data_5GNM # _model_server_result.job_id 5VTf9SM36CZYm1M5Xv4GjQ _model_server_result.datetime_utc '2024-11-18 06:56:37' _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 5gnm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 5GNM # _exptl.entry_id 5GNM _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.19 _cell.angle_gamma 90 _cell.entry_id 5GNM _cell.length_a 81.22 _cell.length_b 107.65 _cell.length_c 88.36 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GNM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I 1 1 B,F,J 2 1 C,G,K 3 1 D,H,L 4 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 E N N ? 2 F N N ? 2 G N N ? 2 H 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 347 A CYS 347 1_555 E FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc2 B SG CYS 347 B CYS 347 1_555 F FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc3 C SG CYS 347 C CYS 347 1_555 G FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc4 D SG CYS 347 D CYS 347 1_555 H FE HEM . D HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? # _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 5GNM _atom_sites.fract_transf_matrix[1][1] 0.012312 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000041 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009289 _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] 0.011317 _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 E 2 HEM A 1 501 412 HEM HEM . F 2 HEM B 1 501 412 HEM HEM . G 2 HEM C 1 501 412 HEM HEM . H 2 HEM D 1 501 412 HEM HEM . I 3 HOH A 1 601 132 HOH HOH . I 3 HOH A 2 602 88 HOH HOH . I 3 HOH A 3 603 87 HOH HOH . I 3 HOH A 4 604 128 HOH HOH . I 3 HOH A 5 605 83 HOH HOH . I 3 HOH A 6 606 108 HOH HOH . I 3 HOH A 7 607 117 HOH HOH . I 3 HOH A 8 608 127 HOH HOH . I 3 HOH A 9 609 116 HOH HOH . I 3 HOH A 10 610 21 HOH HOH . I 3 HOH A 11 611 129 HOH HOH . I 3 HOH A 12 612 133 HOH HOH . I 3 HOH A 13 613 84 HOH HOH . I 3 HOH A 14 614 85 HOH HOH . I 3 HOH A 15 615 81 HOH HOH . I 3 HOH A 16 616 2 HOH HOH . I 3 HOH A 17 617 102 HOH HOH . I 3 HOH A 18 618 80 HOH HOH . I 3 HOH A 19 619 19 HOH HOH . I 3 HOH A 20 620 20 HOH HOH . I 3 HOH A 21 621 1 HOH HOH . I 3 HOH A 22 622 18 HOH HOH . I 3 HOH A 23 623 126 HOH HOH . I 3 HOH A 24 624 82 HOH HOH . I 3 HOH A 25 625 86 HOH HOH . I 3 HOH A 26 626 97 HOH HOH . J 3 HOH B 1 601 24 HOH HOH . J 3 HOH B 2 602 26 HOH HOH . J 3 HOH B 3 603 39 HOH HOH . J 3 HOH B 4 604 35 HOH HOH . J 3 HOH B 5 605 36 HOH HOH . J 3 HOH B 6 606 98 HOH HOH . J 3 HOH B 7 607 89 HOH HOH . J 3 HOH B 8 608 30 HOH HOH . J 3 HOH B 9 609 22 HOH HOH . J 3 HOH B 10 610 92 HOH HOH . J 3 HOH B 11 611 4 HOH HOH . J 3 HOH B 12 612 3 HOH HOH . J 3 HOH B 13 613 27 HOH HOH . J 3 HOH B 14 614 118 HOH HOH . J 3 HOH B 15 615 23 HOH HOH . J 3 HOH B 16 616 25 HOH HOH . J 3 HOH B 17 617 5 HOH HOH . J 3 HOH B 18 618 94 HOH HOH . J 3 HOH B 19 619 101 HOH HOH . J 3 HOH B 20 620 32 HOH HOH . J 3 HOH B 21 621 130 HOH HOH . J 3 HOH B 22 622 93 HOH HOH . J 3 HOH B 23 623 33 HOH HOH . J 3 HOH B 24 624 31 HOH HOH . J 3 HOH B 25 625 47 HOH HOH . J 3 HOH B 26 626 46 HOH HOH . J 3 HOH B 27 627 123 HOH HOH . J 3 HOH B 28 628 28 HOH HOH . J 3 HOH B 29 629 44 HOH HOH . J 3 HOH B 30 630 99 HOH HOH . J 3 HOH B 31 631 37 HOH HOH . J 3 HOH B 32 632 90 HOH HOH . J 3 HOH B 33 633 95 HOH HOH . J 3 HOH B 34 634 41 HOH HOH . J 3 HOH B 35 635 96 HOH HOH . J 3 HOH B 36 636 119 HOH HOH . J 3 HOH B 37 637 38 HOH HOH . J 3 HOH B 38 638 42 HOH HOH . J 3 HOH B 39 639 52 HOH HOH . J 3 HOH B 40 640 40 HOH HOH . J 3 HOH B 41 641 34 HOH HOH . J 3 HOH B 42 642 100 HOH HOH . J 3 HOH B 43 643 43 HOH HOH . J 3 HOH B 44 644 45 HOH HOH . J 3 HOH B 45 645 48 HOH HOH . J 3 HOH B 46 646 29 HOH HOH . K 3 HOH C 1 601 79 HOH HOH . K 3 HOH C 2 602 60 HOH HOH . K 3 HOH C 3 603 10 HOH HOH . K 3 HOH C 4 604 53 HOH HOH . K 3 HOH C 5 605 110 HOH HOH . K 3 HOH C 6 606 49 HOH HOH . K 3 HOH C 7 607 56 HOH HOH . K 3 HOH C 8 608 50 HOH HOH . K 3 HOH C 9 609 9 HOH HOH . K 3 HOH C 10 610 55 HOH HOH . K 3 HOH C 11 611 58 HOH HOH . K 3 HOH C 12 612 54 HOH HOH . K 3 HOH C 13 613 8 HOH HOH . K 3 HOH C 14 614 7 HOH HOH . K 3 HOH C 15 615 122 HOH HOH . K 3 HOH C 16 616 109 HOH HOH . K 3 HOH C 17 617 57 HOH HOH . K 3 HOH C 18 618 6 HOH HOH . K 3 HOH C 19 619 61 HOH HOH . K 3 HOH C 20 620 107 HOH HOH . K 3 HOH C 21 621 78 HOH HOH . K 3 HOH C 22 622 62 HOH HOH . K 3 HOH C 23 623 65 HOH HOH . K 3 HOH C 24 624 106 HOH HOH . K 3 HOH C 25 625 64 HOH HOH . K 3 HOH C 26 626 51 HOH HOH . K 3 HOH C 27 627 59 HOH HOH . K 3 HOH C 28 628 120 HOH HOH . K 3 HOH C 29 629 121 HOH HOH . K 3 HOH C 30 630 63 HOH HOH . L 3 HOH D 1 601 70 HOH HOH . L 3 HOH D 2 602 131 HOH HOH . L 3 HOH D 3 603 111 HOH HOH . L 3 HOH D 4 604 113 HOH HOH . L 3 HOH D 5 605 124 HOH HOH . L 3 HOH D 6 606 77 HOH HOH . L 3 HOH D 7 607 11 HOH HOH . L 3 HOH D 8 608 103 HOH HOH . L 3 HOH D 9 609 125 HOH HOH . L 3 HOH D 10 610 17 HOH HOH . L 3 HOH D 11 611 12 HOH HOH . L 3 HOH D 12 612 72 HOH HOH . L 3 HOH D 13 613 13 HOH HOH . L 3 HOH D 14 614 114 HOH HOH . L 3 HOH D 15 615 15 HOH HOH . L 3 HOH D 16 616 74 HOH HOH . L 3 HOH D 17 617 112 HOH HOH . L 3 HOH D 18 618 73 HOH HOH . L 3 HOH D 19 619 68 HOH HOH . L 3 HOH D 20 620 14 HOH HOH . L 3 HOH D 21 621 104 HOH HOH . L 3 HOH D 22 622 75 HOH HOH . L 3 HOH D 23 623 105 HOH HOH . L 3 HOH D 24 624 66 HOH HOH . L 3 HOH D 25 625 69 HOH HOH . L 3 HOH D 26 626 71 HOH HOH . L 3 HOH D 27 627 76 HOH HOH . L 3 HOH D 28 628 16 HOH HOH . L 3 HOH D 29 629 67 HOH HOH . L 3 HOH D 30 630 115 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 11.355 -5.736 21.469 1 13.54 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . E 2 11.286 -1.083 20.151 1 13.4 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . E 2 14.213 -2.139 16.405 1 13.24 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . E 2 14.143 -6.791 17.655 1 13.27 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . E 2 11.126 -4.387 21.439 1 13.64 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . E 2 10.374 -3.696 22.412 1 13.81 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . E 2 10.351 -2.384 22.049 1 13.74 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . E 2 11.087 -2.266 20.845 1 13.58 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . E 2 9.662 -1.259 22.794 1 13.62 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . E 2 9.736 -4.309 23.638 1 14.27 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . E 2 8.264 -4.647 23.379 1 14.78 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . E 2 7.51 -4.879 24.668 1 15.23 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . E 2 8.056 -4.695 25.784 1 15.6 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . E 2 6.318 -5.261 24.625 1 15.18 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . E 2 12.096 -0.967 19.012 1 13.33 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . E 2 12.346 0.274 18.35 1 13.39 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . E 2 13.173 -0.004 17.291 1 13.27 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . E 2 13.411 -1.465 17.33 1 13.24 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . E 2 11.808 1.635 18.748 1 13.35 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . E 2 13.721 0.927 16.283 1 13.34 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . E 2 14.499 1.944 16.634 1 13.42 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . E 2 14.522 -3.498 16.445 1 13.07 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . E 2 15.487 -4.151 15.647 1 12.95 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . E 2 15.459 -5.496 15.999 1 12.92 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . E 2 14.481 -5.628 17.029 1 13.12 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . E 2 16.365 -3.504 14.595 1 12.85 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . E 2 16.294 -6.588 15.449 1 12.94 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . E 2 16.076 -7.101 14.243 1 13.13 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . E 2 13.363 -6.82 18.808 1 13.31 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . E 2 13.139 -8.098 19.508 1 13.33 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . E 2 12.37 -7.808 20.57 1 13.4 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . E 2 12.129 -6.356 20.504 1 13.47 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . E 2 13.674 -9.457 19.108 1 13.16 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . E 2 11.848 -8.78 21.607 1 13.62 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . E 2 12.772 -8.849 22.827 1 13.9 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . E 2 12.191 -9.762 23.887 1 14 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . E 2 11.022 -9.594 24.306 1 14.11 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . E 2 12.876 -10.692 24.362 1 13.98 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . E 2 11.542 -3.507 20.47 1 13.47 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . E 2 12.734 -1.95 18.373 1 13.2 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . E 2 13.939 -4.405 17.285 1 13.07 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . E 2 12.736 -5.8 19.43 1 13.35 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . E 2 12.721 -3.97 18.929 1 13.64 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 239 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 43 #