67 667 132 HOH HOH . G 6 HOH A 68 668 676 HOH HOH . G 6 HOH A 69 669 689 HOH HOH . G 6 HOH A 70 670 88 HOH HOH . G 6 HOH A 71 671 53 HOH HOH . G 6 HOH A 72 672 651 HOH HOH . G 6 HOH A 73 673 83 HOH HOH . G 6 HOH A 74 674 633 HOH HOH . G 6 HOH A 75 675 683 HOH HOH . G 6 HOH A 76 676 686 HOH HOH . G 6 HOH A 77 677 693 HOH HOH . G 6 HOH A 78 678 666 HOH HOH . G 6 HOH A 79 679 696 HOH HOH . G 6 HOH A 80 680 648 HOH HOH . G 6 HOH A 81 681 108 HOH HOH . G 6 HOH A 82 682 91 HOH HOH . G 6 HOH A 83 683 39 HOH HOH . G 6 HOH A 84 684 119 HOH HOH . G 6 HOH A 85 685 110 HOH HOH . G 6 HOH A 86 686 699 HOH HOH . G 6 HOH A 87 687 690 HOH HOH . G 6 HOH A 88 688 29 HOH HOH . G 6 HOH A 89 689 46 HOH HOH . G 6 HOH A 90 690 667 HOH HOH . G 6 HOH A 91 691 28 HOH HOH . G 6 HOH A 92 692 47 HOH HOH . G 6 HOH A 93 693 680 HOH HOH . G 6 HOH A 94 694 605 HOH HOH . G 6 HOH A 95 695 661 HOH HOH . G 6 HOH A 96 696 684 HOH HOH . G 6 HOH A 97 697 127 HOH HOH . G 6 HOH A 98 698 74 HOH HOH . G 6 HOH A 99 699 125 HOH HOH . G 6 HOH A 100 700 698 HOH HOH . G 6 HOH A 101 701 118 HOH HOH . G 6 HOH A 102 702 703 HOH HOH . G 6 HOH A 103 703 72 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 . . . E 4 -14.013 -20.921 -26.456 1 25.89 ? CHA HEM 504 A 1 HETATM 2 C CHB HEM . . . E 4 -9.976 -23.603 -26.718 1 31.44 ? CHB HEM 504 A 1 HETATM 3 C CHC HEM . . . E 4 -9.92 -23.042 -31.537 1 26.57 ? CHC HEM 504 A 1 HETATM 4 C CHD HEM . . . E 4 -14.219 -20.904 -31.25 1 27.92 ? CHD HEM 504 A 1 HETATM 5 C C1A HEM . . . E 4 -12.905 -21.665 -26.136 1 27.97 ? C1A HEM 504 A 1 HETATM 6 C C2A HEM . . . E 4 -12.495 -21.948 -24.817 1 28.72 ? C2A HEM 504 A 1 HETATM 7 C C3A HEM . . . E 4 -11.374 -22.698 -24.862 1 29.58 ? C3A HEM 504 A 1 HETATM 8 C C4A HEM . . . E 4 -11.076 -22.898 -26.237 1 30.8 ? C4A HEM 504 A 1 HETATM 9 C CMA HEM . . . E 4 -10.627 -23.265 -23.666 1 28.23 ? CMA HEM 504 A 1 HETATM 10 C CAA HEM . . . E 4 -13.178 -21.514 -23.559 1 30.06 ? CAA HEM 504 A 1 HETATM 11 C CBA HEM . . . E 4 -14.286 -22.505 -23.303 1 32.09 ? CBA HEM 504 A 1 HETATM 12 C CGA HEM . . . E 4 -14.954 -22.189 -21.995 1 33.15 ? CGA HEM 504 A 1 HETATM 13 O O1A HEM . . . E 4 -15.011 -23.124 -21.164 1 32.37 ? O1A HEM 504 A 1 HETATM 14 O O2A HEM . . . E 4 -15.435 -21.035 -21.759 1 31.19 ? O2A HEM 504 A 1 HETATM 15 C C1B HEM . . . E 4 -9.57 -23.666 -28.07 1 30.12 ? C1B HEM 504 A 1 HETATM 16 C C2B HEM . . . E 4 -8.358 -24.288 -28.535 1 27.37 ? C2B HEM 504 A 1 HETATM 17 C C3B HEM . . . E 4 -8.34 -24.117 -29.892 1 26.58 ? C3B HEM 504 A 1 HETATM 18 C C4B HEM . . . E 4 -9.573 -23.383 -30.237 1 27.59 ? C4B HEM 504 A 1 HETATM 19 C CMB HEM . . . E 4 -7.326 -24.982 -27.672 1 27.21 ? CMB HEM 504 A 1 HETATM 20 C CAB HEM . . . E 4 -7.39 -24.548 -30.928 1 27.03 ? CAB HEM 504 A 1 HETATM 21 C CBB HEM . . . E 4 -6.324 -25.278 -30.711 1 29.67 ? CBB HEM 504 A 1 HETATM 22 C C1C HEM . . . E 4 -11.088 -22.442 -31.893 1 28.35 ? C1C HEM 504 A 1 HETATM 23 C C2C HEM . . . E 4 -11.49 -22.245 -33.216 1 31.32 ? C2C HEM 504 A 1 HETATM 24 C C3C HEM . . . E 4 -12.731 -21.606 -33.158 1 32.06 ? C3C HEM 504 A 1 HETATM 25 C C4C HEM . . . E 4 -13.082 -21.464 -31.76 1 29.24 ? C4C HEM 504 A 1 HETATM 26 C CMC HEM . . . E 4 -10.761 -22.657 -34.492 1 31.72 ? CMC HEM 504 A 1 HETATM 27 C CAC HEM . . . E 4 -13.505 -21.348 -34.394 1 33.24 ? CAC HEM 504 A 1 HETATM 28 C CBC HEM . . . E 4 -14.832 -21.225 -34.475 1 35.47 ? CBC HEM 504 A 1 HETATM 29 C C1D HEM . . . E 4 -14.47 -20.752 -29.906 1 28.42 ? C1D HEM 504 A 1 HETATM 30 C C2D HEM . . . E 4 -15.64 -20.024 -29.444 1 27.79 ? C2D HEM 504 A 1 HETATM 31 C C3D HEM . . . E 4 -15.559 -20.009 -28.123 1 29.41 ? C3D HEM 504 A 1 HETATM 32 C C4D HEM . . . E 4 -14.362 -20.737 -27.765 1 26.9 ? C4D HEM 504 A 1 HETATM 33 C CMD HEM . . . E 4 -16.737 -19.387 -30.252 1 27.55 ? CMD HEM 504 A 1 HETATM 34 C CAD HEM . . . E 4 -16.58 -19.386 -27.198 1 35.34 ? CAD HEM 504 A 1 HETATM 35 C CBD HEM . . . E 4 -17.533 -20.501 -26.77 1 39.88 ? CBD HEM 504 A 1 HETATM 36 C CGD HEM . . . E 4 -18.586 -20.07 -25.811 1 40.03 ? CGD HEM 504 A 1 HETATM 37 O O1D HEM . . . E 4 -18.31 -19.35 -24.848 1 47.67 ? O1D HEM 504 A 1 HETATM 38 O O2D HEM . . . E 4 -19.742 -20.464 -25.965 1 42.31 ? O2D HEM 504 A 1 HETATM 39 N NA HEM . . . E 4 -12.008 -22.266 -27.001 1 29.01 ? NA HEM 504 A 1 HETATM 40 N NB HEM . . . E 4 -10.246 -23.18 -29.11 1 29.49 ? NB HEM 504 A 1 HETATM 41 N NC HEM . . . E 4 -12.056 -21.991 -31.046 1 28 ? NC HEM 504 A 1 HETATM 42 N ND HEM . . . E 4 -13.74 -21.206 -28.874 1 30.23 ? ND HEM 504 A 1 HETATM 43 FE FE HEM . . . E 4 -12.066 -22.169 -28.985 1 30.35 ? FE HEM 504 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 43 #