data_3TF9 # _model_server_result.job_id wVh8AMCusFFHVjD4bRYrXA _model_server_result.datetime_utc '2024-11-08 09:03:58' _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 3tf9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 3TF9 # _exptl.entry_id 3TF9 _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 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 3TF9 _cell.length_a 124.404 _cell.length_b 124.404 _cell.length_c 124.404 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TF9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # 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,E,I 1 1 B,F,G,H,J 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 ? 2 C N N ? 2 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 O SER 44 A SER 44 1_555 E NA NA . A NA 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.723 ? metalc ? metalc2 A OG1 THR 48 A THR 48 1_555 E NA NA . A NA 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? metalc ? metalc3 A NE2 HIS 105 A HIS 105 1_555 C FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc4 B OD1 ASN 6 B ASN 6 1_555 H NA NA . B NA 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.826 ? metalc ? metalc5 B O SER 44 B SER 44 1_555 H NA NA . B NA 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? metalc ? metalc6 B OG1 THR 48 B THR 48 1_555 H NA NA . B NA 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc7 B NE2 HIS 105 B HIS 105 1_555 F FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? # _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 3TF9 _atom_sites.fract_transf_matrix[1][1] 0.008038 _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] 0.008038 _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] 0.008038 _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 HEM A 1 500 500 HEM HEM . D 3 XE A 1 190 1 XE XE . E 4 NA A 1 191 1 NA NA . F 2 HEM B 1 501 501 HEM HEM . G 3 XE B 1 190 2 XE XE . H 4 NA B 1 191 1 NA NA . I 5 HOH A 1 192 9 HOH HOH . I 5 HOH A 2 193 10 HOH HOH . I 5 HOH A 3 194 11 HOH HOH . I 5 HOH A 4 195 13 HOH HOH . I 5 HOH A 5 196 15 HOH HOH . I 5 HOH A 6 197 18 HOH HOH . I 5 HOH A 7 198 19 HOH HOH . I 5 HOH A 8 199 20 HOH HOH . I 5 HOH A 9 200 21 HOH HOH . I 5 HOH A 10 201 22 HOH HOH . I 5 HOH A 11 202 1 HOH HOH . I 5 HOH A 12 203 2 HOH HOH . I 5 HOH A 13 204 4 HOH HOH . I 5 HOH A 14 205 5 HOH HOH . I 5 HOH A 15 206 7 HOH HOH . J 5 HOH B 1 192 16 HOH HOH . J 5 HOH B 2 193 17 HOH HOH . J 5 HOH B 3 194 23 HOH HOH . J 5 HOH B 4 195 3 HOH HOH . J 5 HOH B 5 196 6 HOH HOH . J 5 HOH B 6 197 8 HOH HOH . J 5 HOH B 7 198 12 HOH HOH . J 5 HOH B 8 199 14 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 2 3.924 20.86 73.229 1 41.16 ? CHA HEM 500 A 1 HETATM 2 C CHB HEM . . . C 2 1.705 16.542 72.357 1 59.27 ? CHB HEM 500 A 1 HETATM 3 C CHC HEM . . . C 2 2.624 17.145 67.599 1 39.2 ? CHC HEM 500 A 1 HETATM 4 C CHD HEM . . . C 2 4.066 21.747 68.364 1 46.76 ? CHD HEM 500 A 1 HETATM 5 C C1A HEM . . . C 2 3.301 19.632 73.37 1 45.8 ? C1A HEM 500 A 1 HETATM 6 C C2A HEM . . . C 2 3.14 18.9 74.612 1 51 ? C2A HEM 500 A 1 HETATM 7 C C3A HEM . . . C 2 2.58 17.738 74.371 1 50.5 ? C3A HEM 500 A 1 HETATM 8 C C4A HEM . . . C 2 2.316 17.641 72.968 1 54.9 ? C4A HEM 500 A 1 HETATM 9 C CMA HEM . . . C 2 2.249 16.691 75.432 1 53.41 ? CMA HEM 500 A 1 HETATM 10 C CAA HEM . . . C 2 3.597 19.389 75.986 1 46.99 ? CAA HEM 500 A 1 HETATM 11 C CBA HEM . . . C 2 2.657 20.484 76.491 1 47.74 ? CBA HEM 500 A 1 HETATM 12 C CGA HEM . . . C 2 2.353 20.377 77.982 1 57.26 ? CGA HEM 500 A 1 HETATM 13 O O1A HEM . . . C 2 2.826 19.446 78.727 1 56.97 ? O1A HEM 500 A 1 HETATM 14 O O2A HEM . . . C 2 1.65 21.319 78.441 1 46.8 ? O2A HEM 500 A 1 HETATM 15 C C1B HEM . . . C 2 1.808 16.249 71.001 1 54.03 ? C1B HEM 500 A 1 HETATM 16 C C2B HEM . . . C 2 1.494 15.013 70.298 1 56.52 ? C2B HEM 500 A 1 HETATM 17 C C3B HEM . . . C 2 1.776 15.238 69.007 1 51.92 ? C3B HEM 500 A 1 HETATM 18 C C4B HEM . . . C 2 2.226 16.589 68.822 1 51.9 ? C4B HEM 500 A 1 HETATM 19 C CMB HEM . . . C 2 0.976 13.71 70.968 1 47.65 ? CMB HEM 500 A 1 HETATM 20 C CAB HEM . . . C 2 1.604 14.353 67.782 1 51.5 ? CAB HEM 500 A 1 HETATM 21 C CBB HEM . . . C 2 0.597 13.499 67.824 1 73.17 ? CBB HEM 500 A 1 HETATM 22 C C1C HEM . . . C 2 3.116 18.399 67.39 1 46.04 ? C1C HEM 500 A 1 HETATM 23 C C2C HEM . . . C 2 3.6 18.875 66.125 1 56.27 ? C2C HEM 500 A 1 HETATM 24 C C3C HEM . . . C 2 3.998 20.152 66.297 1 54.59 ? C3C HEM 500 A 1 HETATM 25 C C4C HEM . . . C 2 3.807 20.543 67.711 1 49.2 ? C4C HEM 500 A 1 HETATM 26 C CMC HEM . . . C 2 3.675 18.018 64.856 1 42.95 ? CMC HEM 500 A 1 HETATM 27 C CAC HEM . . . C 2 4.579 20.97 65.149 1 56.01 ? CAC HEM 500 A 1 HETATM 28 C CBC HEM . . . C 2 4.535 22.308 65.194 1 61.65 ? CBC HEM 500 A 1 HETATM 29 C C1D HEM . . . C 2 4.318 21.938 69.736 1 48.33 ? C1D HEM 500 A 1 HETATM 30 C C2D HEM . . . C 2 5.07 23.013 70.363 1 49.67 ? C2D HEM 500 A 1 HETATM 31 C C3D HEM . . . C 2 5.036 22.742 71.862 1 56.6 ? C3D HEM 500 A 1 HETATM 32 C C4D HEM . . . C 2 4.271 21.509 72.036 1 51.92 ? C4D HEM 500 A 1 HETATM 33 C CMD HEM . . . C 2 5.794 24.213 69.7 1 49.59 ? CMD HEM 500 A 1 HETATM 34 C CAD HEM . . . C 2 5.746 23.623 72.912 1 54.83 ? CAD HEM 500 A 1 HETATM 35 C CBD HEM . . . C 2 4.738 24.072 73.972 1 54.43 ? CBD HEM 500 A 1 HETATM 36 C CGD HEM . . . C 2 4.516 25.547 73.869 1 59.76 ? CGD HEM 500 A 1 HETATM 37 O O1D HEM . . . C 2 4.937 26.144 72.853 1 63.87 ? O1D HEM 500 A 1 HETATM 38 O O2D HEM . . . C 2 3.939 26.108 74.827 1 60.99 ? O2D HEM 500 A 1 HETATM 39 N NA HEM . . . C 2 2.756 18.831 72.385 1 47.71 ? NA HEM 500 A 1 HETATM 40 N NB HEM . . . C 2 2.238 17.176 70.064 1 54.23 ? NB HEM 500 A 1 HETATM 41 N NC HEM . . . C 2 3.254 19.433 68.331 1 53.14 ? NC HEM 500 A 1 HETATM 42 N ND HEM . . . C 2 3.891 21.113 70.765 1 49.55 ? ND HEM 500 A 1 HETATM 43 FE FE HEM . . . C 2 2.758 19.368 70.342 1 51.98 ? FE HEM 500 A 1 HETATM 44 H HHB HEM . . . C 2 0.986 16.099 72.854 1 71.16 ? HHB HEM 500 A 1 HETATM 45 H HHC HEM . . . C 2 2.54 16.571 66.809 1 47.07 ? HHC HEM 500 A 1 HETATM 46 H HHD HEM . . . C 2 4.073 22.552 67.805 1 56.15 ? HHD HEM 500 A 1 HETATM 47 H HMA HEM . . . C 2 3.072 16.416 75.888 1 64.13 ? HMA HEM 500 A 1 HETATM 48 H HMAA HEM . . . C 2 1.837 15.911 75.004 1 64.13 ? HMAA HEM 500 A 1 HETATM 49 H HMAB HEM . . . C 2 1.626 17.072 76.085 1 64.13 ? HMAB HEM 500 A 1 HETATM 50 H HAA HEM . . . C 2 4.497 19.745 75.918 1 56.43 ? HAA HEM 500 A 1 HETATM 51 H HAAA HEM . . . C 2 3.591 18.647 76.611 1 56.43 ? HAAA HEM 500 A 1 HETATM 52 H HBA HEM . . . C 2 1.823 20.429 75.999 1 57.32 ? HBA HEM 500 A 1 HETATM 53 H HBAA HEM . . . C 2 3.064 21.348 76.318 1 57.32 ? HBAA HEM 500 A 1 HETATM 54 H HMB HEM . . . C 2 0.841 13.03 70.29 1 57.21 ? HMB HEM 500 A 1 HETATM 55 H HMBA HEM . . . C 2 0.135 13.89 71.418 1 57.21 ? HMBA HEM 500 A 1 HETATM 56 H HMBB HEM . . . C 2 1.628 13.398 71.614 1 57.21 ? HMBB HEM 500 A 1 HETATM 57 H HAB HEM . . . C 2 1.964 14.63 66.936 1 61.84 ? HAB HEM 500 A 1 HETATM 58 H HBB HEM . . . C 2 0.431 12.908 67.073 1 87.84 ? HBB HEM 500 A 1 HETATM 59 H HBBA HEM . . . C 2 0.022 13.465 68.604 1 87.84 ? HBBA HEM 500 A 1 HETATM 60 H HMC HEM . . . C 2 4.033 18.55 64.128 1 51.58 ? HMC HEM 500 A 1 HETATM 61 H HMCA HEM . . . C 2 2.786 17.708 64.623 1 51.58 ? HMCA HEM 500 A 1 HETATM 62 H HMCB HEM . . . C 2 4.253 17.255 65.014 1 51.58 ? HMCB HEM 500 A 1 HETATM 63 H HAC HEM . . . C 2 5.028 20.529 64.424 1 67.24 ? HAC HEM 500 A 1 HETATM 64 H HBC HEM . . . C 2 4.906 22.83 64.466 1 74.01 ? HBC HEM 500 A 1 HETATM 65 H HBCA HEM . . . C 2 4.134 22.755 65.956 1 74.01 ? HBCA HEM 500 A 1 HETATM 66 H HMD HEM . . . C 2 6.212 24.766 70.393 1 59.54 ? HMD HEM 500 A 1 HETATM 67 H HMDA HEM . . . C 2 5.145 24.751 69.2 1 59.54 ? HMDA HEM 500 A 1 HETATM 68 H HMDB HEM . . . C 2 6.484 23.88 69.087 1 59.54 ? HMDB HEM 500 A 1 HETATM 69 H HAD HEM . . . C 2 6.125 24.402 72.476 1 65.83 ? HAD HEM 500 A 1 HETATM 70 H HADA HEM . . . C 2 6.454 23.113 73.335 1 65.83 ? HADA HEM 500 A 1 HETATM 71 H HBD HEM . . . C 2 5.081 23.859 74.854 1 65.35 ? HBD HEM 500 A 1 HETATM 72 H HBDA HEM . . . C 2 3.897 23.609 73.833 1 65.35 ? HBDA HEM 500 A 1 HETATM 73 H HHA HEM . . . C 2 4.148 21.33 74.059 1 49.42 ? HHA HEM 500 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 73 #