data_5XXI # _model_server_result.job_id T0O6J7wIVmfuGEI8CwbtWw _model_server_result.datetime_utc '2024-12-04 07:47:52' _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 5xxi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":504}' # _entry.id 5XXI # _exptl.entry_id 5XXI _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 90 _cell.entry_id 5XXI _cell.length_a 74.571 _cell.length_b 142.958 _cell.length_c 161.42 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XXI _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 3 _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 408 A CYS 435 1_555 E FE HEM . A HEM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc2 E FE HEM . A HEM 504 1_555 G O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? # _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 5XXI _atom_sites.fract_transf_matrix[1][1] 0.01341 _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] 0.006995 _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] 0.006195 _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 2 LSN A 1 503 504 LSN lsn . E 3 HEM A 1 504 500 HEM HEM . F 4 K A 1 505 1 K K . G 5 HOH A 1 601 57 HOH HOH . G 5 HOH A 2 602 12 HOH HOH . G 5 HOH A 3 603 33 HOH HOH . G 5 HOH A 4 604 113 HOH HOH . G 5 HOH A 5 605 29 HOH HOH . G 5 HOH A 6 606 2 HOH HOH . G 5 HOH A 7 607 139 HOH HOH . G 5 HOH A 8 608 11 HOH HOH . G 5 HOH A 9 609 160 HOH HOH . G 5 HOH A 10 610 91 HOH HOH . G 5 HOH A 11 611 132 HOH HOH . G 5 HOH A 12 612 817 HOH HOH . G 5 HOH A 13 613 144 HOH HOH . G 5 HOH A 14 614 50 HOH HOH . G 5 HOH A 15 615 9 HOH HOH . G 5 HOH A 16 616 1 HOH HOH . G 5 HOH A 17 617 3 HOH HOH . G 5 HOH A 18 618 73 HOH HOH . G 5 HOH A 19 619 31 HOH HOH . G 5 HOH A 20 620 88 HOH HOH . G 5 HOH A 21 621 40 HOH HOH . G 5 HOH A 22 622 810 HOH HOH . G 5 HOH A 23 623 10 HOH HOH . G 5 HOH A 24 624 70 HOH HOH . G 5 HOH A 25 625 109 HOH HOH . G 5 HOH A 26 626 13 HOH HOH . G 5 HOH A 27 627 75 HOH HOH . G 5 HOH A 28 628 5 HOH HOH . G 5 HOH A 29 629 61 HOH HOH . G 5 HOH A 30 630 45 HOH HOH . G 5 HOH A 31 631 18 HOH HOH . G 5 HOH A 32 632 34 HOH HOH . G 5 HOH A 33 633 66 HOH HOH . G 5 HOH A 34 634 24 HOH HOH . G 5 HOH A 35 635 7 HOH HOH . G 5 HOH A 36 636 25 HOH HOH . G 5 HOH A 37 637 41 HOH HOH . G 5 HOH A 38 638 4 HOH HOH . G 5 HOH A 39 639 146 HOH HOH . G 5 HOH A 40 640 21 HOH HOH . G 5 HOH A 41 641 90 HOH HOH . G 5 HOH A 42 642 818 HOH HOH . G 5 HOH A 43 643 22 HOH HOH . G 5 HOH A 44 644 112 HOH HOH . G 5 HOH A 45 645 82 HOH HOH . G 5 HOH A 46 646 161 HOH HOH . G 5 HOH A 47 647 105 HOH HOH . G 5 HOH A 48 648 27 HOH HOH . G 5 HOH A 49 649 28 HOH HOH . G 5 HOH A 50 650 44 HOH HOH . G 5 HOH A 51 651 14 HOH HOH . G 5 HOH A 52 652 43 HOH HOH . G 5 HOH A 53 653 100 HOH HOH . G 5 HOH A 54 654 8 HOH HOH . G 5 HOH A 55 655 51 HOH HOH . G 5 HOH A 56 656 38 HOH HOH . G 5 HOH A 57 657 20 HOH HOH . G 5 HOH A 58 658 811 HOH HOH . G 5 HOH A 59 659 59 HOH HOH . G 5 HOH A 60 660 19 HOH HOH . G 5 HOH A 61 661 140 HOH HOH . G 5 HOH A 62 662 52 HOH HOH . G 5 HOH A 63 663 117 HOH HOH . G 5 HOH A 64 664 37 HOH HOH . G 5 HOH A 65 665 80 HOH HOH . G 5 HOH A 66 666 49 HOH HOH . G 5 HOH A 67 667 78 HOH HOH . G 5 HOH A 68 668 99 HOH HOH . G 5 HOH A 69 669 16 HOH HOH . G 5 HOH A 70 670 55 HOH HOH . G 5 HOH A 71 671 74 HOH HOH . G 5 HOH A 72 672 138 HOH HOH . G 5 HOH A 73 673 143 HOH HOH . G 5 HOH A 74 674 142 HOH HOH . G 5 HOH A 75 675 164 HOH HOH . G 5 HOH A 76 676 26 HOH HOH . G 5 HOH A 77 677 53 HOH HOH . G 5 HOH A 78 678 35 HOH HOH . G 5 HOH A 79 679 69 HOH HOH . G 5 HOH A 80 680 141 HOH HOH . G 5 HOH A 81 681 110 HOH HOH . G 5 HOH A 82 682 118 HOH HOH . G 5 HOH A 83 683 94 HOH HOH . G 5 HOH A 84 684 54 HOH HOH . G 5 HOH A 85 685 114 HOH HOH . G 5 HOH A 86 686 812 HOH HOH . G 5 HOH A 87 687 162 HOH HOH . G 5 HOH A 88 688 42 HOH HOH . G 5 HOH A 89 689 48 HOH HOH . G 5 HOH A 90 690 108 HOH HOH . G 5 HOH A 91 691 129 HOH HOH . G 5 HOH A 92 692 92 HOH HOH . G 5 HOH A 93 693 111 HOH HOH . G 5 HOH A 94 694 136 HOH HOH . G 5 HOH A 95 695 68 HOH HOH . G 5 HOH A 96 696 130 HOH HOH . G 5 HOH A 97 697 127 HOH HOH . G 5 HOH A 98 698 32 HOH HOH . G 5 HOH A 99 699 116 HOH HOH . G 5 HOH A 100 700 149 HOH HOH . G 5 HOH A 101 701 124 HOH HOH . G 5 HOH A 102 702 814 HOH HOH . G 5 HOH A 103 703 107 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 3 23.229 20.98 26.613 1 39.22 ? CHA HEM 504 A 1 HETATM 2 C CHB HEM . . . E 3 27.226 23.613 26.843 1 47.75 ? CHB HEM 504 A 1 HETATM 3 C CHC HEM . . . E 3 27.256 22.895 31.613 1 36.56 ? CHC HEM 504 A 1 HETATM 4 C CHD HEM . . . E 3 22.921 20.871 31.454 1 52.13 ? CHD HEM 504 A 1 HETATM 5 C C1A HEM . . . E 3 24.322 21.653 26.315 1 41.2 ? C1A HEM 504 A 1 HETATM 6 C C2A HEM . . . E 3 24.588 21.961 24.981 1 37.47 ? C2A HEM 504 A 1 HETATM 7 C C3A HEM . . . E 3 25.745 22.711 25.025 1 37.89 ? C3A HEM 504 A 1 HETATM 8 C C4A HEM . . . E 3 26.141 22.9 26.392 1 41.04 ? C4A HEM 504 A 1 HETATM 9 C CMA HEM . . . E 3 26.461 23.225 23.831 1 35.32 ? CMA HEM 504 A 1 HETATM 10 C CAA HEM . . . E 3 23.799 21.479 23.758 1 42.74 ? CAA HEM 504 A 1 HETATM 11 C CBA HEM . . . E 3 22.788 22.485 23.193 1 41.33 ? CBA HEM 504 A 1 HETATM 12 C CGA HEM . . . E 3 22.185 22.06 21.873 1 55.3 ? CGA HEM 504 A 1 HETATM 13 O O1A HEM . . . E 3 22.218 22.824 20.846 1 42.58 ? O1A HEM 504 A 1 HETATM 14 O O2A HEM . . . E 3 21.634 20.925 21.835 1 39.43 ? O2A HEM 504 A 1 HETATM 15 C C1B HEM . . . E 3 27.598 23.592 28.175 1 38.36 ? C1B HEM 504 A 1 HETATM 16 C C2B HEM . . . E 3 28.766 24.253 28.675 1 38.69 ? C2B HEM 504 A 1 HETATM 17 C C3B HEM . . . E 3 28.767 24.016 30.042 1 34.17 ? C3B HEM 504 A 1 HETATM 18 C C4B HEM . . . E 3 27.573 23.217 30.338 1 40.13 ? C4B HEM 504 A 1 HETATM 19 C CMB HEM . . . E 3 29.847 25.017 27.866 1 33.26 ? CMB HEM 504 A 1 HETATM 20 C CAB HEM . . . E 3 29.734 24.41 31.072 1 41.4 ? CAB HEM 504 A 1 HETATM 21 C CBB HEM . . . E 3 30.713 25.286 30.75 1 35.1 ? CBB HEM 504 A 1 HETATM 22 C C1C HEM . . . E 3 26.032 22.374 31.992 1 35.47 ? C1C HEM 504 A 1 HETATM 23 C C2C HEM . . . E 3 25.636 22.196 33.355 1 39 ? C2C HEM 504 A 1 HETATM 24 C C3C HEM . . . E 3 24.339 21.645 33.338 1 31.76 ? C3C HEM 504 A 1 HETATM 25 C C4C HEM . . . E 3 24.046 21.435 31.927 1 43.68 ? C4C HEM 504 A 1 HETATM 26 C CMC HEM . . . E 3 26.413 22.737 34.562 1 37.74 ? CMC HEM 504 A 1 HETATM 27 C CAC HEM . . . E 3 23.543 21.371 34.597 1 38.6 ? CAC HEM 504 A 1 HETATM 28 C CBC HEM . . . E 3 22.236 21.587 34.58 1 41.46 ? CBC HEM 504 A 1 HETATM 29 C C1D HEM . . . E 3 22.747 20.76 30.09 1 46.65 ? C1D HEM 504 A 1 HETATM 30 C C2D HEM . . . E 3 21.546 20.087 29.595 1 43.92 ? C2D HEM 504 A 1 HETATM 31 C C3D HEM . . . E 3 21.643 20.129 28.238 1 36.5 ? C3D HEM 504 A 1 HETATM 32 C C4D HEM . . . E 3 22.883 20.81 27.938 1 37.45 ? C4D HEM 504 A 1 HETATM 33 C CMD HEM . . . E 3 20.483 19.434 30.456 1 42.47 ? CMD HEM 504 A 1 HETATM 34 C CAD HEM . . . E 3 20.708 19.574 27.214 1 45.15 ? CAD HEM 504 A 1 HETATM 35 C CBD HEM . . . E 3 19.659 20.635 26.756 1 42.79 ? CBD HEM 504 A 1 HETATM 36 C CGD HEM . . . E 3 18.501 20.052 25.918 1 65.6 ? CGD HEM 504 A 1 HETATM 37 O O1D HEM . . . E 3 18.796 19.238 25 1 44.74 ? O1D HEM 504 A 1 HETATM 38 O O2D HEM . . . E 3 17.274 20.388 26.108 1 51.67 ? O2D HEM 504 A 1 HETATM 39 N NA HEM . . . E 3 25.235 22.299 27.195 1 38.97 ? NA HEM 504 A 1 HETATM 40 N NB HEM . . . E 3 26.943 22.989 29.183 1 41.19 ? NB HEM 504 A 1 HETATM 41 N NC HEM . . . E 3 25.09 21.875 31.148 1 40.89 ? NC HEM 504 A 1 HETATM 42 N ND HEM . . . E 3 23.504 21.231 29.071 1 40.31 ? ND HEM 504 A 1 HETATM 43 FE FE HEM . . . E 3 25.133 22.123 29.125 1 43.72 ? FE HEM 504 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #