data_5DYP # _model_server_result.job_id av26HfGeBu84eqV1n2LtPg _model_server_result.datetime_utc '2024-11-28 19:14:01' _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 5dyp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5DYP # _exptl.entry_id 5DYP _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 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5DYP _cell.length_a 61.134 _cell.length_b 118.448 _cell.length_c 146.947 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DYP _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 D 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 400 A CYS 400 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc2 B SG CYS 400 C CYS 400 1_555 D FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? # _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 5DYP _atom_sites.fract_transf_matrix[1][1] 0.016358 _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] 0.008443 _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] 0.006805 _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 1 501 471 HEM HEM . D 2 HEM C 1 501 471 HEM HEM . E 3 HOH A 1 601 115 HOH HOH . E 3 HOH A 2 602 69 HOH HOH . E 3 HOH A 3 603 41 HOH HOH . E 3 HOH A 4 604 88 HOH HOH . E 3 HOH A 5 605 100 HOH HOH . E 3 HOH A 6 606 23 HOH HOH . E 3 HOH A 7 607 141 HOH HOH . E 3 HOH A 8 608 93 HOH HOH . E 3 HOH A 9 609 101 HOH HOH . E 3 HOH A 10 610 96 HOH HOH . E 3 HOH A 11 611 90 HOH HOH . E 3 HOH A 12 612 36 HOH HOH . E 3 HOH A 13 613 146 HOH HOH . E 3 HOH A 14 614 112 HOH HOH . E 3 HOH A 15 615 87 HOH HOH . E 3 HOH A 16 616 9 HOH HOH . E 3 HOH A 17 617 119 HOH HOH . E 3 HOH A 18 618 7 HOH HOH . E 3 HOH A 19 619 31 HOH HOH . E 3 HOH A 20 620 86 HOH HOH . E 3 HOH A 21 621 19 HOH HOH . E 3 HOH A 22 622 14 HOH HOH . E 3 HOH A 23 623 27 HOH HOH . E 3 HOH A 24 624 30 HOH HOH . E 3 HOH A 25 625 95 HOH HOH . E 3 HOH A 26 626 81 HOH HOH . E 3 HOH A 27 627 136 HOH HOH . E 3 HOH A 28 628 50 HOH HOH . E 3 HOH A 29 629 65 HOH HOH . E 3 HOH A 30 630 21 HOH HOH . E 3 HOH A 31 631 143 HOH HOH . E 3 HOH A 32 632 15 HOH HOH . E 3 HOH A 33 633 49 HOH HOH . E 3 HOH A 34 634 109 HOH HOH . E 3 HOH A 35 635 25 HOH HOH . E 3 HOH A 36 636 110 HOH HOH . E 3 HOH A 37 637 67 HOH HOH . E 3 HOH A 38 638 71 HOH HOH . E 3 HOH A 39 639 13 HOH HOH . E 3 HOH A 40 640 62 HOH HOH . E 3 HOH A 41 641 83 HOH HOH . E 3 HOH A 42 642 3 HOH HOH . E 3 HOH A 43 643 2 HOH HOH . E 3 HOH A 44 644 73 HOH HOH . E 3 HOH A 45 645 32 HOH HOH . E 3 HOH A 46 646 35 HOH HOH . E 3 HOH A 47 647 11 HOH HOH . E 3 HOH A 48 648 4 HOH HOH . E 3 HOH A 49 649 39 HOH HOH . E 3 HOH A 50 650 82 HOH HOH . E 3 HOH A 51 651 64 HOH HOH . E 3 HOH A 52 652 78 HOH HOH . E 3 HOH A 53 653 105 HOH HOH . E 3 HOH A 54 654 8 HOH HOH . E 3 HOH A 55 655 45 HOH HOH . E 3 HOH A 56 656 24 HOH HOH . E 3 HOH A 57 657 52 HOH HOH . E 3 HOH A 58 658 56 HOH HOH . E 3 HOH A 59 659 108 HOH HOH . E 3 HOH A 60 660 124 HOH HOH . E 3 HOH A 61 661 44 HOH HOH . E 3 HOH A 62 662 114 HOH HOH . E 3 HOH A 63 663 40 HOH HOH . E 3 HOH A 64 664 54 HOH HOH . E 3 HOH A 65 665 22 HOH HOH . E 3 HOH A 66 666 92 HOH HOH . E 3 HOH A 67 667 38 HOH HOH . E 3 HOH A 68 668 1 HOH HOH . E 3 HOH A 69 669 16 HOH HOH . E 3 HOH A 70 670 147 HOH HOH . E 3 HOH A 71 671 70 HOH HOH . E 3 HOH A 72 672 72 HOH HOH . E 3 HOH A 73 673 47 HOH HOH . E 3 HOH A 74 674 84 HOH HOH . E 3 HOH A 75 675 37 HOH HOH . E 3 HOH A 76 676 29 HOH HOH . E 3 HOH A 77 677 79 HOH HOH . E 3 HOH A 78 678 46 HOH HOH . E 3 HOH A 79 679 68 HOH HOH . E 3 HOH A 80 680 20 HOH HOH . E 3 HOH A 81 681 89 HOH HOH . E 3 HOH A 82 682 28 HOH HOH . E 3 HOH A 83 683 102 HOH HOH . E 3 HOH A 84 684 26 HOH HOH . E 3 HOH A 85 685 43 HOH HOH . E 3 HOH A 86 686 60 HOH HOH . E 3 HOH A 87 687 111 HOH HOH . E 3 HOH A 88 688 97 HOH HOH . E 3 HOH A 89 689 132 HOH HOH . E 3 HOH A 90 690 42 HOH HOH . E 3 HOH A 91 691 130 HOH HOH . E 3 HOH A 92 692 135 HOH HOH . E 3 HOH A 93 693 85 HOH HOH . E 3 HOH A 94 694 107 HOH HOH . E 3 HOH A 95 695 117 HOH HOH . E 3 HOH A 96 696 142 HOH HOH . E 3 HOH A 97 697 133 HOH HOH . E 3 HOH A 98 698 144 HOH HOH . F 3 HOH C 1 601 131 HOH HOH . F 3 HOH C 2 602 139 HOH HOH . F 3 HOH C 3 603 140 HOH HOH . F 3 HOH C 4 604 129 HOH HOH . F 3 HOH C 5 605 120 HOH HOH . F 3 HOH C 6 606 128 HOH HOH . F 3 HOH C 7 607 17 HOH HOH . F 3 HOH C 8 608 134 HOH HOH . F 3 HOH C 9 609 58 HOH HOH . F 3 HOH C 10 610 59 HOH HOH . F 3 HOH C 11 611 125 HOH HOH . F 3 HOH C 12 612 66 HOH HOH . F 3 HOH C 13 613 106 HOH HOH . F 3 HOH C 14 614 51 HOH HOH . F 3 HOH C 15 615 63 HOH HOH . F 3 HOH C 16 616 55 HOH HOH . F 3 HOH C 17 617 57 HOH HOH . F 3 HOH C 18 618 126 HOH HOH . F 3 HOH C 19 619 123 HOH HOH . F 3 HOH C 20 620 80 HOH HOH . F 3 HOH C 21 621 53 HOH HOH . F 3 HOH C 22 622 113 HOH HOH . F 3 HOH C 23 623 34 HOH HOH . F 3 HOH C 24 624 121 HOH HOH . F 3 HOH C 25 625 77 HOH HOH . F 3 HOH C 26 626 5 HOH HOH . F 3 HOH C 27 627 75 HOH HOH . F 3 HOH C 28 628 12 HOH HOH . F 3 HOH C 29 629 76 HOH HOH . F 3 HOH C 30 630 18 HOH HOH . F 3 HOH C 31 631 91 HOH HOH . F 3 HOH C 32 632 104 HOH HOH . F 3 HOH C 33 633 99 HOH HOH . F 3 HOH C 34 634 94 HOH HOH . F 3 HOH C 35 635 6 HOH HOH . F 3 HOH C 36 636 137 HOH HOH . F 3 HOH C 37 637 127 HOH HOH . F 3 HOH C 38 638 74 HOH HOH . F 3 HOH C 39 639 122 HOH HOH . F 3 HOH C 40 640 148 HOH HOH . F 3 HOH C 41 641 33 HOH HOH . F 3 HOH C 42 642 98 HOH HOH . F 3 HOH C 43 643 145 HOH HOH . F 3 HOH C 44 644 48 HOH HOH . F 3 HOH C 45 645 10 HOH HOH . F 3 HOH C 46 646 116 HOH HOH . F 3 HOH C 47 647 61 HOH HOH . F 3 HOH C 48 648 138 HOH HOH . F 3 HOH C 49 649 118 HOH HOH . F 3 HOH C 50 650 103 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 . . . C 2 14.24 19.596 -12.836 1 37.41 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . C 2 9.493 20.622 -13.045 1 42.47 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . C 2 10.022 22.199 -17.603 1 45.36 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . C 2 14.572 20.529 -17.635 1 27.02 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . C 2 12.914 19.732 -12.49 1 35.93 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . C 2 12.329 19.377 -11.213 1 47.93 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . C 2 11.024 19.662 -11.267 1 49.25 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . C 2 10.728 20.207 -12.581 1 44.39 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . C 2 10.009 19.443 -10.122 1 30.88 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . C 2 13.087 18.784 -10.001 1 30.73 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . C 2 13.131 17.258 -10.079 1 25.52 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . C 2 13.627 16.684 -8.769 1 46.6 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . C 2 13.776 15.434 -8.68 1 38.72 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . C 2 13.881 17.467 -7.814 1 32.85 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . C 2 9.226 21.187 -14.278 1 30.92 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . C 2 7.974 21.792 -14.701 1 45.64 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . C 2 8.13 22.214 -15.97 1 28.88 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . C 2 9.48 21.906 -16.372 1 42.1 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . C 2 6.707 21.884 -13.811 1 35.93 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . C 2 7.144 22.94 -16.92 1 30.01 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . C 2 6.006 23.522 -16.526 1 53.66 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . C 2 11.309 21.912 -17.998 1 44.6 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . C 2 11.908 22.288 -19.259 1 44.85 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . C 2 13.171 21.823 -19.271 1 47.72 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . C 2 13.398 21.146 -18.011 1 27.48 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . C 2 11.155 23.08 -20.351 1 20.82 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . C 2 14.266 21.938 -20.363 1 37.66 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . C 2 14.133 22.63 -21.501 1 47.73 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . C 2 14.921 20.132 -16.362 1 29.46 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . C 2 16.213 19.612 -15.983 1 42.24 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . C 2 16.109 19.318 -14.486 1 36.71 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . C 2 14.766 19.696 -14.108 1 43.56 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . C 2 17.44 19.39 -16.893 1 51.61 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . C 2 17.22 18.761 -13.573 1 36.01 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . C 2 17.891 19.979 -12.934 1 33.33 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . C 2 19.266 19.647 -12.417 1 42.62 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . C 2 19.396 18.679 -11.623 1 37.51 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . C 2 20.231 20.365 -12.792 1 47.9 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . C 2 11.911 20.235 -13.3 1 57.91 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . C 2 10.124 21.279 -15.324 1 52.84 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . C 2 12.243 21.219 -17.257 1 41 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . C 2 14.1 20.165 -15.237 1 46.69 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . C 2 12.127 20.873 -15.249 1 88.54 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #