data_3DDR # _model_server_result.job_id QuB5IRugs26SWYcy2f7G9Q _model_server_result.datetime_utc '2024-12-12 02:54:09' _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 3ddr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":200}' # _entry.id 3DDR # _exptl.entry_id 3DDR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 5 _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 3DDR _cell.length_a 157.41 _cell.length_b 162.72 _cell.length_c 597.01 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DDR _symmetry.cell_setting ? _symmetry.Int_Tables_number 22 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'F 2 2 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,E,F,M,O 1 1 B,D,G,H,I,J,K,L,N,P,Q 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 ? 5 M N N ? 5 N 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 538 A CYS 538 1_555 A SG CYS 546 A CYS 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 715 A CYS 715 1_555 A SG CYS 750 A CYS 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 B SG CYS 538 B CYS 538 1_555 B SG CYS 546 B CYS 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 715 B CYS 715 1_555 B SG CYS 750 B CYS 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc1 C OH TYR 93 C TYR 75 1_555 M FE HEM . C HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc2 D OH TYR 93 D TYR 75 1_555 N FE HEM . D HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? # _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 142 n n CHA C4D HEM doub 143 n n CHA HHA HEM sing 144 n n CHB C4A HEM sing 145 n n CHB C1B HEM doub 146 n n CHB HHB HEM sing 147 n n CHC C4B HEM sing 148 n n CHC C1C HEM doub 149 n n CHC HHC HEM sing 150 n n CHD C4C HEM doub 151 n n CHD C1D HEM sing 152 n n CHD HHD HEM sing 153 n n C1A C2A HEM doub 154 n y C1A NA HEM sing 155 n y C2A C3A HEM sing 156 n y C2A CAA HEM sing 157 n n C3A C4A HEM doub 158 n y C3A CMA HEM sing 159 n n C4A NA HEM sing 160 n y CMA HMA HEM sing 161 n n CMA HMAA HEM sing 162 n n CMA HMAB HEM sing 163 n n CAA CBA HEM sing 164 n n CAA HAA HEM sing 165 n n CAA HAAA HEM sing 166 n n CBA CGA HEM sing 167 n n CBA HBA HEM sing 168 n n CBA HBAA HEM sing 169 n n CGA O1A HEM doub 170 n n CGA O2A HEM sing 171 n n C1B C2B HEM sing 172 n n C1B NB HEM sing 173 n n C2B C3B HEM doub 174 n n C2B CMB HEM sing 175 n n C3B C4B HEM sing 176 n n C3B CAB HEM sing 177 n n C4B NB HEM doub 178 n n CMB HMB HEM sing 179 n n CMB HMBA HEM sing 180 n n CMB HMBB HEM sing 181 n n CAB CBB HEM doub 182 n n CAB HAB HEM sing 183 n n CBB HBB HEM sing 184 n n CBB HBBA HEM sing 185 n n C1C C2C HEM sing 186 n y C1C NC HEM sing 187 n y C2C C3C HEM doub 188 n y C2C CMC HEM sing 189 n n C3C C4C HEM sing 190 n y C3C CAC HEM sing 191 n n C4C NC HEM sing 192 n y CMC HMC HEM sing 193 n n CMC HMCA HEM sing 194 n n CMC HMCB HEM sing 195 n n CAC CBC HEM doub 196 n n CAC HAC HEM sing 197 n n CBC HBC HEM sing 198 n n CBC HBCA HEM sing 199 n n C1D C2D HEM sing 200 n n C1D ND HEM doub 201 n n C2D C3D HEM doub 202 n n C2D CMD HEM sing 203 n n C3D C4D HEM sing 204 n n C3D CAD HEM sing 205 n n C4D ND HEM sing 206 n n CMD HMD HEM sing 207 n n CMD HMDA HEM sing 208 n n CMD HMDB HEM sing 209 n n CAD CBD HEM sing 210 n n CAD HAD HEM sing 211 n n CAD HADA HEM sing 212 n n CBD CGD HEM sing 213 n n CBD HBD HEM sing 214 n n CBD HBDA HEM sing 215 n n CGD O1D HEM doub 216 n n CGD O2D HEM sing 217 n n O2A H2A HEM sing 218 n n O2D H2D HEM sing 219 n n FE NA HEM sing 220 n n FE NB HEM sing 221 n n FE NC HEM sing 222 n n FE ND HEM sing 223 n n # _atom_sites.entry_id 3DDR _atom_sites.fract_transf_matrix[1][1] 0.006353 _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] 0.006146 _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] 0.001675 _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 E 3 NA A 1 866 1 NA NA . F 4 GOL A 1 867 2 GOL GOL . G 3 NA B 1 866 2 NA NA . H 4 GOL B 1 867 1 GOL GOL . I 4 GOL B 1 868 3 GOL GOL . J 4 GOL B 1 869 4 GOL GOL . K 4 GOL B 1 870 5 GOL GOL . L 4 GOL B 1 871 6 GOL GOL . M 5 HEM C 1 200 200 HEM HEM . N 5 HEM D 1 200 200 HEM HEM . O 6 HOH A 1 868 1 HOH HOH . O 6 HOH A 2 869 3 HOH HOH . O 6 HOH A 3 870 4 HOH HOH . O 6 HOH A 4 871 6 HOH HOH . O 6 HOH A 5 872 9 HOH HOH . O 6 HOH A 6 873 11 HOH HOH . P 6 HOH B 1 872 5 HOH HOH . P 6 HOH B 2 873 7 HOH HOH . P 6 HOH B 3 874 8 HOH HOH . P 6 HOH B 4 875 10 HOH HOH . P 6 HOH B 5 876 12 HOH HOH . P 6 HOH B 6 877 13 HOH HOH . Q 6 HOH D 1 201 2 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 . . . M 5 48.75 54.788 270.414 0.89 118.71 ? CHA HEM 200 C 1 HETATM 2 C CHB HEM . . . M 5 51.102 58.856 269.155 0.89 102.32 ? CHB HEM 200 C 1 HETATM 3 C CHC HEM . . . M 5 53.18 59.104 273.518 0.89 77.65 ? CHC HEM 200 C 1 HETATM 4 C CHD HEM . . . M 5 50.855 55.026 274.823 0.89 104.22 ? CHD HEM 200 C 1 HETATM 5 C C1A HEM . . . M 5 49.199 55.874 269.691 0.89 120.28 ? C1A HEM 200 C 1 HETATM 6 C C2A HEM . . . M 5 48.824 56.214 268.329 0.89 125.58 ? C2A HEM 200 C 1 HETATM 7 C C3A HEM . . . M 5 49.478 57.331 267.995 0.89 130.64 ? C3A HEM 200 C 1 HETATM 8 C C4A HEM . . . M 5 50.287 57.746 269.122 0.89 105.41 ? C4A HEM 200 C 1 HETATM 9 C CMA HEM . . . M 5 49.385 58.07 266.642 0.89 129.5 ? CMA HEM 200 C 1 HETATM 10 C CAA HEM . . . M 5 47.84 55.442 267.417 0.89 117.86 ? CAA HEM 200 C 1 HETATM 11 C CBA HEM . . . M 5 46.685 54.859 268.23 0.89 147.36 ? CBA HEM 200 C 1 HETATM 12 C CGA HEM . . . M 5 45.982 53.788 267.433 0.89 157.32 ? CGA HEM 200 C 1 HETATM 13 O O1A HEM . . . M 5 46.238 53.687 266.203 0.89 129.08 ? O1A HEM 200 C 1 HETATM 14 O O2A HEM . . . M 5 45.163 53.038 268.032 0.89 151.98 ? O2A HEM 200 C 1 HETATM 15 C C1B HEM . . . M 5 51.875 59.281 270.212 0.89 96.97 ? C1B HEM 200 C 1 HETATM 16 C C2B HEM . . . M 5 52.731 60.454 270.232 0.89 108.75 ? C2B HEM 200 C 1 HETATM 17 C C3B HEM . . . M 5 53.305 60.531 271.429 0.89 113.51 ? C3B HEM 200 C 1 HETATM 18 C C4B HEM . . . M 5 52.835 59.405 272.222 0.89 102.88 ? C4B HEM 200 C 1 HETATM 19 C CMB HEM . . . M 5 52.965 61.458 269.081 0.89 72.38 ? CMB HEM 200 C 1 HETATM 20 C CAB HEM . . . M 5 54.297 61.644 271.842 0.89 111.22 ? CAB HEM 200 C 1 HETATM 21 C CBB HEM . . . M 5 54.704 61.776 273.107 0.89 121.76 ? CBB HEM 200 C 1 HETATM 22 C C1C HEM . . . M 5 52.728 58.024 274.249 0.89 114.15 ? C1C HEM 200 C 1 HETATM 23 C C2C HEM . . . M 5 53.097 57.704 275.616 0.89 116.68 ? C2C HEM 200 C 1 HETATM 24 C C3C HEM . . . M 5 52.461 56.588 275.968 0.89 110.48 ? C3C HEM 200 C 1 HETATM 25 C C4C HEM . . . M 5 51.658 56.146 274.847 0.89 103.54 ? C4C HEM 200 C 1 HETATM 26 C CMC HEM . . . M 5 54.07 58.494 276.52 0.89 83.84 ? CMC HEM 200 C 1 HETATM 27 C CAC HEM . . . M 5 52.583 55.895 277.339 0.89 133.08 ? CAC HEM 200 C 1 HETATM 28 C CBC HEM . . . M 5 52.061 54.68 277.52 0.89 141.01 ? CBC HEM 200 C 1 HETATM 29 C C1D HEM . . . M 5 50.078 54.57 273.781 0.89 88.91 ? C1D HEM 200 C 1 HETATM 30 C C2D HEM . . . M 5 49.252 53.38 273.816 0.89 94.59 ? C2D HEM 200 C 1 HETATM 31 C C3D HEM . . . M 5 48.591 53.3 272.433 0.89 128.71 ? C3D HEM 200 C 1 HETATM 32 C C4D HEM . . . M 5 49.091 54.454 271.709 0.89 129.56 ? C4D HEM 200 C 1 HETATM 33 C CMD HEM . . . M 5 49.091 52.402 275 0.89 137.72 ? CMD HEM 200 C 1 HETATM 34 C CAD HEM . . . M 5 47.603 52.223 271.924 0.89 135.42 ? CAD HEM 200 C 1 HETATM 35 C CBD HEM . . . M 5 46.664 51.817 273.057 0.89 146.44 ? CBD HEM 200 C 1 HETATM 36 C CGD HEM . . . M 5 46.038 50.478 272.763 0.89 156.07 ? CGD HEM 200 C 1 HETATM 37 O O1D HEM . . . M 5 46.09 50.045 271.579 0.89 152.52 ? O1D HEM 200 C 1 HETATM 38 O O2D HEM . . . M 5 45.485 49.851 273.711 0.89 123.16 ? O2D HEM 200 C 1 HETATM 39 N NA HEM . . . M 5 50.098 56.83 270.14 0.89 120.26 ? NA HEM 200 C 1 HETATM 40 N NB HEM . . . M 5 51.962 58.666 271.445 0.89 101.31 ? NB HEM 200 C 1 HETATM 41 N NC HEM . . . M 5 51.842 57.051 273.819 0.89 113.77 ? NC HEM 200 C 1 HETATM 42 N ND HEM . . . M 5 49.96 55.17 272.532 0.89 86.15 ? ND HEM 200 C 1 HETATM 43 FE FE HEM . . . M 5 50.985 56.916 272.03 0.89 117.46 ? FE HEM 200 C 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 69 _model_server_stats.query_time_ms 449 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #