data_3KHM # _model_server_result.job_id 3GluW1pMvH93bU5BSwzGww _model_server_result.datetime_utc '2024-10-13 13:18:43' _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 3khm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 3KHM # _exptl.entry_id 3KHM _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 120 _cell.entry_id 3KHM _cell.length_a 62.591 _cell.length_b 62.591 _cell.length_c 222.248 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KHM _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _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 # 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 399 A CYS 422 1_555 B FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc2 B FE HEM . A HEM 500 1_555 C N5 TPF . A TPF 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? # _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 3KHM _atom_sites.fract_transf_matrix[1][1] 0.015977 _atom_sites.fract_transf_matrix[1][2] 0.009224 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018448 _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] 0.004499 _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 1 500 500 HEM HEM . C 3 TPF A 1 501 501 TPF TPF . # 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 3.79 -24.648 23.545 1 37.23 ? CHA HEM 500 A 1 HETATM 2 C CHB HEM . . . B 2 8.207 -23.557 21.856 1 30.38 ? CHB HEM 500 A 1 HETATM 3 C CHC HEM . . . B 2 8.933 -28.25 20.848 1 35.76 ? CHC HEM 500 A 1 HETATM 4 C CHD HEM . . . B 2 4.253 -29.184 21.767 1 35.17 ? CHD HEM 500 A 1 HETATM 5 C C1A HEM . . . B 2 4.905 -23.943 23.154 1 34.26 ? C1A HEM 500 A 1 HETATM 6 C C2A HEM . . . B 2 5.07 -22.507 23.225 1 34.74 ? C2A HEM 500 A 1 HETATM 7 C C3A HEM . . . B 2 6.284 -22.207 22.76 1 34.54 ? C3A HEM 500 A 1 HETATM 8 C C4A HEM . . . B 2 6.939 -23.44 22.377 1 31.4 ? C4A HEM 500 A 1 HETATM 9 C CMA HEM . . . B 2 6.887 -20.79 22.65 1 36.16 ? CMA HEM 500 A 1 HETATM 10 C CAA HEM . . . B 2 4.023 -21.502 23.745 1 34.81 ? CAA HEM 500 A 1 HETATM 11 C CBA HEM . . . B 2 2.781 -21.559 22.863 1 36.78 ? CBA HEM 500 A 1 HETATM 12 C CGA HEM . . . B 2 1.825 -20.471 23.277 1 37.12 ? CGA HEM 500 A 1 HETATM 13 O O1A HEM . . . B 2 2.119 -19.761 24.272 1 39.3 ? O1A HEM 500 A 1 HETATM 14 O O2A HEM . . . B 2 0.77 -20.315 22.61 1 36.88 ? O2A HEM 500 A 1 HETATM 15 C C1B HEM . . . B 2 8.808 -24.734 21.469 1 33.94 ? C1B HEM 500 A 1 HETATM 16 C C2B HEM . . . B 2 10.17 -24.886 20.995 1 34.39 ? C2B HEM 500 A 1 HETATM 17 C C3B HEM . . . B 2 10.369 -26.178 20.718 1 35.22 ? C3B HEM 500 A 1 HETATM 18 C C4B HEM . . . B 2 9.142 -26.897 21.004 1 35.13 ? C4B HEM 500 A 1 HETATM 19 C CMB HEM . . . B 2 11.208 -23.752 20.839 1 27.49 ? CMB HEM 500 A 1 HETATM 20 C CAB HEM . . . B 2 11.678 -26.797 20.184 1 33.64 ? CAB HEM 500 A 1 HETATM 21 C CBB HEM . . . B 2 12.859 -26.372 20.645 1 33.47 ? CBB HEM 500 A 1 HETATM 22 C C1C HEM . . . B 2 7.722 -28.902 20.96 1 36.88 ? C1C HEM 500 A 1 HETATM 23 C C2C HEM . . . B 2 7.455 -30.286 20.609 1 36.2 ? C2C HEM 500 A 1 HETATM 24 C C3C HEM . . . B 2 6.168 -30.537 20.864 1 35.57 ? C3C HEM 500 A 1 HETATM 25 C C4C HEM . . . B 2 5.568 -29.327 21.385 1 34.29 ? C4C HEM 500 A 1 HETATM 26 C CMC HEM . . . B 2 8.48 -31.293 20.041 1 32.77 ? CMC HEM 500 A 1 HETATM 27 C CAC HEM . . . B 2 5.437 -31.879 20.644 1 35.16 ? CAC HEM 500 A 1 HETATM 28 C CBC HEM . . . B 2 6.136 -33.006 20.481 1 38.14 ? CBC HEM 500 A 1 HETATM 29 C C1D HEM . . . B 2 3.677 -28.058 22.313 1 34.88 ? C1D HEM 500 A 1 HETATM 30 C C2D HEM . . . B 2 2.285 -27.925 22.672 1 32.71 ? C2D HEM 500 A 1 HETATM 31 C C3D HEM . . . B 2 2.137 -26.508 23.229 1 34.98 ? C3D HEM 500 A 1 HETATM 32 C C4D HEM . . . B 2 3.457 -25.925 23.15 1 35.18 ? C4D HEM 500 A 1 HETATM 33 C CMD HEM . . . B 2 1.18 -28.992 22.523 1 33.73 ? CMD HEM 500 A 1 HETATM 34 C CAD HEM . . . B 2 0.849 -25.838 23.761 1 37.1 ? CAD HEM 500 A 1 HETATM 35 C CBD HEM . . . B 2 0.324 -26.615 24.963 1 39.54 ? CBD HEM 500 A 1 HETATM 36 C CGD HEM . . . B 2 -0.209 -25.654 25.994 1 41.75 ? CGD HEM 500 A 1 HETATM 37 O O1D HEM . . . B 2 0.007 -25.896 27.21 1 44.77 ? O1D HEM 500 A 1 HETATM 38 O O2D HEM . . . B 2 -0.85 -24.648 25.599 1 42.56 ? O2D HEM 500 A 1 HETATM 39 N NA HEM . . . B 2 6.063 -24.48 22.628 1 32.12 ? NA HEM 500 A 1 HETATM 40 N NB HEM . . . B 2 8.211 -25.983 21.459 1 33.95 ? NB HEM 500 A 1 HETATM 41 N NC HEM . . . B 2 6.543 -28.349 21.427 1 33.27 ? NC HEM 500 A 1 HETATM 42 N ND HEM . . . B 2 4.332 -26.862 22.606 1 33.81 ? ND HEM 500 A 1 HETATM 43 FE FE HEM . . . B 2 6.306 -26.431 22.076 1 34.92 ? FE HEM 500 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #