data_3DAX # _model_server_result.job_id fG1awkl1zWtrOT7ZXW4w7w _model_server_result.datetime_utc '2024-12-02 23:00:01' _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 3dax # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 3DAX # _exptl.entry_id 3DAX _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 64.36 _cell.angle_beta 75.23 _cell.angle_gamma 72.17 _cell.entry_id 3DAX _cell.length_a 55.339 _cell.length_b 80.159 _cell.length_c 84.937 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DAX _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 427 A CYS 444 1_555 C FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc2 B SG CYS 427 B CYS 444 1_555 E FE HEM . B HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? # _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 3DAX _atom_sites.fract_transf_matrix[1][1] 0.01807 _atom_sites.fract_transf_matrix[1][2] -0.005812 _atom_sites.fract_transf_matrix[1][3] -0.002739 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013105 _atom_sites.fract_transf_matrix[2][3] -0.00547 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.013194 _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 C 2 HEM A 1 601 601 HEM HEM . D 3 UNX A 1 1 1 UNX UNX . E 2 HEM B 1 601 601 HEM HEM . F 3 UNX B 1 2 2 UNX UNX . G 4 HOH A 1 602 5 HOH HOH . G 4 HOH A 2 603 7 HOH HOH . G 4 HOH A 3 604 8 HOH HOH . G 4 HOH A 4 605 9 HOH HOH . G 4 HOH A 5 606 12 HOH HOH . G 4 HOH A 6 607 15 HOH HOH . G 4 HOH A 7 608 18 HOH HOH . G 4 HOH A 8 609 19 HOH HOH . G 4 HOH A 9 610 20 HOH HOH . G 4 HOH A 10 611 21 HOH HOH . G 4 HOH A 11 612 23 HOH HOH . G 4 HOH A 12 613 24 HOH HOH . G 4 HOH A 13 614 25 HOH HOH . G 4 HOH A 14 615 27 HOH HOH . G 4 HOH A 15 616 31 HOH HOH . G 4 HOH A 16 617 34 HOH HOH . G 4 HOH A 17 618 36 HOH HOH . G 4 HOH A 18 619 37 HOH HOH . G 4 HOH A 19 620 40 HOH HOH . G 4 HOH A 20 621 41 HOH HOH . G 4 HOH A 21 622 42 HOH HOH . G 4 HOH A 22 623 44 HOH HOH . G 4 HOH A 23 624 45 HOH HOH . G 4 HOH A 24 625 51 HOH HOH . G 4 HOH A 25 626 52 HOH HOH . G 4 HOH A 26 627 53 HOH HOH . G 4 HOH A 27 628 55 HOH HOH . G 4 HOH A 28 629 56 HOH HOH . G 4 HOH A 29 630 57 HOH HOH . G 4 HOH A 30 631 60 HOH HOH . G 4 HOH A 31 632 64 HOH HOH . G 4 HOH A 32 633 67 HOH HOH . G 4 HOH A 33 634 74 HOH HOH . G 4 HOH A 34 635 75 HOH HOH . G 4 HOH A 35 636 76 HOH HOH . G 4 HOH A 36 637 77 HOH HOH . G 4 HOH A 37 638 78 HOH HOH . G 4 HOH A 38 639 96 HOH HOH . G 4 HOH A 39 640 97 HOH HOH . G 4 HOH A 40 641 98 HOH HOH . G 4 HOH A 41 642 99 HOH HOH . G 4 HOH A 42 643 100 HOH HOH . G 4 HOH A 43 644 101 HOH HOH . G 4 HOH A 44 645 102 HOH HOH . G 4 HOH A 45 646 103 HOH HOH . G 4 HOH A 46 647 104 HOH HOH . G 4 HOH A 47 648 105 HOH HOH . G 4 HOH A 48 649 106 HOH HOH . G 4 HOH A 49 650 107 HOH HOH . G 4 HOH A 50 651 108 HOH HOH . G 4 HOH A 51 652 109 HOH HOH . G 4 HOH A 52 653 110 HOH HOH . G 4 HOH A 53 654 111 HOH HOH . G 4 HOH A 54 655 112 HOH HOH . G 4 HOH A 55 656 113 HOH HOH . G 4 HOH A 56 657 114 HOH HOH . G 4 HOH A 57 658 115 HOH HOH . G 4 HOH A 58 659 117 HOH HOH . G 4 HOH A 59 660 122 HOH HOH . G 4 HOH A 60 661 126 HOH HOH . G 4 HOH A 61 662 128 HOH HOH . G 4 HOH A 62 663 129 HOH HOH . H 4 HOH B 1 602 1 HOH HOH . H 4 HOH B 2 603 2 HOH HOH . H 4 HOH B 3 604 3 HOH HOH . H 4 HOH B 4 605 4 HOH HOH . H 4 HOH B 5 606 6 HOH HOH . H 4 HOH B 6 607 10 HOH HOH . H 4 HOH B 7 608 11 HOH HOH . H 4 HOH B 8 609 13 HOH HOH . H 4 HOH B 9 610 14 HOH HOH . H 4 HOH B 10 611 16 HOH HOH . H 4 HOH B 11 612 17 HOH HOH . H 4 HOH B 12 613 22 HOH HOH . H 4 HOH B 13 614 26 HOH HOH . H 4 HOH B 14 615 28 HOH HOH . H 4 HOH B 15 616 29 HOH HOH . H 4 HOH B 16 617 30 HOH HOH . H 4 HOH B 17 618 32 HOH HOH . H 4 HOH B 18 619 33 HOH HOH . H 4 HOH B 19 620 35 HOH HOH . H 4 HOH B 20 621 38 HOH HOH . H 4 HOH B 21 622 39 HOH HOH . H 4 HOH B 22 623 43 HOH HOH . H 4 HOH B 23 624 46 HOH HOH . H 4 HOH B 24 625 47 HOH HOH . H 4 HOH B 25 626 48 HOH HOH . H 4 HOH B 26 627 49 HOH HOH . H 4 HOH B 27 628 50 HOH HOH . H 4 HOH B 28 629 54 HOH HOH . H 4 HOH B 29 630 58 HOH HOH . H 4 HOH B 30 631 59 HOH HOH . H 4 HOH B 31 632 61 HOH HOH . H 4 HOH B 32 633 62 HOH HOH . H 4 HOH B 33 634 63 HOH HOH . H 4 HOH B 34 635 65 HOH HOH . H 4 HOH B 35 636 66 HOH HOH . H 4 HOH B 36 637 68 HOH HOH . H 4 HOH B 37 638 69 HOH HOH . H 4 HOH B 38 639 70 HOH HOH . H 4 HOH B 39 640 71 HOH HOH . H 4 HOH B 40 641 72 HOH HOH . H 4 HOH B 41 642 73 HOH HOH . H 4 HOH B 42 643 79 HOH HOH . H 4 HOH B 43 644 80 HOH HOH . H 4 HOH B 44 645 81 HOH HOH . H 4 HOH B 45 646 82 HOH HOH . H 4 HOH B 46 647 83 HOH HOH . H 4 HOH B 47 648 84 HOH HOH . H 4 HOH B 48 649 85 HOH HOH . H 4 HOH B 49 650 86 HOH HOH . H 4 HOH B 50 651 87 HOH HOH . H 4 HOH B 51 652 88 HOH HOH . H 4 HOH B 52 653 89 HOH HOH . H 4 HOH B 53 654 90 HOH HOH . H 4 HOH B 54 655 91 HOH HOH . H 4 HOH B 55 656 92 HOH HOH . H 4 HOH B 56 657 93 HOH HOH . H 4 HOH B 57 658 94 HOH HOH . H 4 HOH B 58 659 95 HOH HOH . H 4 HOH B 59 660 116 HOH HOH . H 4 HOH B 60 661 118 HOH HOH . H 4 HOH B 61 662 119 HOH HOH . H 4 HOH B 62 663 120 HOH HOH . H 4 HOH B 63 664 121 HOH HOH . H 4 HOH B 64 665 123 HOH HOH . H 4 HOH B 65 666 124 HOH HOH . H 4 HOH B 66 667 125 HOH HOH . H 4 HOH B 67 668 127 HOH HOH . H 4 HOH B 68 669 130 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 2 0.962 -7.216 -1.277 1 24.85 ? CHA HEM 601 B 1 HETATM 2 C CHB HEM . . . E 2 -1.628 -3.226 -0.48 1 22.54 ? CHB HEM 601 B 1 HETATM 3 C CHC HEM . . . E 2 0.755 -2.459 3.643 1 25.79 ? CHC HEM 601 B 1 HETATM 4 C CHD HEM . . . E 2 2.871 -6.715 3.199 1 24.7 ? CHD HEM 601 B 1 HETATM 5 C C1A HEM . . . E 2 0.063 -6.203 -1.438 1 24.49 ? C1A HEM 601 B 1 HETATM 6 C C2A HEM . . . E 2 -0.797 -5.972 -2.575 1 26.88 ? C2A HEM 601 B 1 HETATM 7 C C3A HEM . . . E 2 -1.507 -4.88 -2.361 1 25.08 ? C3A HEM 601 B 1 HETATM 8 C C4A HEM . . . E 2 -1.113 -4.352 -1.076 1 26.52 ? C4A HEM 601 B 1 HETATM 9 C CMA HEM . . . E 2 -2.545 -4.271 -3.333 1 22.6 ? CMA HEM 601 B 1 HETATM 10 C CAA HEM . . . E 2 -0.908 -6.834 -3.847 1 32.71 ? CAA HEM 601 B 1 HETATM 11 C CBA HEM . . . E 2 -2.213 -7.61 -3.792 1 39.88 ? CBA HEM 601 B 1 HETATM 12 C CGA HEM . . . E 2 -2.328 -8.533 -5.007 1 46.15 ? CGA HEM 601 B 1 HETATM 13 O O1A HEM . . . E 2 -1.534 -9.511 -5.064 1 48.81 ? O1A HEM 601 B 1 HETATM 14 O O2A HEM . . . E 2 -3.223 -8.303 -5.901 1 46.47 ? O2A HEM 601 B 1 HETATM 15 C C1B HEM . . . E 2 -1.201 -2.68 0.703 1 21.37 ? C1B HEM 601 B 1 HETATM 16 C C2B HEM . . . E 2 -1.689 -1.451 1.293 1 25.57 ? C2B HEM 601 B 1 HETATM 17 C C3B HEM . . . E 2 -1.022 -1.248 2.434 1 19.39 ? C3B HEM 601 B 1 HETATM 18 C C4B HEM . . . E 2 -0.109 -2.324 2.585 1 22.35 ? C4B HEM 601 B 1 HETATM 19 C CMB HEM . . . E 2 -2.778 -0.572 0.65 1 23.53 ? CMB HEM 601 B 1 HETATM 20 C CAB HEM . . . E 2 -1.109 -0.102 3.452 1 22.31 ? CAB HEM 601 B 1 HETATM 21 C CBB HEM . . . E 2 -2.113 0.743 3.468 1 26.07 ? CBB HEM 601 B 1 HETATM 22 C C1C HEM . . . E 2 1.477 -3.566 3.932 1 24.78 ? C1C HEM 601 B 1 HETATM 23 C C2C HEM . . . E 2 2.162 -3.813 5.169 1 24.33 ? C2C HEM 601 B 1 HETATM 24 C C3C HEM . . . E 2 2.75 -5.008 5.062 1 24.08 ? C3C HEM 601 B 1 HETATM 25 C C4C HEM . . . E 2 2.467 -5.526 3.737 1 25.22 ? C4C HEM 601 B 1 HETATM 26 C CMC HEM . . . E 2 2.222 -2.855 6.393 1 17.67 ? CMC HEM 601 B 1 HETATM 27 C CAC HEM . . . E 2 3.607 -5.618 6.179 1 27.83 ? CAC HEM 601 B 1 HETATM 28 C CBC HEM . . . E 2 4.378 -6.676 5.931 1 34.26 ? CBC HEM 601 B 1 HETATM 29 C C1D HEM . . . E 2 2.655 -7.152 1.928 1 24.14 ? C1D HEM 601 B 1 HETATM 30 C C2D HEM . . . E 2 3.37 -8.258 1.335 1 24.01 ? C2D HEM 601 B 1 HETATM 31 C C3D HEM . . . E 2 2.782 -8.446 -0.061 1 26.89 ? C3D HEM 601 B 1 HETATM 32 C C4D HEM . . . E 2 1.756 -7.412 -0.184 1 25.76 ? C4D HEM 601 B 1 HETATM 33 C CMD HEM . . . E 2 4.503 -9.086 2.007 1 25.66 ? CMD HEM 601 B 1 HETATM 34 C CAD HEM . . . E 2 3.201 -9.48 -1.134 1 30.83 ? CAD HEM 601 B 1 HETATM 35 C CBD HEM . . . E 2 2.083 -10.51 -1.266 1 40.72 ? CBD HEM 601 B 1 HETATM 36 C CGD HEM . . . E 2 2.575 -11.871 -1.76 1 46.25 ? CGD HEM 601 B 1 HETATM 37 O O1D HEM . . . E 2 2.35 -12.922 -1.056 1 50.69 ? O1D HEM 601 B 1 HETATM 38 O O2D HEM . . . E 2 3.178 -11.903 -2.867 1 49.54 ? O2D HEM 601 B 1 HETATM 39 N NA HEM . . . E 2 -0.144 -5.212 -0.525 1 24.47 ? NA HEM 601 B 1 HETATM 40 N NB HEM . . . E 2 -0.238 -3.171 1.544 1 23.05 ? NB HEM 601 B 1 HETATM 41 N NC HEM . . . E 2 1.64 -4.628 3.103 1 23.93 ? NC HEM 601 B 1 HETATM 42 N ND HEM . . . E 2 1.705 -6.673 1.006 1 26.09 ? ND HEM 601 B 1 HETATM 43 FE FE HEM . . . E 2 0.592 -4.969 1.354 1 25.06 ? FE HEM 601 B 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 82 _model_server_stats.create_model_time_ms 71 _model_server_stats.query_time_ms 670 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #