data_5EK2 # _model_server_result.job_id n3rZYTemVvvOqVzQwIgTtA _model_server_result.datetime_utc '2024-12-02 11:00:34' _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 5ek2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5EK2 # _exptl.entry_id 5EK2 _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 5EK2 _cell.length_a 86.005 _cell.length_b 96.985 _cell.length_c 131.206 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EK2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 disulf ? disulf1 A SG CYS 308 A CYS 308 1_555 B SG CYS 308 B CYS 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc1 A NE2 HIS 346 A HIS 346 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc2 C FE HEM . A HEM 501 1_555 D NAP 5PJ . A 5PJ 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc3 B NE2 HIS 346 B HIS 346 1_555 E FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc4 E FE HEM . B HEM 501 1_555 F NAP 5PJ . B 5PJ 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? # _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 173 n n CHA C4D HEM doub 174 n n CHA HHA HEM sing 175 n n CHB C4A HEM sing 176 n n CHB C1B HEM doub 177 n n CHB HHB HEM sing 178 n n CHC C4B HEM sing 179 n n CHC C1C HEM doub 180 n n CHC HHC HEM sing 181 n n CHD C4C HEM doub 182 n n CHD C1D HEM sing 183 n n CHD HHD HEM sing 184 n n C1A C2A HEM doub 185 n y C1A NA HEM sing 186 n y C2A C3A HEM sing 187 n y C2A CAA HEM sing 188 n n C3A C4A HEM doub 189 n y C3A CMA HEM sing 190 n n C4A NA HEM sing 191 n y CMA HMA HEM sing 192 n n CMA HMAA HEM sing 193 n n CMA HMAB HEM sing 194 n n CAA CBA HEM sing 195 n n CAA HAA HEM sing 196 n n CAA HAAA HEM sing 197 n n CBA CGA HEM sing 198 n n CBA HBA HEM sing 199 n n CBA HBAA HEM sing 200 n n CGA O1A HEM doub 201 n n CGA O2A HEM sing 202 n n C1B C2B HEM sing 203 n n C1B NB HEM sing 204 n n C2B C3B HEM doub 205 n n C2B CMB HEM sing 206 n n C3B C4B HEM sing 207 n n C3B CAB HEM sing 208 n n C4B NB HEM doub 209 n n CMB HMB HEM sing 210 n n CMB HMBA HEM sing 211 n n CMB HMBB HEM sing 212 n n CAB CBB HEM doub 213 n n CAB HAB HEM sing 214 n n CBB HBB HEM sing 215 n n CBB HBBA HEM sing 216 n n C1C C2C HEM sing 217 n y C1C NC HEM sing 218 n y C2C C3C HEM doub 219 n y C2C CMC HEM sing 220 n n C3C C4C HEM sing 221 n y C3C CAC HEM sing 222 n n C4C NC HEM sing 223 n y CMC HMC HEM sing 224 n n CMC HMCA HEM sing 225 n n CMC HMCB HEM sing 226 n n CAC CBC HEM doub 227 n n CAC HAC HEM sing 228 n n CBC HBC HEM sing 229 n n CBC HBCA HEM sing 230 n n C1D C2D HEM sing 231 n n C1D ND HEM doub 232 n n C2D C3D HEM doub 233 n n C2D CMD HEM sing 234 n n C3D C4D HEM sing 235 n n C3D CAD HEM sing 236 n n C4D ND HEM sing 237 n n CMD HMD HEM sing 238 n n CMD HMDA HEM sing 239 n n CMD HMDB HEM sing 240 n n CAD CBD HEM sing 241 n n CAD HAD HEM sing 242 n n CAD HADA HEM sing 243 n n CBD CGD HEM sing 244 n n CBD HBD HEM sing 245 n n CBD HBDA HEM sing 246 n n CGD O1D HEM doub 247 n n CGD O2D HEM sing 248 n n O2A H2A HEM sing 249 n n O2D H2D HEM sing 250 n n FE NA HEM sing 251 n n FE NB HEM sing 252 n n FE NC HEM sing 253 n n FE ND HEM sing 254 n n # _atom_sites.entry_id 5EK2 _atom_sites.fract_transf_matrix[1][1] 0.011627 _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] 0.010311 _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] 0.007622 _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 1 501 404 HEM HEM . D 3 5PJ A 1 502 501 5PJ 5PJ . E 2 HEM B 1 501 404 HEM HEM . F 3 5PJ B 1 502 501 5PJ 5PJ . G 4 HOH A 1 601 20 HOH HOH . G 4 HOH A 2 602 30 HOH HOH . G 4 HOH A 3 603 24 HOH HOH . G 4 HOH A 4 604 151 HOH HOH . G 4 HOH A 5 605 34 HOH HOH . G 4 HOH A 6 606 3 HOH HOH . G 4 HOH A 7 607 68 HOH HOH . G 4 HOH A 8 608 110 HOH HOH . G 4 HOH A 9 609 73 HOH HOH . G 4 HOH A 10 610 49 HOH HOH . G 4 HOH A 11 611 100 HOH HOH . G 4 HOH A 12 612 90 HOH HOH . G 4 HOH A 13 613 26 HOH HOH . G 4 HOH A 14 614 12 HOH HOH . G 4 HOH A 15 615 67 HOH HOH . G 4 HOH A 16 616 44 HOH HOH . G 4 HOH A 17 617 108 HOH HOH . G 4 HOH A 18 618 174 HOH HOH . G 4 HOH A 19 619 154 HOH HOH . G 4 HOH A 20 620 23 HOH HOH . G 4 HOH A 21 621 4 HOH HOH . G 4 HOH A 22 622 127 HOH HOH . G 4 HOH A 23 623 10 HOH HOH . G 4 HOH A 24 624 79 HOH HOH . G 4 HOH A 25 625 65 HOH HOH . G 4 HOH A 26 626 40 HOH HOH . G 4 HOH A 27 627 58 HOH HOH . G 4 HOH A 28 628 11 HOH HOH . G 4 HOH A 29 629 47 HOH HOH . G 4 HOH A 30 630 131 HOH HOH . G 4 HOH A 31 631 182 HOH HOH . G 4 HOH A 32 632 165 HOH HOH . G 4 HOH A 33 633 129 HOH HOH . G 4 HOH A 34 634 132 HOH HOH . G 4 HOH A 35 635 15 HOH HOH . G 4 HOH A 36 636 160 HOH HOH . G 4 HOH A 37 637 94 HOH HOH . H 4 HOH B 1 601 35 HOH HOH . H 4 HOH B 2 602 21 HOH HOH . H 4 HOH B 3 603 128 HOH HOH . H 4 HOH B 4 604 6 HOH HOH . H 4 HOH B 5 605 27 HOH HOH . H 4 HOH B 6 606 84 HOH HOH . H 4 HOH B 7 607 19 HOH HOH . H 4 HOH B 8 608 48 HOH HOH . H 4 HOH B 9 609 7 HOH HOH . H 4 HOH B 10 610 1 HOH HOH . H 4 HOH B 11 611 164 HOH HOH . H 4 HOH B 12 612 17 HOH HOH . H 4 HOH B 13 613 168 HOH HOH . H 4 HOH B 14 614 113 HOH HOH . H 4 HOH B 15 615 2 HOH HOH . H 4 HOH B 16 616 82 HOH HOH . H 4 HOH B 17 617 72 HOH HOH . H 4 HOH B 18 618 16 HOH HOH . H 4 HOH B 19 619 56 HOH HOH . H 4 HOH B 20 620 43 HOH HOH . H 4 HOH B 21 621 14 HOH HOH . H 4 HOH B 22 622 88 HOH HOH . H 4 HOH B 23 623 74 HOH HOH . H 4 HOH B 24 624 147 HOH HOH . H 4 HOH B 25 625 13 HOH HOH . H 4 HOH B 26 626 60 HOH HOH . H 4 HOH B 27 627 150 HOH HOH . H 4 HOH B 28 628 59 HOH HOH . H 4 HOH B 29 629 157 HOH HOH . H 4 HOH B 30 630 76 HOH HOH . H 4 HOH B 31 631 5 HOH HOH . H 4 HOH B 32 632 42 HOH HOH . H 4 HOH B 33 633 45 HOH HOH . H 4 HOH B 34 634 87 HOH HOH . H 4 HOH B 35 635 134 HOH HOH . H 4 HOH B 36 636 55 HOH HOH . H 4 HOH B 37 637 36 HOH HOH . H 4 HOH B 38 638 130 HOH HOH . H 4 HOH B 39 639 81 HOH HOH . H 4 HOH B 40 640 75 HOH HOH . H 4 HOH B 41 641 143 HOH HOH . H 4 HOH B 42 642 85 HOH HOH . H 4 HOH B 43 643 33 HOH HOH . H 4 HOH B 44 644 8 HOH HOH . H 4 HOH B 45 645 61 HOH HOH . H 4 HOH B 46 646 115 HOH HOH . H 4 HOH B 47 647 50 HOH HOH . H 4 HOH B 48 648 37 HOH HOH . H 4 HOH B 49 649 38 HOH HOH . H 4 HOH B 50 650 32 HOH HOH . H 4 HOH B 51 651 119 HOH HOH . H 4 HOH B 52 652 46 HOH HOH . H 4 HOH B 53 653 28 HOH HOH . H 4 HOH B 54 654 29 HOH HOH . H 4 HOH B 55 655 22 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 22.26 -2.499 -20.402 1 49.64 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . C 2 20.749 -6.894 -21.785 1 49.64 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . C 2 19.57 -7.919 -17.19 1 49.64 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . C 2 21.357 -3.628 -15.763 1 49.64 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . C 2 21.927 -3.588 -21.171 1 49.64 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . C 2 22.075 -3.68 -22.603 1 49.64 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . C 2 21.676 -4.9 -22.981 1 49.64 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . C 2 21.245 -5.61 -21.802 1 49.64 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . C 2 21.638 -5.51 -24.399 1 49.64 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . C 2 22.642 -2.537 -23.466 1 51.87 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . C 2 21.608 -2.01 -24.456 1 58.97 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . C 2 20.809 -0.862 -23.864 1 65.77 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . C 2 20.161 -0.122 -24.661 1 70.68 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . C 2 20.803 -0.685 -22.613 1 65.28 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . C 2 20.254 -7.543 -20.675 1 49.64 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . C 2 19.584 -8.833 -20.65 1 50.89 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . C 2 19.264 -9.118 -19.372 1 52.49 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . C 2 19.711 -8.008 -18.557 1 52 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . C 2 19.345 -9.687 -21.913 1 53.34 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . C 2 18.531 -10.334 -18.752 1 53.41 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . C 2 17.771 -11.198 -19.432 1 54.31 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . C 2 19.89 -6.827 -16.417 1 52.61 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . C 2 19.562 -6.656 -15.015 1 49.64 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . C 2 20.023 -5.475 -14.624 1 49.64 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . C 2 20.708 -4.844 -15.747 1 50.08 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . C 2 18.788 -7.646 -14.116 1 50.42 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . C 2 19.853 -4.975 -13.179 1 49.64 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . C 2 19.606 -3.691 -12.956 1 49.64 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . C 2 21.818 -2.962 -16.878 1 49.64 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . C 2 22.537 -1.681 -16.912 1 49.64 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . C 2 22.793 -1.379 -18.186 1 49.64 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . C 2 22.236 -2.441 -19.016 1 49.64 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . C 2 22.953 -0.796 -15.695 1 49.64 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . C 2 23.517 -0.093 -18.655 1 52.39 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . C 2 24.956 -0.344 -19.102 1 56.04 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . C 2 25.855 -0.523 -17.895 1 60 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . C 2 26.692 -1.469 -17.91 1 57.06 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . C 2 25.738 0.261 -16.907 1 60.7 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . C 2 21.417 -4.782 -20.711 1 49.64 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . C 2 20.311 -7.073 -19.38 1 51.98 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . C 2 20.599 -5.706 -16.829 1 55.64 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . C 2 21.65 -3.386 -18.179 1 51.15 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . C 2 20.937 -5.288 -18.79 1 49.64 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #