data_1HDA # _model_server_result.job_id '_Vj3hLQ3f5tbllwyay3ECw' _model_server_result.datetime_utc '2024-11-26 05:35:40' _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 1hda # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":143}' # _entry.id 1HDA # _exptl.entry_id 1HDA _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 4 _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 1HDA _cell.length_a 63.82 _cell.length_b 95.51 _cell.length_c 105.32 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1HDA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H 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 NE2 HIS 87 A HIS 87 1_555 E FE HEM . A HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc2 B NE2 HIS 91 B HIS 92 1_555 F FE HEM . B HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc3 C NE2 HIS 87 C HIS 87 1_555 G FE HEM . C HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc4 D NE2 HIS 91 D HIS 92 1_555 H FE HEM . D HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? # _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 1HDA _atom_sites.fract_transf_matrix[1][1] 0.015669 _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] 0.01047 _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] 0.009495 _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 HEM A 1 143 143 HEM HEM . F 3 HEM B 1 148 148 HEM HEM . G 3 HEM C 1 143 143 HEM HEM . H 3 HEM D 1 148 148 HEM HEM . I 4 HOH A 1 752 752 HOH HOH . I 4 HOH A 2 758 758 HOH HOH . I 4 HOH A 3 759 759 HOH HOH . I 4 HOH A 4 762 762 HOH HOH . I 4 HOH A 5 764 764 HOH HOH . I 4 HOH A 6 765 765 HOH HOH . I 4 HOH A 7 769 769 HOH HOH . I 4 HOH A 8 770 770 HOH HOH . I 4 HOH A 9 771 771 HOH HOH . I 4 HOH A 10 772 772 HOH HOH . I 4 HOH A 11 773 773 HOH HOH . I 4 HOH A 12 776 776 HOH HOH . I 4 HOH A 13 781 781 HOH HOH . I 4 HOH A 14 782 782 HOH HOH . I 4 HOH A 15 785 785 HOH HOH . I 4 HOH A 16 786 786 HOH HOH . I 4 HOH A 17 788 788 HOH HOH . I 4 HOH A 18 789 789 HOH HOH . I 4 HOH A 19 790 790 HOH HOH . J 4 HOH B 1 751 751 HOH HOH . J 4 HOH B 2 753 753 HOH HOH . J 4 HOH B 3 754 754 HOH HOH . J 4 HOH B 4 763 763 HOH HOH . J 4 HOH B 5 766 766 HOH HOH . J 4 HOH B 6 775 775 HOH HOH . J 4 HOH B 7 777 777 HOH HOH . J 4 HOH B 8 783 783 HOH HOH . K 4 HOH C 1 756 756 HOH HOH . K 4 HOH C 2 761 761 HOH HOH . K 4 HOH C 3 774 774 HOH HOH . K 4 HOH C 4 778 778 HOH HOH . K 4 HOH C 5 779 779 HOH HOH . K 4 HOH C 6 780 780 HOH HOH . K 4 HOH C 7 784 784 HOH HOH . K 4 HOH C 8 787 787 HOH HOH . K 4 HOH C 9 791 791 HOH HOH . K 4 HOH C 10 792 792 HOH HOH . L 4 HOH D 1 760 760 HOH HOH . L 4 HOH D 2 767 767 HOH HOH . L 4 HOH D 3 768 768 HOH HOH . L 4 HOH D 4 793 793 HOH HOH . L 4 HOH D 5 794 794 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 . . . E 3 25.244 53.18 2.308 1 17.03 ? CHA HEM 143 A 1 HETATM 2 C CHB HEM . . . E 3 27.947 53.682 6.302 1 15.45 ? CHB HEM 143 A 1 HETATM 3 C CHC HEM . . . E 3 25.875 49.754 8.193 1 14.31 ? CHC HEM 143 A 1 HETATM 4 C CHD HEM . . . E 3 23.516 49.015 4.059 1 15.29 ? CHD HEM 143 A 1 HETATM 5 C C1A HEM . . . E 3 26.195 53.614 3.209 1 18.13 ? C1A HEM 143 A 1 HETATM 6 C C2A HEM . . . E 3 27.151 54.681 2.977 1 19.59 ? C2A HEM 143 A 1 HETATM 7 C C3A HEM . . . E 3 27.882 54.836 4.074 1 17.23 ? C3A HEM 143 A 1 HETATM 8 C C4A HEM . . . E 3 27.411 53.853 5.033 1 17.4 ? C4A HEM 143 A 1 HETATM 9 C CMA HEM . . . E 3 29.052 55.808 4.344 1 15.65 ? CMA HEM 143 A 1 HETATM 10 C CAA HEM . . . E 3 27.247 55.454 1.641 1 22.93 ? CAA HEM 143 A 1 HETATM 11 C CBA HEM . . . E 3 26.445 56.731 1.458 1 28.08 ? CBA HEM 143 A 1 HETATM 12 C CGA HEM . . . E 3 26.611 57.366 0.097 1 30.71 ? CGA HEM 143 A 1 HETATM 13 O O1A HEM . . . E 3 26.116 56.814 -0.914 1 33.32 ? O1A HEM 143 A 1 HETATM 14 O O2A HEM . . . E 3 27.289 58.403 0.043 1 31.88 ? O2A HEM 143 A 1 HETATM 15 C C1B HEM . . . E 3 27.632 52.641 7.15 1 13.3 ? C1B HEM 143 A 1 HETATM 16 C C2B HEM . . . E 3 28.219 52.421 8.46 1 12.38 ? C2B HEM 143 A 1 HETATM 17 C C3B HEM . . . E 3 27.643 51.336 8.967 1 12.53 ? C3B HEM 143 A 1 HETATM 18 C C4B HEM . . . E 3 26.689 50.853 8 1 12.99 ? C4B HEM 143 A 1 HETATM 19 C CMB HEM . . . E 3 29.321 53.33 9.052 1 10.01 ? CMB HEM 143 A 1 HETATM 20 C CAB HEM . . . E 3 27.84 50.61 10.316 1 12.47 ? CAB HEM 143 A 1 HETATM 21 C CBB HEM . . . E 3 28.98 50.717 10.976 1 13.6 ? CBB HEM 143 A 1 HETATM 22 C C1C HEM . . . E 3 25.086 49.181 7.218 1 13.43 ? C1C HEM 143 A 1 HETATM 23 C C2C HEM . . . E 3 24.505 47.855 7.301 1 12.29 ? C2C HEM 143 A 1 HETATM 24 C C3C HEM . . . E 3 23.872 47.642 6.144 1 12.69 ? C3C HEM 143 A 1 HETATM 25 C C4C HEM . . . E 3 24.04 48.835 5.321 1 14.6 ? C4C HEM 143 A 1 HETATM 26 C CMC HEM . . . E 3 24.674 46.936 8.524 1 9.68 ? CMC HEM 143 A 1 HETATM 27 C CAC HEM . . . E 3 23.069 46.421 5.676 1 11.65 ? CAC HEM 143 A 1 HETATM 28 C CBC HEM . . . E 3 23.436 45.211 6.102 1 11.61 ? CBC HEM 143 A 1 HETATM 29 C C1D HEM . . . E 3 23.772 50.088 3.232 1 15.76 ? C1D HEM 143 A 1 HETATM 30 C C2D HEM . . . E 3 23.246 50.236 1.884 1 16.71 ? C2D HEM 143 A 1 HETATM 31 C C3D HEM . . . E 3 23.714 51.393 1.417 1 18.22 ? C3D HEM 143 A 1 HETATM 32 C C4D HEM . . . E 3 24.556 51.987 2.442 1 17.43 ? C4D HEM 143 A 1 HETATM 33 C CMD HEM . . . E 3 22.324 49.197 1.206 1 14.33 ? CMD HEM 143 A 1 HETATM 34 C CAD HEM . . . E 3 23.531 52.031 0.012 1 19.42 ? CAD HEM 143 A 1 HETATM 35 C CBD HEM . . . E 3 24.467 51.414 -1.046 1 23.21 ? CBD HEM 143 A 1 HETATM 36 C CGD HEM . . . E 3 24.148 51.649 -2.497 1 25.56 ? CGD HEM 143 A 1 HETATM 37 O O1D HEM . . . E 3 24.879 52.469 -3.116 1 26.88 ? O1D HEM 143 A 1 HETATM 38 O O2D HEM . . . E 3 23.18 51.015 -3.02 1 26.7 ? O2D HEM 143 A 1 HETATM 39 N NA HEM . . . E 3 26.369 53.121 4.488 1 17.23 ? NA HEM 143 A 1 HETATM 40 N NB HEM . . . E 3 26.696 51.662 6.883 1 14.39 ? NB HEM 143 A 1 HETATM 41 N NC HEM . . . E 3 24.798 49.779 6.005 1 14.3 ? NC HEM 143 A 1 HETATM 42 N ND HEM . . . E 3 24.56 51.164 3.558 1 16.44 ? ND HEM 143 A 1 HETATM 43 FE FE HEM . . . E 3 25.288 51.654 5.398 1 16.04 ? FE HEM 143 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 238 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 43 #