data_5Z9I # _model_server_result.job_id 4CStRWU10QHNWZw4aMku_g _model_server_result.datetime_utc '2024-10-19 20:17:47' _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 5z9i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5Z9I # _exptl.entry_id 5Z9I _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 5Z9I _cell.length_a 57.987 _cell.length_b 72.492 _cell.length_c 98.829 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Z9I _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 _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 347 A CYS 347 1_555 B FE HEM . A HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc2 B FE HEM . A HEM 401 1_555 C O HOH . A HOH 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? # _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 5Z9I _atom_sites.fract_transf_matrix[1][1] 0.017245 _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] 0.013795 _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] 0.010118 _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 1 401 1 HEM HEM . C 3 HOH A 1 501 36 HOH HOH . C 3 HOH A 2 502 108 HOH HOH . C 3 HOH A 3 503 41 HOH HOH . C 3 HOH A 4 504 100 HOH HOH . C 3 HOH A 5 505 8 HOH HOH . C 3 HOH A 6 506 103 HOH HOH . C 3 HOH A 7 507 7 HOH HOH . C 3 HOH A 8 508 23 HOH HOH . C 3 HOH A 9 509 94 HOH HOH . C 3 HOH A 10 510 31 HOH HOH . C 3 HOH A 11 511 5 HOH HOH . C 3 HOH A 12 512 46 HOH HOH . C 3 HOH A 13 513 73 HOH HOH . C 3 HOH A 14 514 10 HOH HOH . C 3 HOH A 15 515 1 HOH HOH . C 3 HOH A 16 516 38 HOH HOH . C 3 HOH A 17 517 107 HOH HOH . C 3 HOH A 18 518 2 HOH HOH . C 3 HOH A 19 519 35 HOH HOH . C 3 HOH A 20 520 60 HOH HOH . C 3 HOH A 21 521 34 HOH HOH . C 3 HOH A 22 522 32 HOH HOH . C 3 HOH A 23 523 117 HOH HOH . C 3 HOH A 24 524 61 HOH HOH . C 3 HOH A 25 525 104 HOH HOH . C 3 HOH A 26 526 50 HOH HOH . C 3 HOH A 27 527 19 HOH HOH . C 3 HOH A 28 528 26 HOH HOH . C 3 HOH A 29 529 20 HOH HOH . C 3 HOH A 30 530 30 HOH HOH . C 3 HOH A 31 531 79 HOH HOH . C 3 HOH A 32 532 56 HOH HOH . C 3 HOH A 33 533 12 HOH HOH . C 3 HOH A 34 534 95 HOH HOH . C 3 HOH A 35 535 14 HOH HOH . C 3 HOH A 36 536 22 HOH HOH . C 3 HOH A 37 537 3 HOH HOH . C 3 HOH A 38 538 21 HOH HOH . C 3 HOH A 39 539 13 HOH HOH . C 3 HOH A 40 540 72 HOH HOH . C 3 HOH A 41 541 24 HOH HOH . C 3 HOH A 42 542 17 HOH HOH . C 3 HOH A 43 543 6 HOH HOH . C 3 HOH A 44 544 15 HOH HOH . C 3 HOH A 45 545 16 HOH HOH . C 3 HOH A 46 546 51 HOH HOH . C 3 HOH A 47 547 54 HOH HOH . C 3 HOH A 48 548 53 HOH HOH . C 3 HOH A 49 549 85 HOH HOH . C 3 HOH A 50 550 48 HOH HOH . C 3 HOH A 51 551 93 HOH HOH . C 3 HOH A 52 552 18 HOH HOH . C 3 HOH A 53 553 58 HOH HOH . C 3 HOH A 54 554 29 HOH HOH . C 3 HOH A 55 555 25 HOH HOH . C 3 HOH A 56 556 84 HOH HOH . C 3 HOH A 57 557 52 HOH HOH . C 3 HOH A 58 558 37 HOH HOH . C 3 HOH A 59 559 9 HOH HOH . C 3 HOH A 60 560 109 HOH HOH . C 3 HOH A 61 561 90 HOH HOH . C 3 HOH A 62 562 27 HOH HOH . C 3 HOH A 63 563 71 HOH HOH . C 3 HOH A 64 564 33 HOH HOH . C 3 HOH A 65 565 63 HOH HOH . C 3 HOH A 66 566 83 HOH HOH . C 3 HOH A 67 567 55 HOH HOH . C 3 HOH A 68 568 65 HOH HOH . C 3 HOH A 69 569 40 HOH HOH . C 3 HOH A 70 570 43 HOH HOH . C 3 HOH A 71 571 68 HOH HOH . C 3 HOH A 72 572 28 HOH HOH . C 3 HOH A 73 573 47 HOH HOH . C 3 HOH A 74 574 57 HOH HOH . C 3 HOH A 75 575 91 HOH HOH . C 3 HOH A 76 576 69 HOH HOH . C 3 HOH A 77 577 74 HOH HOH . C 3 HOH A 78 578 66 HOH HOH . C 3 HOH A 79 579 98 HOH HOH . C 3 HOH A 80 580 45 HOH HOH . C 3 HOH A 81 581 11 HOH HOH . C 3 HOH A 82 582 76 HOH HOH . C 3 HOH A 83 583 87 HOH HOH . C 3 HOH A 84 584 81 HOH HOH . C 3 HOH A 85 585 77 HOH HOH . C 3 HOH A 86 586 44 HOH HOH . C 3 HOH A 87 587 64 HOH HOH . C 3 HOH A 88 588 82 HOH HOH . C 3 HOH A 89 589 115 HOH HOH . C 3 HOH A 90 590 96 HOH HOH . C 3 HOH A 91 591 62 HOH HOH . C 3 HOH A 92 592 112 HOH HOH . C 3 HOH A 93 593 78 HOH HOH . C 3 HOH A 94 594 80 HOH HOH . C 3 HOH A 95 595 4 HOH HOH . C 3 HOH A 96 596 70 HOH HOH . C 3 HOH A 97 597 75 HOH HOH . C 3 HOH A 98 598 42 HOH HOH . C 3 HOH A 99 599 49 HOH HOH . C 3 HOH A 100 600 92 HOH HOH . C 3 HOH A 101 601 111 HOH HOH . C 3 HOH A 102 602 67 HOH HOH . C 3 HOH A 103 603 86 HOH HOH . C 3 HOH A 104 604 39 HOH HOH . C 3 HOH A 105 605 88 HOH HOH . C 3 HOH A 106 606 105 HOH HOH . C 3 HOH A 107 607 113 HOH HOH . C 3 HOH A 108 608 59 HOH HOH . C 3 HOH A 109 609 116 HOH HOH . C 3 HOH A 110 610 114 HOH HOH . C 3 HOH A 111 611 89 HOH HOH . C 3 HOH A 112 612 101 HOH HOH . C 3 HOH A 113 613 110 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 -13.426 -15.653 18.453 1 20 ? CHA HEM 401 A 1 HETATM 2 C CHB HEM . . . B 2 -12.112 -11.476 20.207 1 20 ? CHB HEM 401 A 1 HETATM 3 C CHC HEM . . . B 2 -10.609 -10.152 15.862 1 20 ? CHC HEM 401 A 1 HETATM 4 C CHD HEM . . . B 2 -12.642 -14.01 14.083 1 20 ? CHD HEM 401 A 1 HETATM 5 C C1A HEM . . . B 2 -13.123 -14.649 19.299 1 20 ? C1A HEM 401 A 1 HETATM 6 C C2A HEM . . . B 2 -13.334 -14.723 20.655 1 20 ? C2A HEM 401 A 1 HETATM 7 C C3A HEM . . . B 2 -12.983 -13.542 21.137 1 20 ? C3A HEM 401 A 1 HETATM 8 C C4A HEM . . . B 2 -12.572 -12.754 20.09 1 20 ? C4A HEM 401 A 1 HETATM 9 C CMA HEM . . . B 2 -13.009 -13.093 22.552 1 20 ? CMA HEM 401 A 1 HETATM 10 C CAA HEM . . . B 2 -13.851 -15.921 21.412 1 20 ? CAA HEM 401 A 1 HETATM 11 C CBA HEM . . . B 2 -15.329 -15.909 21.743 1 20 ? CBA HEM 401 A 1 HETATM 12 C CGA HEM . . . B 2 -15.778 -17.065 22.59 1 20 ? CGA HEM 401 A 1 HETATM 13 O O1A HEM . . . B 2 -16.945 -17.312 22.71 1 20 ? O1A HEM 401 A 1 HETATM 14 O O2A HEM . . . B 2 -15.009 -17.768 23.183 1 20 ? O2A HEM 401 A 1 HETATM 15 C C1B HEM . . . B 2 -11.574 -10.762 19.143 1 20 ? C1B HEM 401 A 1 HETATM 16 C C2B HEM . . . B 2 -11.023 -9.505 19.291 1 20 ? C2B HEM 401 A 1 HETATM 17 C C3B HEM . . . B 2 -10.604 -9.128 18.087 1 20 ? C3B HEM 401 A 1 HETATM 18 C C4B HEM . . . B 2 -10.895 -10.204 17.193 1 20 ? C4B HEM 401 A 1 HETATM 19 C CMB HEM . . . B 2 -10.948 -8.739 20.556 1 20 ? CMB HEM 401 A 1 HETATM 20 C CAB HEM . . . B 2 -9.907 -7.936 17.64 1 20 ? CAB HEM 401 A 1 HETATM 21 C CBB HEM . . . B 2 -9.368 -7.064 18.422 1 20 ? CBB HEM 401 A 1 HETATM 22 C C1C HEM . . . B 2 -11.027 -11.088 14.979 1 20 ? C1C HEM 401 A 1 HETATM 23 C C2C HEM . . . B 2 -10.848 -11.066 13.633 1 20 ? C2C HEM 401 A 1 HETATM 24 C C3C HEM . . . B 2 -11.454 -12.155 13.138 1 20 ? C3C HEM 401 A 1 HETATM 25 C C4C HEM . . . B 2 -11.991 -12.828 14.201 1 20 ? C4C HEM 401 A 1 HETATM 26 C CMC HEM . . . B 2 -10.131 -10.012 12.888 1 20 ? CMC HEM 401 A 1 HETATM 27 C CAC HEM . . . B 2 -11.53 -12.674 11.778 1 20 ? CAC HEM 401 A 1 HETATM 28 C CBC HEM . . . B 2 -10.84 -12.236 10.777 1 20 ? CBC HEM 401 A 1 HETATM 29 C C1D HEM . . . B 2 -13.007 -14.755 15.162 1 20 ? C1D HEM 401 A 1 HETATM 30 C C2D HEM . . . B 2 -13.635 -16.019 14.992 1 20 ? C2D HEM 401 A 1 HETATM 31 C C3D HEM . . . B 2 -13.837 -16.484 16.187 1 20 ? C3D HEM 401 A 1 HETATM 32 C C4D HEM . . . B 2 -13.335 -15.494 17.098 1 20 ? C4D HEM 401 A 1 HETATM 33 C CMD HEM . . . B 2 -13.987 -16.69 13.712 1 20 ? CMD HEM 401 A 1 HETATM 34 C CAD HEM . . . B 2 -14.508 -17.775 16.495 1 20 ? CAD HEM 401 A 1 HETATM 35 C CBD HEM . . . B 2 -13.559 -18.891 16.819 1 20 ? CBD HEM 401 A 1 HETATM 36 C CGD HEM . . . B 2 -14.24 -20.121 17.314 1 20 ? CGD HEM 401 A 1 HETATM 37 O O1D HEM . . . B 2 -15.329 -20.134 17.831 1 20 ? O1D HEM 401 A 1 HETATM 38 O O2D HEM . . . B 2 -13.686 -21.162 17.208 1 20 ? O2D HEM 401 A 1 HETATM 39 N NA HEM . . . B 2 -12.672 -13.436 18.967 1 20 ? NA HEM 401 A 1 HETATM 40 N NB HEM . . . B 2 -11.471 -11.134 17.895 1 20 ? NB HEM 401 A 1 HETATM 41 N NC HEM . . . B 2 -11.718 -12.156 15.306 1 20 ? NC HEM 401 A 1 HETATM 42 N ND HEM . . . B 2 -12.848 -14.474 16.43 1 20 ? ND HEM 401 A 1 HETATM 43 FE FE HEM . . . B 2 -12.109 -12.951 17.167 1 20 ? FE HEM 401 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 43 #