data_9NNJ # _model_server_result.job_id q9sz8n7i3CMGtg4_hnLoEQ _model_server_result.datetime_utc '2025-06-28 19:45:52' _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 9nnj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 9NNJ # _exptl.entry_id 9NNJ _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 90 _cell.angle_gamma 90 _cell.entry_id 9NNJ _cell.length_a 58.104 _cell.length_b 63.626 _cell.length_c 123.138 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9NNJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 417 A CYS 437 1_555 B FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc2 B FE HEM . A HEM 501 1_555 C N13 A1BZB . A A1BZB 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? # _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 182 n n CHA C4D HEM doub 183 n n CHA HHA HEM sing 184 n n CHB C4A HEM sing 185 n n CHB C1B HEM doub 186 n n CHB HHB HEM sing 187 n n CHC C4B HEM sing 188 n n CHC C1C HEM doub 189 n n CHC HHC HEM sing 190 n n CHD C4C HEM doub 191 n n CHD C1D HEM sing 192 n n CHD HHD HEM sing 193 n n C1A C2A HEM doub 194 n y C1A NA HEM sing 195 n y C2A C3A HEM sing 196 n y C2A CAA HEM sing 197 n n C3A C4A HEM doub 198 n y C3A CMA HEM sing 199 n n C4A NA HEM sing 200 n y CMA HMA HEM sing 201 n n CMA HMAA HEM sing 202 n n CMA HMAB HEM sing 203 n n CAA CBA HEM sing 204 n n CAA HAA HEM sing 205 n n CAA HAAA HEM sing 206 n n CBA CGA HEM sing 207 n n CBA HBA HEM sing 208 n n CBA HBAA HEM sing 209 n n CGA O1A HEM doub 210 n n CGA O2A HEM sing 211 n n C1B C2B HEM sing 212 n n C1B NB HEM sing 213 n n C2B C3B HEM doub 214 n n C2B CMB HEM sing 215 n n C3B C4B HEM sing 216 n n C3B CAB HEM sing 217 n n C4B NB HEM doub 218 n n CMB HMB HEM sing 219 n n CMB HMBA HEM sing 220 n n CMB HMBB HEM sing 221 n n CAB CBB HEM doub 222 n n CAB HAB HEM sing 223 n n CBB HBB HEM sing 224 n n CBB HBBA HEM sing 225 n n C1C C2C HEM sing 226 n y C1C NC HEM sing 227 n y C2C C3C HEM doub 228 n y C2C CMC HEM sing 229 n n C3C C4C HEM sing 230 n y C3C CAC HEM sing 231 n n C4C NC HEM sing 232 n y CMC HMC HEM sing 233 n n CMC HMCA HEM sing 234 n n CMC HMCB HEM sing 235 n n CAC CBC HEM doub 236 n n CAC HAC HEM sing 237 n n CBC HBC HEM sing 238 n n CBC HBCA HEM sing 239 n n C1D C2D HEM sing 240 n n C1D ND HEM doub 241 n n C2D C3D HEM doub 242 n n C2D CMD HEM sing 243 n n C3D C4D HEM sing 244 n n C3D CAD HEM sing 245 n n C4D ND HEM sing 246 n n CMD HMD HEM sing 247 n n CMD HMDA HEM sing 248 n n CMD HMDB HEM sing 249 n n CAD CBD HEM sing 250 n n CAD HAD HEM sing 251 n n CAD HADA HEM sing 252 n n CBD CGD HEM sing 253 n n CBD HBD HEM sing 254 n n CBD HBDA HEM sing 255 n n CGD O1D HEM doub 256 n n CGD O2D HEM sing 257 n n O2A H2A HEM sing 258 n n O2D H2D HEM sing 259 n n FE NA HEM sing 260 n n FE NB HEM sing 261 n n FE NC HEM sing 262 n n FE ND HEM sing 263 n n # _atom_sites.entry_id 9NNJ _atom_sites.fract_transf_matrix[1][1] 0.017211 _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] 0.015717 _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] 0.008121 _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 1 501 602 HEM HEM . C 3 A1BZB A 1 502 901 A1BZB LIG . D 4 EDO A 1 503 902 EDO EDO . E 5 HOH A 1 601 21 HOH HOH . E 5 HOH A 2 602 121 HOH HOH . E 5 HOH A 3 603 22 HOH HOH . E 5 HOH A 4 604 100 HOH HOH . E 5 HOH A 5 605 7 HOH HOH . E 5 HOH A 6 606 35 HOH HOH . E 5 HOH A 7 607 63 HOH HOH . E 5 HOH A 8 608 73 HOH HOH . E 5 HOH A 9 609 139 HOH HOH . E 5 HOH A 10 610 154 HOH HOH . E 5 HOH A 11 611 129 HOH HOH . E 5 HOH A 12 612 34 HOH HOH . E 5 HOH A 13 613 85 HOH HOH . E 5 HOH A 14 614 10 HOH HOH . E 5 HOH A 15 615 131 HOH HOH . E 5 HOH A 16 616 165 HOH HOH . E 5 HOH A 17 617 40 HOH HOH . E 5 HOH A 18 618 83 HOH HOH . E 5 HOH A 19 619 117 HOH HOH . E 5 HOH A 20 620 51 HOH HOH . E 5 HOH A 21 621 75 HOH HOH . E 5 HOH A 22 622 95 HOH HOH . E 5 HOH A 23 623 41 HOH HOH . E 5 HOH A 24 624 16 HOH HOH . E 5 HOH A 25 625 68 HOH HOH . E 5 HOH A 26 626 143 HOH HOH . E 5 HOH A 27 627 39 HOH HOH . E 5 HOH A 28 628 29 HOH HOH . E 5 HOH A 29 629 71 HOH HOH . E 5 HOH A 30 630 79 HOH HOH . E 5 HOH A 31 631 28 HOH HOH . E 5 HOH A 32 632 168 HOH HOH . E 5 HOH A 33 633 84 HOH HOH . E 5 HOH A 34 634 109 HOH HOH . E 5 HOH A 35 635 54 HOH HOH . E 5 HOH A 36 636 56 HOH HOH . E 5 HOH A 37 637 157 HOH HOH . E 5 HOH A 38 638 128 HOH HOH . E 5 HOH A 39 639 8 HOH HOH . E 5 HOH A 40 640 130 HOH HOH . E 5 HOH A 41 641 152 HOH HOH . E 5 HOH A 42 642 50 HOH HOH . E 5 HOH A 43 643 11 HOH HOH . E 5 HOH A 44 644 4 HOH HOH . E 5 HOH A 45 645 156 HOH HOH . E 5 HOH A 46 646 89 HOH HOH . E 5 HOH A 47 647 136 HOH HOH . E 5 HOH A 48 648 69 HOH HOH . E 5 HOH A 49 649 5 HOH HOH . E 5 HOH A 50 650 6 HOH HOH . E 5 HOH A 51 651 12 HOH HOH . E 5 HOH A 52 652 123 HOH HOH . E 5 HOH A 53 653 164 HOH HOH . E 5 HOH A 54 654 3 HOH HOH . E 5 HOH A 55 655 27 HOH HOH . E 5 HOH A 56 656 64 HOH HOH . E 5 HOH A 57 657 97 HOH HOH . E 5 HOH A 58 658 36 HOH HOH . E 5 HOH A 59 659 137 HOH HOH . E 5 HOH A 60 660 163 HOH HOH . E 5 HOH A 61 661 124 HOH HOH . E 5 HOH A 62 662 96 HOH HOH . E 5 HOH A 63 663 42 HOH HOH . E 5 HOH A 64 664 116 HOH HOH . E 5 HOH A 65 665 119 HOH HOH . E 5 HOH A 66 666 38 HOH HOH . E 5 HOH A 67 667 120 HOH HOH . E 5 HOH A 68 668 90 HOH HOH . E 5 HOH A 69 669 106 HOH HOH . E 5 HOH A 70 670 9 HOH HOH . E 5 HOH A 71 671 45 HOH HOH . E 5 HOH A 72 672 107 HOH HOH . E 5 HOH A 73 673 47 HOH HOH . E 5 HOH A 74 674 32 HOH HOH . E 5 HOH A 75 675 33 HOH HOH . E 5 HOH A 76 676 94 HOH HOH . E 5 HOH A 77 677 14 HOH HOH . E 5 HOH A 78 678 101 HOH HOH . E 5 HOH A 79 679 46 HOH HOH . E 5 HOH A 80 680 53 HOH HOH . E 5 HOH A 81 681 155 HOH HOH . E 5 HOH A 82 682 37 HOH HOH . E 5 HOH A 83 683 60 HOH HOH . E 5 HOH A 84 684 61 HOH HOH . E 5 HOH A 85 685 105 HOH HOH . E 5 HOH A 86 686 19 HOH HOH . E 5 HOH A 87 687 132 HOH HOH . E 5 HOH A 88 688 153 HOH HOH . E 5 HOH A 89 689 147 HOH HOH . E 5 HOH A 90 690 166 HOH HOH . E 5 HOH A 91 691 25 HOH HOH . E 5 HOH A 92 692 162 HOH HOH . E 5 HOH A 93 693 102 HOH HOH . E 5 HOH A 94 694 118 HOH HOH . E 5 HOH A 95 695 31 HOH HOH . E 5 HOH A 96 696 88 HOH HOH . E 5 HOH A 97 697 167 HOH HOH . E 5 HOH A 98 698 115 HOH HOH . E 5 HOH A 99 699 98 HOH HOH . E 5 HOH A 100 700 30 HOH HOH . E 5 HOH A 101 701 15 HOH HOH . E 5 HOH A 102 702 20 HOH HOH . E 5 HOH A 103 703 43 HOH HOH . E 5 HOH A 104 704 23 HOH HOH . E 5 HOH A 105 705 138 HOH HOH . E 5 HOH A 106 706 80 HOH HOH . E 5 HOH A 107 707 126 HOH HOH . E 5 HOH A 108 708 18 HOH HOH . E 5 HOH A 109 709 127 HOH HOH . E 5 HOH A 110 710 65 HOH HOH . E 5 HOH A 111 711 77 HOH HOH . E 5 HOH A 112 712 146 HOH HOH . E 5 HOH A 113 713 159 HOH HOH . E 5 HOH A 114 714 134 HOH HOH . E 5 HOH A 115 715 66 HOH HOH . E 5 HOH A 116 716 82 HOH HOH . E 5 HOH A 117 717 44 HOH HOH . E 5 HOH A 118 718 49 HOH HOH . E 5 HOH A 119 719 13 HOH HOH . E 5 HOH A 120 720 2 HOH HOH . E 5 HOH A 121 721 145 HOH HOH . E 5 HOH A 122 722 135 HOH HOH . E 5 HOH A 123 723 58 HOH HOH . E 5 HOH A 124 724 158 HOH HOH . E 5 HOH A 125 725 59 HOH HOH . E 5 HOH A 126 726 72 HOH HOH . E 5 HOH A 127 727 103 HOH HOH . E 5 HOH A 128 728 161 HOH HOH . E 5 HOH A 129 729 92 HOH HOH . E 5 HOH A 130 730 151 HOH HOH . E 5 HOH A 131 731 17 HOH HOH . E 5 HOH A 132 732 86 HOH HOH . E 5 HOH A 133 733 93 HOH HOH . E 5 HOH A 134 734 62 HOH HOH . E 5 HOH A 135 735 70 HOH HOH . E 5 HOH A 136 736 57 HOH HOH . E 5 HOH A 137 737 26 HOH HOH . E 5 HOH A 138 738 55 HOH HOH . E 5 HOH A 139 739 24 HOH HOH . E 5 HOH A 140 740 81 HOH HOH . E 5 HOH A 141 741 140 HOH HOH . E 5 HOH A 142 742 48 HOH HOH . E 5 HOH A 143 743 74 HOH HOH . E 5 HOH A 144 744 125 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 10.712 1.085 -22.733 1 19.54 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . B 2 11.411 -1.225 -18.503 1 18.19 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . B 2 9.945 -5.36 -20.713 1 20.04 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . B 2 10.142 -3.15 -24.985 1 20.09 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . B 2 11.032 0.8 -21.425 1 18.69 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . B 2 11.485 1.767 -20.496 1 18.85 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . B 2 11.677 1.124 -19.291 1 18.56 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . B 2 11.335 -0.238 -19.474 1 18.24 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . B 2 12.179 1.733 -17.994 1 17.86 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . B 2 11.745 3.227 -20.82 1 18.59 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . B 2 13.052 3.306 -21.639 1 19.02 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . B 2 13.636 4.708 -21.636 1 19.89 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . B 2 14.671 4.994 -22.296 1 19.2 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . B 2 13.06 5.599 -20.961 1 20.36 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . B 2 11.042 -2.567 -18.775 1 18.88 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . B 2 11.015 -3.587 -17.78 1 18.53 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . B 2 10.588 -4.746 -18.371 1 18.92 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . B 2 10.369 -4.403 -19.784 1 19.47 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . B 2 11.379 -3.419 -16.326 1 18.51 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . B 2 10.412 -6.102 -17.789 1 18.57 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . B 2 10.24 -6.273 -16.484 1 17.64 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . B 2 9.826 -5.12 -22.072 1 19.89 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . B 2 9.321 -6.027 -23.018 1 20.67 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . B 2 9.375 -5.394 -24.258 1 20.49 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . B 2 9.91 -4.091 -24.013 1 20.19 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . B 2 8.837 -7.426 -22.69 1 20.29 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . B 2 8.984 -5.912 -25.592 1 20.58 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . B 2 8.152 -6.942 -25.774 1 20.92 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . B 2 10.285 -1.804 -24.676 1 19.86 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . B 2 10.287 -0.79 -25.738 1 20.08 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . B 2 10.442 0.393 -25.121 1 20.03 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . B 2 10.529 0.089 -23.684 1 20.03 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . B 2 10.162 -1.031 -27.235 1 19.59 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . B 2 10.459 1.752 -25.795 1 20.78 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . B 2 8.983 2.223 -25.804 1 21.56 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . B 2 8.751 3.633 -26.318 1 23.27 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . B 2 7.696 3.885 -26.953 1 24.23 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . B 2 9.584 4.562 -26.132 1 23.45 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . B 2 10.942 -0.409 -20.785 1 18.7 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . B 2 10.654 -3.099 -19.949 1 19 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . B 2 10.172 -3.956 -22.674 1 19.69 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . B 2 10.442 -1.237 -23.466 1 19.67 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . B 2 10.524 -2.082 -21.776 1 18.89 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 78 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 360 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #