data_3DY5 # _model_server_result.job_id Ah1P5CsOMLEH9HJfGwidEA _model_server_result.datetime_utc '2024-12-21 14:15:09' _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 3dy5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1100}' # _entry.id 3DY5 # _exptl.entry_id 3DY5 _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 112.45 _cell.angle_gamma 90 _cell.entry_id 3DY5 _cell.length_a 235.52 _cell.length_b 77.493 _cell.length_c 157.966 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DY5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 1 1 B,E,F 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 ? 3 D N N ? 3 F 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 metalc ? metalc1 A OH TYR 353 A TYR 353 1_555 D FE HEM . A HEM 1100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.912 ? metalc ? metalc2 A NE2 HIS 757 A HIS 757 1_555 C FE FE2 . A FE2 1099 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.885 ? metalc ? metalc3 A NE2 HIS 762 A HIS 762 1_555 C FE FE2 . A FE2 1099 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc4 A NE2 HIS 943 A HIS 943 1_555 C FE FE2 . A FE2 1099 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc5 A ND2 ASN 947 A ASN 947 1_555 C FE FE2 . A FE2 1099 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? metalc ? metalc6 A OXT ILE 1066 A ILE 1066 1_555 C FE FE2 . A FE2 1099 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc7 B OH TYR 353 C TYR 353 1_555 F FE HEM . C HEM 1100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc8 B NE2 HIS 757 C HIS 757 1_555 E FE FE2 . C FE2 1099 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.886 ? metalc ? metalc9 B NE2 HIS 762 C HIS 762 1_555 E FE FE2 . C FE2 1099 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc10 B NE2 HIS 943 C HIS 943 1_555 E FE FE2 . C FE2 1099 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc11 B ND2 ASN 947 C ASN 947 1_555 E FE FE2 . C FE2 1099 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.805 ? metalc ? metalc12 B OXT ILE 1066 C ILE 1066 1_555 E FE FE2 . C FE2 1099 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? # _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 3DY5 _atom_sites.fract_transf_matrix[1][1] 0.004246 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001754 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012904 _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] 0.00685 _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 FE2 A 1 1099 1099 FE2 FE2 . D 3 HEM A 1 1100 1100 HEM HEM . E 2 FE2 C 1 1099 1099 FE2 FE2 . F 3 HEM C 1 1100 1100 HEM HEM . # 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 . . . D 3 37.351 -75.24 -52.089 1 2 ? CHA HEM 1100 A 1 HETATM 2 C CHB HEM . . . D 3 38.169 -79.262 -49.59 1 2 ? CHB HEM 1100 A 1 HETATM 3 C CHC HEM . . . D 3 39.392 -76.667 -45.715 1 2 ? CHC HEM 1100 A 1 HETATM 4 C CHD HEM . . . D 3 38.898 -72.621 -48.284 1 2 ? CHD HEM 1100 A 1 HETATM 5 C C1A HEM . . . D 3 37.478 -76.564 -51.748 1 2 ? C1A HEM 1100 A 1 HETATM 6 C C2A HEM . . . D 3 37.239 -77.703 -52.614 1 2 ? C2A HEM 1100 A 1 HETATM 7 C C3A HEM . . . D 3 37.463 -78.805 -51.918 1 2 ? C3A HEM 1100 A 1 HETATM 8 C C4A HEM . . . D 3 37.85 -78.402 -50.595 1 2 ? C4A HEM 1100 A 1 HETATM 9 C CMA HEM . . . D 3 37.334 -80.26 -52.417 1 2 ? CMA HEM 1100 A 1 HETATM 10 C CAA HEM . . . D 3 36.796 -77.67 -54.082 1 2 ? CAA HEM 1100 A 1 HETATM 11 C CBA HEM . . . D 3 35.28 -77.74 -54.153 1 2 ? CBA HEM 1100 A 1 HETATM 12 C CGA HEM . . . D 3 34.965 -77.47 -55.591 1 2 ? CGA HEM 1100 A 1 HETATM 13 O O1A HEM . . . D 3 34.254 -76.477 -55.899 1 2 ? O1A HEM 1100 A 1 HETATM 14 O O2A HEM . . . D 3 35.467 -78.258 -56.431 1 2 ? O2A HEM 1100 A 1 HETATM 15 C C1B HEM . . . D 3 38.583 -78.901 -48.334 1 2 ? C1B HEM 1100 A 1 HETATM 16 C C2B HEM . . . D 3 38.958 -79.832 -47.291 1 2 ? C2B HEM 1100 A 1 HETATM 17 C C3B HEM . . . D 3 39.294 -79.118 -46.217 1 2 ? C3B HEM 1100 A 1 HETATM 18 C C4B HEM . . . D 3 39.147 -77.718 -46.554 1 2 ? C4B HEM 1100 A 1 HETATM 19 C CMB HEM . . . D 3 38.952 -81.378 -47.419 1 2 ? CMB HEM 1100 A 1 HETATM 20 C CAB HEM . . . D 3 39.764 -79.672 -44.852 1 2 ? CAB HEM 1100 A 1 HETATM 21 C CBB HEM . . . D 3 38.995 -80.499 -44.13 1 2 ? CBB HEM 1100 A 1 HETATM 22 C C1C HEM . . . D 3 39.31 -75.341 -46.05 1 2 ? C1C HEM 1100 A 1 HETATM 23 C C2C HEM . . . D 3 39.467 -74.223 -45.137 1 2 ? C2C HEM 1100 A 1 HETATM 24 C C3C HEM . . . D 3 39.329 -73.109 -45.858 1 2 ? C3C HEM 1100 A 1 HETATM 25 C C4C HEM . . . D 3 39.086 -73.484 -47.232 1 2 ? C4C HEM 1100 A 1 HETATM 26 C CMC HEM . . . D 3 39.752 -74.312 -43.606 1 2 ? CMC HEM 1100 A 1 HETATM 27 C CAC HEM . . . D 3 39.415 -71.673 -45.316 1 2 ? CAC HEM 1100 A 1 HETATM 28 C CBC HEM . . . D 3 38.96 -71.422 -44.085 1 2 ? CBC HEM 1100 A 1 HETATM 29 C C1D HEM . . . D 3 38.373 -72.927 -49.52 1 2 ? C1D HEM 1100 A 1 HETATM 30 C C2D HEM . . . D 3 37.897 -71.967 -50.476 1 2 ? C2D HEM 1100 A 1 HETATM 31 C C3D HEM . . . D 3 37.409 -72.769 -51.666 1 2 ? C3D HEM 1100 A 1 HETATM 32 C C4D HEM . . . D 3 37.638 -74.149 -51.302 1 2 ? C4D HEM 1100 A 1 HETATM 33 C CMD HEM . . . D 3 37.884 -70.443 -50.333 1 2 ? CMD HEM 1100 A 1 HETATM 34 C CAD HEM . . . D 3 36.81 -72.205 -52.97 1 2 ? CAD HEM 1100 A 1 HETATM 35 C CBD HEM . . . D 3 35.368 -71.776 -52.728 1 2 ? CBD HEM 1100 A 1 HETATM 36 C CGD HEM . . . D 3 34.776 -71.254 -54.009 1 2 ? CGD HEM 1100 A 1 HETATM 37 O O1D HEM . . . D 3 33.759 -71.834 -54.465 1 2 ? O1D HEM 1100 A 1 HETATM 38 O O2D HEM . . . D 3 35.321 -70.264 -54.564 1 2 ? O2D HEM 1100 A 1 HETATM 39 N NA HEM . . . D 3 37.852 -77.028 -50.509 1 2 ? NA HEM 1100 A 1 HETATM 40 N NB HEM . . . D 3 38.709 -77.614 -47.854 1 2 ? NB HEM 1100 A 1 HETATM 41 N NC HEM . . . D 3 39.08 -74.856 -47.316 1 2 ? NC HEM 1100 A 1 HETATM 42 N ND HEM . . . D 3 38.201 -74.203 -50.036 1 2 ? ND HEM 1100 A 1 HETATM 43 FE FE HEM . . . D 3 38.295 -75.905 -48.813 1 2 ? FE HEM 1100 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 62 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #