data_2DY5 # _model_server_result.job_id BIvjeXUacDfbno-jZ8q5Jg _model_server_result.datetime_utc '2024-11-15 03:00:40' _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 2dy5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":300}' # _entry.id 2DY5 # _exptl.entry_id 2DY5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 3 _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 2DY5 _cell.length_a 66.78 _cell.length_b 66.78 _cell.length_c 121.39 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DY5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 3 _struct_asym.id C _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 NE2 HIS 25 A HIS 25 1_555 C FE HEM . A HEM 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc2 C FE HEM . A HEM 300 1_555 D N2 224 . A 224 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? # _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 155 n n CHA C4D HEM doub 156 n n CHA HHA HEM sing 157 n n CHB C4A HEM sing 158 n n CHB C1B HEM doub 159 n n CHB HHB HEM sing 160 n n CHC C4B HEM sing 161 n n CHC C1C HEM doub 162 n n CHC HHC HEM sing 163 n n CHD C4C HEM doub 164 n n CHD C1D HEM sing 165 n n CHD HHD HEM sing 166 n n C1A C2A HEM doub 167 n y C1A NA HEM sing 168 n y C2A C3A HEM sing 169 n y C2A CAA HEM sing 170 n n C3A C4A HEM doub 171 n y C3A CMA HEM sing 172 n n C4A NA HEM sing 173 n y CMA HMA HEM sing 174 n n CMA HMAA HEM sing 175 n n CMA HMAB HEM sing 176 n n CAA CBA HEM sing 177 n n CAA HAA HEM sing 178 n n CAA HAAA HEM sing 179 n n CBA CGA HEM sing 180 n n CBA HBA HEM sing 181 n n CBA HBAA HEM sing 182 n n CGA O1A HEM doub 183 n n CGA O2A HEM sing 184 n n C1B C2B HEM sing 185 n n C1B NB HEM sing 186 n n C2B C3B HEM doub 187 n n C2B CMB HEM sing 188 n n C3B C4B HEM sing 189 n n C3B CAB HEM sing 190 n n C4B NB HEM doub 191 n n CMB HMB HEM sing 192 n n CMB HMBA HEM sing 193 n n CMB HMBB HEM sing 194 n n CAB CBB HEM doub 195 n n CAB HAB HEM sing 196 n n CBB HBB HEM sing 197 n n CBB HBBA HEM sing 198 n n C1C C2C HEM sing 199 n y C1C NC HEM sing 200 n y C2C C3C HEM doub 201 n y C2C CMC HEM sing 202 n n C3C C4C HEM sing 203 n y C3C CAC HEM sing 204 n n C4C NC HEM sing 205 n y CMC HMC HEM sing 206 n n CMC HMCA HEM sing 207 n n CMC HMCB HEM sing 208 n n CAC CBC HEM doub 209 n n CAC HAC HEM sing 210 n n CBC HBC HEM sing 211 n n CBC HBCA HEM sing 212 n n C1D C2D HEM sing 213 n n C1D ND HEM doub 214 n n C2D C3D HEM doub 215 n n C2D CMD HEM sing 216 n n C3D C4D HEM sing 217 n n C3D CAD HEM sing 218 n n C4D ND HEM sing 219 n n CMD HMD HEM sing 220 n n CMD HMDA HEM sing 221 n n CMD HMDB HEM sing 222 n n CAD CBD HEM sing 223 n n CAD HAD HEM sing 224 n n CAD HADA HEM sing 225 n n CBD CGD HEM sing 226 n n CBD HBD HEM sing 227 n n CBD HBDA HEM sing 228 n n CGD O1D HEM doub 229 n n CGD O2D HEM sing 230 n n O2A H2A HEM sing 231 n n O2D H2D HEM sing 232 n n FE NA HEM sing 233 n n FE NB HEM sing 234 n n FE NC HEM sing 235 n n FE ND HEM sing 236 n n # _atom_sites.entry_id 2DY5 _atom_sites.fract_transf_matrix[1][1] 0.014975 _atom_sites.fract_transf_matrix[1][2] 0.008646 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017291 _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] 0.008238 _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 CL A 1 302 302 CL CL . C 3 HEM A 1 300 300 HEM HEM . D 4 224 A 1 301 301 224 224 . E 5 HOH A 1 303 303 HOH HOH . E 5 HOH A 2 304 304 HOH HOH . E 5 HOH A 3 305 305 HOH HOH . E 5 HOH A 4 306 306 HOH HOH . E 5 HOH A 5 307 307 HOH HOH . E 5 HOH A 6 308 308 HOH HOH . E 5 HOH A 7 309 309 HOH HOH . E 5 HOH A 8 310 310 HOH HOH . E 5 HOH A 9 311 311 HOH HOH . E 5 HOH A 10 312 312 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 3 29.323 -31.806 27.622 1 42.71 ? CHA HEM 300 A 1 HETATM 2 C CHB HEM . . . C 3 32.27 -30.224 31.085 1 45.52 ? CHB HEM 300 A 1 HETATM 3 C CHC HEM . . . C 3 33.338 -26.359 28.419 1 42.75 ? CHC HEM 300 A 1 HETATM 4 C CHD HEM . . . C 3 30.382 -27.879 24.958 1 43.38 ? CHD HEM 300 A 1 HETATM 5 C C1A HEM . . . C 3 30.039 -31.731 28.816 1 44.22 ? C1A HEM 300 A 1 HETATM 6 C C2A HEM . . . C 3 30.002 -32.712 29.879 1 46.58 ? C2A HEM 300 A 1 HETATM 7 C C3A HEM . . . C 3 30.826 -32.264 30.853 1 45.4 ? C3A HEM 300 A 1 HETATM 8 C C4A HEM . . . C 3 31.374 -31.004 30.376 1 44.75 ? C4A HEM 300 A 1 HETATM 9 C CMA HEM . . . C 3 31.154 -32.892 32.173 1 43.35 ? CMA HEM 300 A 1 HETATM 10 C CAA HEM . . . C 3 29.188 -33.998 29.884 1 52.44 ? CAA HEM 300 A 1 HETATM 11 C CBA HEM . . . C 3 30.052 -35.268 29.63 1 59.42 ? CBA HEM 300 A 1 HETATM 12 C CGA HEM . . . C 3 29.379 -36.375 29.071 1 64.58 ? CGA HEM 300 A 1 HETATM 13 O O1A HEM . . . C 3 29.1 -37.339 29.903 1 65.51 ? O1A HEM 300 A 1 HETATM 14 O O2A HEM . . . C 3 29.064 -36.455 27.855 1 66.8 ? O2A HEM 300 A 1 HETATM 15 C C1B HEM . . . C 3 32.814 -29.023 30.653 1 45.09 ? C1B HEM 300 A 1 HETATM 16 C C2B HEM . . . C 3 33.757 -28.24 31.437 1 46.63 ? C2B HEM 300 A 1 HETATM 17 C C3B HEM . . . C 3 34.062 -27.149 30.682 1 47.05 ? C3B HEM 300 A 1 HETATM 18 C C4B HEM . . . C 3 33.297 -27.275 29.445 1 43.64 ? C4B HEM 300 A 1 HETATM 19 C CMB HEM . . . C 3 34.257 -28.625 32.814 1 44.05 ? CMB HEM 300 A 1 HETATM 20 C CAB HEM . . . C 3 34.999 -26.004 31.004 1 48.96 ? CAB HEM 300 A 1 HETATM 21 C CBB HEM . . . C 3 34.518 -25.108 32.172 1 52.03 ? CBB HEM 300 A 1 HETATM 22 C C1C HEM . . . C 3 32.646 -26.425 27.26 1 42.56 ? C1C HEM 300 A 1 HETATM 23 C C2C HEM . . . C 3 32.717 -25.43 26.201 1 44.44 ? C2C HEM 300 A 1 HETATM 24 C C3C HEM . . . C 3 31.882 -25.862 25.244 1 43.4 ? C3C HEM 300 A 1 HETATM 25 C C4C HEM . . . C 3 31.3 -27.111 25.683 1 43.64 ? C4C HEM 300 A 1 HETATM 26 C CMC HEM . . . C 3 33.585 -24.171 26.24 1 43.92 ? CMC HEM 300 A 1 HETATM 27 C CAC HEM . . . C 3 31.587 -25.172 23.92 1 44.65 ? CAC HEM 300 A 1 HETATM 28 C CBC HEM . . . C 3 30.625 -23.957 24.134 1 48.05 ? CBC HEM 300 A 1 HETATM 29 C C1D HEM . . . C 3 29.818 -29.096 25.376 1 41.68 ? C1D HEM 300 A 1 HETATM 30 C C2D HEM . . . C 3 28.865 -29.879 24.579 1 41.05 ? C2D HEM 300 A 1 HETATM 31 C C3D HEM . . . C 3 28.573 -30.973 25.328 1 42.15 ? C3D HEM 300 A 1 HETATM 32 C C4D HEM . . . C 3 29.35 -30.862 26.584 1 41.96 ? C4D HEM 300 A 1 HETATM 33 C CMD HEM . . . C 3 28.382 -29.465 23.226 1 38.39 ? CMD HEM 300 A 1 HETATM 34 C CAD HEM . . . C 3 27.652 -32.148 25.045 1 43.07 ? CAD HEM 300 A 1 HETATM 35 C CBD HEM . . . C 3 28.317 -33.304 24.165 1 45.63 ? CBD HEM 300 A 1 HETATM 36 C CGD HEM . . . C 3 27.471 -34.444 24.015 1 48.45 ? CGD HEM 300 A 1 HETATM 37 O O1D HEM . . . C 3 27.171 -34.863 22.846 1 48.58 ? O1D HEM 300 A 1 HETATM 38 O O2D HEM . . . C 3 27.004 -35.06 25.025 1 50.3 ? O2D HEM 300 A 1 HETATM 39 N NA HEM . . . C 3 30.883 -30.692 29.129 1 43.3 ? NA HEM 300 A 1 HETATM 40 N NB HEM . . . C 3 32.534 -28.423 29.437 1 43.52 ? NB HEM 300 A 1 HETATM 41 N NC HEM . . . C 3 31.766 -27.469 26.928 1 42.57 ? NC HEM 300 A 1 HETATM 42 N ND HEM . . . C 3 30.096 -29.717 26.589 1 41.89 ? ND HEM 300 A 1 HETATM 43 FE FE HEM . . . C 3 31.314 -29.076 28.017 1 40.38 ? FE HEM 300 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #