data_5EK2 # _model_server_result.job_id Tm4HnEGhHQ1kE637bALneQ _model_server_result.datetime_utc '2024-10-20 03:26:21' _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":"E","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 . . . E 2 25.186 31.234 -32.714 1 55.07 ? CHA HEM 501 B 1 HETATM 2 C CHB HEM . . . E 2 27.283 33.73 -36.293 1 49.64 ? CHB HEM 501 B 1 HETATM 3 C CHC HEM . . . E 2 28.54 37.177 -33.132 1 49.64 ? CHC HEM 501 B 1 HETATM 4 C CHD HEM . . . E 2 26.373 34.674 -29.559 1 49.64 ? CHD HEM 501 B 1 HETATM 5 C C1A HEM . . . E 2 25.651 31.607 -33.952 1 50.92 ? C1A HEM 501 B 1 HETATM 6 C C2A HEM . . . E 2 25.486 30.831 -35.168 1 49.64 ? C2A HEM 501 B 1 HETATM 7 C C3A HEM . . . E 2 26.05 31.523 -36.157 1 49.64 ? C3A HEM 501 B 1 HETATM 8 C C4A HEM . . . E 2 26.618 32.746 -35.599 1 49.64 ? C4A HEM 501 B 1 HETATM 9 C CMA HEM . . . E 2 26.11 31.09 -37.64 1 49.64 ? CMA HEM 501 B 1 HETATM 10 C CAA HEM . . . E 2 24.762 29.474 -35.276 1 49.64 ? CAA HEM 501 B 1 HETATM 11 C CBA HEM . . . E 2 25.649 28.269 -35.621 1 53.78 ? CBA HEM 501 B 1 HETATM 12 C CGA HEM . . . E 2 26.353 27.703 -34.396 1 61.15 ? CGA HEM 501 B 1 HETATM 13 O O1A HEM . . . E 2 26.772 26.514 -34.407 1 61.83 ? O1A HEM 501 B 1 HETATM 14 O O2A HEM . . . E 2 26.522 28.438 -33.39 1 67.82 ? O2A HEM 501 B 1 HETATM 15 C C1B HEM . . . E 2 27.798 34.881 -35.746 1 49.64 ? C1B HEM 501 B 1 HETATM 16 C C2B HEM . . . E 2 28.531 35.906 -36.459 1 49.64 ? C2B HEM 501 B 1 HETATM 17 C C3B HEM . . . E 2 28.879 36.865 -35.587 1 49.64 ? C3B HEM 501 B 1 HETATM 18 C C4B HEM . . . E 2 28.384 36.465 -34.293 1 49.64 ? C4B HEM 501 B 1 HETATM 19 C CMB HEM . . . E 2 28.811 35.847 -37.97 1 50.95 ? CMB HEM 501 B 1 HETATM 20 C CAB HEM . . . E 2 29.684 38.169 -35.806 1 55.58 ? CAB HEM 501 B 1 HETATM 21 C CBB HEM . . . E 2 30.426 38.428 -36.903 1 56.63 ? CBB HEM 501 B 1 HETATM 22 C C1C HEM . . . E 2 28.129 36.753 -31.886 1 49.64 ? C1C HEM 501 B 1 HETATM 23 C C2C HEM . . . E 2 28.453 37.389 -30.625 1 49.64 ? C2C HEM 501 B 1 HETATM 24 C C3C HEM . . . E 2 27.885 36.696 -29.643 1 49.64 ? C3C HEM 501 B 1 HETATM 25 C C4C HEM . . . E 2 27.144 35.595 -30.235 1 49.64 ? C4C HEM 501 B 1 HETATM 26 C CMC HEM . . . E 2 29.336 38.634 -30.428 1 49.64 ? CMC HEM 501 B 1 HETATM 27 C CAC HEM . . . E 2 28.01 37.062 -28.149 1 53.15 ? CAC HEM 501 B 1 HETATM 28 C CBC HEM . . . E 2 28.068 36.102 -27.221 1 54.04 ? CBC HEM 501 B 1 HETATM 29 C C1D HEM . . . E 2 25.797 33.556 -30.095 1 49.64 ? C1D HEM 501 B 1 HETATM 30 C C2D HEM . . . E 2 24.981 32.572 -29.396 1 49.64 ? C2D HEM 501 B 1 HETATM 31 C C3D HEM . . . E 2 24.65 31.614 -30.283 1 49.64 ? C3D HEM 501 B 1 HETATM 32 C C4D HEM . . . E 2 25.263 31.963 -31.555 1 51.87 ? C4D HEM 501 B 1 HETATM 33 C CMD HEM . . . E 2 24.559 32.645 -27.914 1 49.64 ? CMD HEM 501 B 1 HETATM 34 C CAD HEM . . . E 2 23.796 30.35 -30.029 1 50.74 ? CAD HEM 501 B 1 HETATM 35 C CBD HEM . . . E 2 22.359 30.53 -30.52 1 60.15 ? CBD HEM 501 B 1 HETATM 36 C CGD HEM . . . E 2 21.534 31.158 -29.427 1 64.32 ? CGD HEM 501 B 1 HETATM 37 O O1D HEM . . . E 2 20.811 32.127 -29.74 1 62.43 ? O1D HEM 501 B 1 HETATM 38 O O2D HEM . . . E 2 21.614 30.718 -28.246 1 70.04 ? O2D HEM 501 B 1 HETATM 39 N NA HEM . . . E 2 26.346 32.765 -34.24 1 49.64 ? NA HEM 501 B 1 HETATM 40 N NB HEM . . . E 2 27.725 35.257 -34.421 1 49.64 ? NB HEM 501 B 1 HETATM 41 N NC HEM . . . E 2 27.316 35.659 -31.612 1 49.64 ? NC HEM 501 B 1 HETATM 42 N ND HEM . . . E 2 25.953 33.149 -31.41 1 51.28 ? ND HEM 501 B 1 HETATM 43 FE FE HEM . . . E 2 26.797 34.268 -32.931 1 49.64 ? FE HEM 501 B 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #