data_5EK4 # _model_server_result.job_id dFrSbVvj1zTJ4XdgyksscA _model_server_result.datetime_utc '2024-11-15 09:32:56' _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 5ek4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5EK4 # _exptl.entry_id 5EK4 _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 5EK4 _cell.length_a 85.768 _cell.length_b 92.357 _cell.length_c 129.928 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EK4 _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 metalc ? metalc1 A NE2 HIS 346 A HIS 346 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc2 C FE HEM . A HEM 501 1_555 D NAO 5PF . A 5PF 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc3 B NE2 HIS 346 B HIS 346 1_555 E FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc4 E FE HEM . B HEM 501 1_555 F NAO 5PF . B 5PF 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? # _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 175 n n CHA C4D HEM doub 176 n n CHA HHA HEM sing 177 n n CHB C4A HEM sing 178 n n CHB C1B HEM doub 179 n n CHB HHB HEM sing 180 n n CHC C4B HEM sing 181 n n CHC C1C HEM doub 182 n n CHC HHC HEM sing 183 n n CHD C4C HEM doub 184 n n CHD C1D HEM sing 185 n n CHD HHD HEM sing 186 n n C1A C2A HEM doub 187 n y C1A NA HEM sing 188 n y C2A C3A HEM sing 189 n y C2A CAA HEM sing 190 n n C3A C4A HEM doub 191 n y C3A CMA HEM sing 192 n n C4A NA HEM sing 193 n y CMA HMA HEM sing 194 n n CMA HMAA HEM sing 195 n n CMA HMAB HEM sing 196 n n CAA CBA HEM sing 197 n n CAA HAA HEM sing 198 n n CAA HAAA HEM sing 199 n n CBA CGA HEM sing 200 n n CBA HBA HEM sing 201 n n CBA HBAA HEM sing 202 n n CGA O1A HEM doub 203 n n CGA O2A HEM sing 204 n n C1B C2B HEM sing 205 n n C1B NB HEM sing 206 n n C2B C3B HEM doub 207 n n C2B CMB HEM sing 208 n n C3B C4B HEM sing 209 n n C3B CAB HEM sing 210 n n C4B NB HEM doub 211 n n CMB HMB HEM sing 212 n n CMB HMBA HEM sing 213 n n CMB HMBB HEM sing 214 n n CAB CBB HEM doub 215 n n CAB HAB HEM sing 216 n n CBB HBB HEM sing 217 n n CBB HBBA HEM sing 218 n n C1C C2C HEM sing 219 n y C1C NC HEM sing 220 n y C2C C3C HEM doub 221 n y C2C CMC HEM sing 222 n n C3C C4C HEM sing 223 n y C3C CAC HEM sing 224 n n C4C NC HEM sing 225 n y CMC HMC HEM sing 226 n n CMC HMCA HEM sing 227 n n CMC HMCB HEM sing 228 n n CAC CBC HEM doub 229 n n CAC HAC HEM sing 230 n n CBC HBC HEM sing 231 n n CBC HBCA HEM sing 232 n n C1D C2D HEM sing 233 n n C1D ND HEM doub 234 n n C2D C3D HEM doub 235 n n C2D CMD HEM sing 236 n n C3D C4D HEM sing 237 n n C3D CAD HEM sing 238 n n C4D ND HEM sing 239 n n CMD HMD HEM sing 240 n n CMD HMDA HEM sing 241 n n CMD HMDB HEM sing 242 n n CAD CBD HEM sing 243 n n CAD HAD HEM sing 244 n n CAD HADA HEM sing 245 n n CBD CGD HEM sing 246 n n CBD HBD HEM sing 247 n n CBD HBDA HEM sing 248 n n CGD O1D HEM doub 249 n n CGD O2D HEM sing 250 n n O2A H2A HEM sing 251 n n O2D H2D HEM sing 252 n n FE NA HEM sing 253 n n FE NB HEM sing 254 n n FE NC HEM sing 255 n n FE ND HEM sing 256 n n # _atom_sites.entry_id 5EK4 _atom_sites.fract_transf_matrix[1][1] 0.011659 _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] 0.010828 _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] 0.007697 _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 5PF A 1 502 501 5PF 5PF . E 2 HEM B 1 501 404 HEM HEM . F 3 5PF B 1 502 501 5PF 5PF . G 4 HOH A 1 601 77 HOH HOH . G 4 HOH A 2 602 84 HOH HOH . G 4 HOH A 3 603 62 HOH HOH . G 4 HOH A 4 604 39 HOH HOH . G 4 HOH A 5 605 23 HOH HOH . G 4 HOH A 6 606 40 HOH HOH . G 4 HOH A 7 607 63 HOH HOH . G 4 HOH A 8 608 15 HOH HOH . G 4 HOH A 9 609 4 HOH HOH . G 4 HOH A 10 610 12 HOH HOH . G 4 HOH A 11 611 90 HOH HOH . G 4 HOH A 12 612 96 HOH HOH . G 4 HOH A 13 613 37 HOH HOH . G 4 HOH A 14 614 53 HOH HOH . G 4 HOH A 15 615 51 HOH HOH . G 4 HOH A 16 616 19 HOH HOH . G 4 HOH A 17 617 8 HOH HOH . G 4 HOH A 18 618 94 HOH HOH . G 4 HOH A 19 619 64 HOH HOH . G 4 HOH A 20 620 9 HOH HOH . G 4 HOH A 21 621 49 HOH HOH . G 4 HOH A 22 622 79 HOH HOH . G 4 HOH A 23 623 28 HOH HOH . G 4 HOH A 24 624 27 HOH HOH . G 4 HOH A 25 625 50 HOH HOH . G 4 HOH A 26 626 47 HOH HOH . G 4 HOH A 27 627 36 HOH HOH . G 4 HOH A 28 628 16 HOH HOH . G 4 HOH A 29 629 55 HOH HOH . G 4 HOH A 30 630 95 HOH HOH . G 4 HOH A 31 631 93 HOH HOH . G 4 HOH A 32 632 85 HOH HOH . G 4 HOH A 33 633 56 HOH HOH . G 4 HOH A 34 634 92 HOH HOH . G 4 HOH A 35 635 97 HOH HOH . H 4 HOH B 1 601 59 HOH HOH . H 4 HOH B 2 602 70 HOH HOH . H 4 HOH B 3 603 72 HOH HOH . H 4 HOH B 4 604 71 HOH HOH . H 4 HOH B 5 605 5 HOH HOH . H 4 HOH B 6 606 43 HOH HOH . H 4 HOH B 7 607 46 HOH HOH . H 4 HOH B 8 608 48 HOH HOH . H 4 HOH B 9 609 35 HOH HOH . H 4 HOH B 10 610 86 HOH HOH . H 4 HOH B 11 611 88 HOH HOH . H 4 HOH B 12 612 13 HOH HOH . H 4 HOH B 13 613 33 HOH HOH . H 4 HOH B 14 614 61 HOH HOH . H 4 HOH B 15 615 3 HOH HOH . H 4 HOH B 16 616 2 HOH HOH . H 4 HOH B 17 617 83 HOH HOH . H 4 HOH B 18 618 11 HOH HOH . H 4 HOH B 19 619 1 HOH HOH . H 4 HOH B 20 620 34 HOH HOH . H 4 HOH B 21 621 22 HOH HOH . H 4 HOH B 22 622 52 HOH HOH . H 4 HOH B 23 623 6 HOH HOH . H 4 HOH B 24 624 26 HOH HOH . H 4 HOH B 25 625 29 HOH HOH . H 4 HOH B 26 626 38 HOH HOH . H 4 HOH B 27 627 24 HOH HOH . H 4 HOH B 28 628 32 HOH HOH . H 4 HOH B 29 629 7 HOH HOH . H 4 HOH B 30 630 44 HOH HOH . H 4 HOH B 31 631 21 HOH HOH . H 4 HOH B 32 632 65 HOH HOH . H 4 HOH B 33 633 66 HOH HOH . H 4 HOH B 34 634 60 HOH HOH . H 4 HOH B 35 635 68 HOH HOH . H 4 HOH B 36 636 87 HOH HOH . H 4 HOH B 37 637 78 HOH HOH . H 4 HOH B 38 638 57 HOH HOH . H 4 HOH B 39 639 17 HOH HOH . H 4 HOH B 40 640 82 HOH HOH . H 4 HOH B 41 641 42 HOH HOH . H 4 HOH B 42 642 20 HOH HOH . H 4 HOH B 43 643 30 HOH HOH . H 4 HOH B 44 644 10 HOH HOH . H 4 HOH B 45 645 31 HOH HOH . H 4 HOH B 46 646 74 HOH HOH . H 4 HOH B 47 647 58 HOH HOH . H 4 HOH B 48 648 14 HOH HOH . H 4 HOH B 49 649 80 HOH HOH . H 4 HOH B 50 650 81 HOH HOH . H 4 HOH B 51 651 67 HOH HOH . H 4 HOH B 52 652 76 HOH HOH . H 4 HOH B 53 653 73 HOH HOH . H 4 HOH B 54 654 69 HOH HOH . H 4 HOH B 55 655 25 HOH HOH . H 4 HOH B 56 656 18 HOH HOH . H 4 HOH B 57 657 41 HOH HOH . H 4 HOH B 58 658 91 HOH HOH . H 4 HOH B 59 659 89 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 21.8 2.946 20.28 1 47.72 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . C 2 19.931 7.166 21.777 1 45.08 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . C 2 18.69 8.232 17.192 1 39.82 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . C 2 20.743 4.113 15.65 1 38.18 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . C 2 21.371 3.957 21.129 1 50.45 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . C 2 21.391 4 22.594 1 52.78 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . C 2 20.873 5.169 22.979 1 52.18 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . C 2 20.504 5.916 21.796 1 49 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . C 2 20.689 5.639 24.442 1 54.77 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . C 2 21.886 2.948 23.61 1 56.8 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . C 2 21.61 1.521 23.155 1 60.9 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . C 2 20.136 1.295 23.168 1 64.09 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . C 2 19.492 1.221 22.082 1 64.18 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . C 2 19.636 1.212 24.31 1 67.31 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . C 2 19.436 7.815 20.673 1 42.29 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . C 2 18.772 9.092 20.697 1 43.13 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . C 2 18.423 9.4 19.429 1 42.13 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . C 2 18.849 8.308 18.566 1 41.27 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . C 2 18.56 9.889 22.009 1 44.72 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . C 2 17.675 10.649 18.899 1 43.18 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . C 2 16.991 11.49 19.686 1 44.62 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . C 2 19.084 7.197 16.37 1 40.15 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . C 2 18.8 7.049 14.954 1 41.38 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . C 2 19.345 5.913 14.52 1 40.23 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . C 2 20.032 5.289 15.638 1 38.73 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . C 2 17.978 8.014 14.076 1 44.36 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . C 2 19.235 5.428 13.06 1 43.34 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . C 2 19.288 4.125 12.765 1 44.67 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . C 2 21.213 3.464 16.771 1 39.51 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . C 2 21.904 2.185 16.778 1 41.5 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . C 2 22.19 1.865 18.041 1 44.14 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . C 2 21.692 2.919 18.902 1 43.75 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . C 2 22.26 1.338 15.542 1 40.16 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . C 2 22.924 0.593 18.486 1 47.79 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . C 2 24.32 1.002 18.939 1 49.87 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . C 2 25.247 0.94 17.752 1 52.81 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . C 2 26.133 1.826 17.674 1 52.21 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . C 2 25.106 0.03 16.881 1 56.69 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . C 2 20.825 5.155 20.691 1 50.3 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . C 2 19.472 7.374 19.368 1 41.96 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . C 2 19.839 6.097 16.742 1 39.76 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . C 2 21.101 3.879 18.088 1 40.31 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . C 2 20.255 5.652 18.721 1 44.2 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 43 #