data_5JOM # _model_server_result.job_id YQPiiZEI2Z6D43XkcnTElA _model_server_result.datetime_utc '2025-02-22 16:26:07' _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 5jom # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5JOM # _exptl.entry_id 5JOM _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 1 _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 5JOM _cell.length_a 38.13 _cell.length_b 46.483 _cell.length_c 84.521 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JOM _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NE2 _struct_conn.ptnr1_label_comp_id HIS _struct_conn.ptnr1_label_seq_id 94 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id HIS _struct_conn.ptnr1_auth_seq_id 93 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id FE _struct_conn.ptnr2_label_comp_id HEM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id HEM _struct_conn.ptnr2_auth_seq_id 201 _struct_conn.ptnr2_symmetry 1_555 _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 2.099 _struct_conn.pdbx_value_order ? # _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 117 n n CHA C4D HEM doub 118 n n CHA HHA HEM sing 119 n n CHB C4A HEM sing 120 n n CHB C1B HEM doub 121 n n CHB HHB HEM sing 122 n n CHC C4B HEM sing 123 n n CHC C1C HEM doub 124 n n CHC HHC HEM sing 125 n n CHD C4C HEM doub 126 n n CHD C1D HEM sing 127 n n CHD HHD HEM sing 128 n n C1A C2A HEM doub 129 n y C1A NA HEM sing 130 n y C2A C3A HEM sing 131 n y C2A CAA HEM sing 132 n n C3A C4A HEM doub 133 n y C3A CMA HEM sing 134 n n C4A NA HEM sing 135 n y CMA HMA HEM sing 136 n n CMA HMAA HEM sing 137 n n CMA HMAB HEM sing 138 n n CAA CBA HEM sing 139 n n CAA HAA HEM sing 140 n n CAA HAAA HEM sing 141 n n CBA CGA HEM sing 142 n n CBA HBA HEM sing 143 n n CBA HBAA HEM sing 144 n n CGA O1A HEM doub 145 n n CGA O2A HEM sing 146 n n C1B C2B HEM sing 147 n n C1B NB HEM sing 148 n n C2B C3B HEM doub 149 n n C2B CMB HEM sing 150 n n C3B C4B HEM sing 151 n n C3B CAB HEM sing 152 n n C4B NB HEM doub 153 n n CMB HMB HEM sing 154 n n CMB HMBA HEM sing 155 n n CMB HMBB HEM sing 156 n n CAB CBB HEM doub 157 n n CAB HAB HEM sing 158 n n CBB HBB HEM sing 159 n n CBB HBBA HEM sing 160 n n C1C C2C HEM sing 161 n y C1C NC HEM sing 162 n y C2C C3C HEM doub 163 n y C2C CMC HEM sing 164 n n C3C C4C HEM sing 165 n y C3C CAC HEM sing 166 n n C4C NC HEM sing 167 n y CMC HMC HEM sing 168 n n CMC HMCA HEM sing 169 n n CMC HMCB HEM sing 170 n n CAC CBC HEM doub 171 n n CAC HAC HEM sing 172 n n CBC HBC HEM sing 173 n n CBC HBCA HEM sing 174 n n C1D C2D HEM sing 175 n n C1D ND HEM doub 176 n n C2D C3D HEM doub 177 n n C2D CMD HEM sing 178 n n C3D C4D HEM sing 179 n n C3D CAD HEM sing 180 n n C4D ND HEM sing 181 n n CMD HMD HEM sing 182 n n CMD HMDA HEM sing 183 n n CMD HMDB HEM sing 184 n n CAD CBD HEM sing 185 n n CAD HAD HEM sing 186 n n CAD HADA HEM sing 187 n n CBD CGD HEM sing 188 n n CBD HBD HEM sing 189 n n CBD HBDA HEM sing 190 n n CGD O1D HEM doub 191 n n CGD O2D HEM sing 192 n n O2A H2A HEM sing 193 n n O2D H2D HEM sing 194 n n FE NA HEM sing 195 n n FE NB HEM sing 196 n n FE NC HEM sing 197 n n FE ND HEM sing 198 n n # _atom_sites.entry_id 5JOM _atom_sites.fract_transf_matrix[1][1] 0.026226 _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] 0.021513 _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] 0.011831 _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 B 2 HEM A 1 201 155 HEM HEM . C 3 SO4 A 1 202 1 SO4 SO4 . D 4 CMO A 1 203 1 CMO CMO . E 5 HOH A 1 301 16 HOH HOH . E 5 HOH A 2 302 20 HOH HOH . E 5 HOH A 3 303 4 HOH HOH . E 5 HOH A 4 304 5 HOH HOH . E 5 HOH A 5 305 2 HOH HOH . E 5 HOH A 6 306 21 HOH HOH . E 5 HOH A 7 307 6 HOH HOH . E 5 HOH A 8 308 1 HOH HOH . E 5 HOH A 9 309 17 HOH HOH . E 5 HOH A 10 310 12 HOH HOH . E 5 HOH A 11 311 18 HOH HOH . E 5 HOH A 12 312 15 HOH HOH . E 5 HOH A 13 313 13 HOH HOH . E 5 HOH A 14 314 7 HOH HOH . E 5 HOH A 15 315 3 HOH HOH . E 5 HOH A 16 316 10 HOH HOH . E 5 HOH A 17 317 9 HOH HOH . E 5 HOH A 18 318 14 HOH HOH . E 5 HOH A 19 319 8 HOH HOH . E 5 HOH A 20 320 19 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 . . . B 2 -15.773 -5.577 19.616 1 34.99 ? CHA HEM 201 A 1 HETATM 2 C CHB HEM . . . B 2 -13.624 -1.885 17.426 1 27.49 ? CHB HEM 201 A 1 HETATM 3 C CHC HEM . . . B 2 -9.713 -4.582 16.579 1 29.72 ? CHC HEM 201 A 1 HETATM 4 C CHD HEM . . . B 2 -11.753 -8.256 18.958 1 32.25 ? CHD HEM 201 A 1 HETATM 5 C C1A HEM . . . B 2 -15.519 -4.347 19.074 1 34.56 ? C1A HEM 201 A 1 HETATM 6 C C2A HEM . . . B 2 -16.414 -3.268 19.084 1 33.97 ? C2A HEM 201 A 1 HETATM 7 C C3A HEM . . . B 2 -15.806 -2.225 18.489 1 31.47 ? C3A HEM 201 A 1 HETATM 8 C C4A HEM . . . B 2 -14.541 -2.654 18.103 1 30.78 ? C4A HEM 201 A 1 HETATM 9 C CMA HEM . . . B 2 -16.363 -0.852 18.249 1 32.94 ? CMA HEM 201 A 1 HETATM 10 C CAA HEM . . . B 2 -17.797 -3.32 19.711 1 36.49 ? CAA HEM 201 A 1 HETATM 11 C CBA HEM . . . B 2 -17.824 -2.745 21.108 1 34.93 ? CBA HEM 201 A 1 HETATM 12 C CGA HEM . . . B 2 -16.742 -3.239 22 1 40.11 ? CGA HEM 201 A 1 HETATM 13 O O1A HEM . . . B 2 -16.8 -4.406 22.4 1 41.16 ? O1A HEM 201 A 1 HETATM 14 O O2A HEM . . . B 2 -15.805 -2.49 22.306 1 39.82 ? O2A HEM 201 A 1 HETATM 15 C C1B HEM . . . B 2 -12.387 -2.298 16.997 1 28.19 ? C1B HEM 201 A 1 HETATM 16 C C2B HEM . . . B 2 -11.475 -1.486 16.258 1 30.11 ? C2B HEM 201 A 1 HETATM 17 C C3B HEM . . . B 2 -10.342 -2.223 16.018 1 31.79 ? C3B HEM 201 A 1 HETATM 18 C C4B HEM . . . B 2 -10.618 -3.538 16.629 1 31.26 ? C4B HEM 201 A 1 HETATM 19 C CMB HEM . . . B 2 -11.72 -0.081 15.845 1 30.1 ? CMB HEM 201 A 1 HETATM 20 C CAB HEM . . . B 2 -9.137 -1.909 15.204 1 33.14 ? CAB HEM 201 A 1 HETATM 21 C CBB HEM . . . B 2 -9.055 -0.907 14.341 1 33.12 ? CBB HEM 201 A 1 HETATM 22 C C1C HEM . . . B 2 -9.9 -5.834 17.129 1 28.66 ? C1C HEM 201 A 1 HETATM 23 C C2C HEM . . . B 2 -9.059 -6.941 16.955 1 26.5 ? C2C HEM 201 A 1 HETATM 24 C C3C HEM . . . B 2 -9.634 -8.021 17.67 1 29.39 ? C3C HEM 201 A 1 HETATM 25 C C4C HEM . . . B 2 -10.84 -7.519 18.231 1 29.97 ? C4C HEM 201 A 1 HETATM 26 C CMC HEM . . . B 2 -7.773 -6.963 16.196 1 27.76 ? CMC HEM 201 A 1 HETATM 27 C CAC HEM . . . B 2 -9.238 -9.464 17.838 1 35.9 ? CAC HEM 201 A 1 HETATM 28 C CBC HEM . . . B 2 -8.248 -10.087 17.22 1 43.69 ? CBC HEM 201 A 1 HETATM 29 C C1D HEM . . . B 2 -13.03 -7.76 19.308 1 30.9 ? C1D HEM 201 A 1 HETATM 30 C C2D HEM . . . B 2 -14.014 -8.627 19.983 1 32.42 ? C2D HEM 201 A 1 HETATM 31 C C3D HEM . . . B 2 -15.131 -7.907 20.158 1 34.21 ? C3D HEM 201 A 1 HETATM 32 C C4D HEM . . . B 2 -14.82 -6.583 19.593 1 35.21 ? C4D HEM 201 A 1 HETATM 33 C CMD HEM . . . B 2 -13.862 -10.051 20.38 1 34.87 ? CMD HEM 201 A 1 HETATM 34 C CAD HEM . . . B 2 -16.421 -8.378 20.749 1 36.14 ? CAD HEM 201 A 1 HETATM 35 C CBD HEM . . . B 2 -17.172 -8.85 19.48 1 40.23 ? CBD HEM 201 A 1 HETATM 36 C CGD HEM . . . B 2 -18.608 -9.38 19.687 1 45.94 ? CGD HEM 201 A 1 HETATM 37 O O1D HEM . . . B 2 -18.832 -10.562 19.931 1 46.66 ? O1D HEM 201 A 1 HETATM 38 O O2D HEM . . . B 2 -19.623 -8.684 19.573 1 46.91 ? O2D HEM 201 A 1 HETATM 39 N NA HEM . . . B 2 -14.379 -3.954 18.472 1 31.43 ? NA HEM 201 A 1 HETATM 40 N NB HEM . . . B 2 -11.844 -3.481 17.186 1 29.75 ? NB HEM 201 A 1 HETATM 41 N NC HEM . . . B 2 -10.997 -6.206 17.858 1 27.51 ? NC HEM 201 A 1 HETATM 42 N ND HEM . . . B 2 -13.539 -6.54 19.114 1 32.79 ? ND HEM 201 A 1 HETATM 43 FE FE HEM . . . B 2 -12.726 -5.058 18.206 1 30.9 ? FE HEM 201 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #