data_1ABY # _model_server_result.job_id S3snhYMR0AZT70U6Xn1ClQ _model_server_result.datetime_utc '2025-03-06 04:26:06' _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 1aby # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":286}' # _entry.id 1ABY # _exptl.entry_id 1ABY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 4 _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 1ABY _cell.length_a 102.54 _cell.length_b 115.17 _cell.length_c 56.7 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ABY _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,M,N _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 ? 4 F N N ? 4 G N N ? 4 I N N ? 4 K 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 F FE HEM . A HEM 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc2 A NE2 HIS 229 A HIS 229 1_555 G FE HEM . A HEM 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc3 D C CYN . A CYN 284 1_555 F FE HEM . A HEM 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc4 D N CYN . A CYN 284 1_555 F FE HEM . A HEM 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc5 E C CYN . A CYN 285 1_555 G FE HEM . A HEM 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc6 E N CYN . A CYN 285 1_555 G FE HEM . A HEM 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.126 ? metalc ? metalc7 B NE2 HIS 92 B HIS 92 1_555 I FE HEM . B HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc8 H C CYN . B CYN 147 1_555 I FE HEM . B HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc9 C NE2 HIS 92 D HIS 92 1_555 K FE HEM . D HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc10 J C CYN . D CYN 147 1_555 K FE HEM . D HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc11 J N CYN . D CYN 147 1_555 K FE HEM . D HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? # _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 130 n n CHA C4D HEM doub 131 n n CHA HHA HEM sing 132 n n CHB C4A HEM sing 133 n n CHB C1B HEM doub 134 n n CHB HHB HEM sing 135 n n CHC C4B HEM sing 136 n n CHC C1C HEM doub 137 n n CHC HHC HEM sing 138 n n CHD C4C HEM doub 139 n n CHD C1D HEM sing 140 n n CHD HHD HEM sing 141 n n C1A C2A HEM doub 142 n y C1A NA HEM sing 143 n y C2A C3A HEM sing 144 n y C2A CAA HEM sing 145 n n C3A C4A HEM doub 146 n y C3A CMA HEM sing 147 n n C4A NA HEM sing 148 n y CMA HMA HEM sing 149 n n CMA HMAA HEM sing 150 n n CMA HMAB HEM sing 151 n n CAA CBA HEM sing 152 n n CAA HAA HEM sing 153 n n CAA HAAA HEM sing 154 n n CBA CGA HEM sing 155 n n CBA HBA HEM sing 156 n n CBA HBAA HEM sing 157 n n CGA O1A HEM doub 158 n n CGA O2A HEM sing 159 n n C1B C2B HEM sing 160 n n C1B NB HEM sing 161 n n C2B C3B HEM doub 162 n n C2B CMB HEM sing 163 n n C3B C4B HEM sing 164 n n C3B CAB HEM sing 165 n n C4B NB HEM doub 166 n n CMB HMB HEM sing 167 n n CMB HMBA HEM sing 168 n n CMB HMBB HEM sing 169 n n CAB CBB HEM doub 170 n n CAB HAB HEM sing 171 n n CBB HBB HEM sing 172 n n CBB HBBA HEM sing 173 n n C1C C2C HEM sing 174 n y C1C NC HEM sing 175 n y C2C C3C HEM doub 176 n y C2C CMC HEM sing 177 n n C3C C4C HEM sing 178 n y C3C CAC HEM sing 179 n n C4C NC HEM sing 180 n y CMC HMC HEM sing 181 n n CMC HMCA HEM sing 182 n n CMC HMCB HEM sing 183 n n CAC CBC HEM doub 184 n n CAC HAC HEM sing 185 n n CBC HBC HEM sing 186 n n CBC HBCA HEM sing 187 n n C1D C2D HEM sing 188 n n C1D ND HEM doub 189 n n C2D C3D HEM doub 190 n n C2D CMD HEM sing 191 n n C3D C4D HEM sing 192 n n C3D CAD HEM sing 193 n n C4D ND HEM sing 194 n n CMD HMD HEM sing 195 n n CMD HMDA HEM sing 196 n n CMD HMDB HEM sing 197 n n CAD CBD HEM sing 198 n n CAD HAD HEM sing 199 n n CAD HADA HEM sing 200 n n CBD CGD HEM sing 201 n n CBD HBD HEM sing 202 n n CBD HBDA HEM sing 203 n n CGD O1D HEM doub 204 n n CGD O2D HEM sing 205 n n O2A H2A HEM sing 206 n n O2D H2D HEM sing 207 n n FE NA HEM sing 208 n n FE NB HEM sing 209 n n FE NC HEM sing 210 n n FE ND HEM sing 211 n n # _atom_sites.entry_id 1ABY _atom_sites.fract_transf_matrix[1][1] 0.009752 _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] 0.008683 _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] 0.017637 _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 D 3 CYN A 1 284 2 CYN CYN . E 3 CYN A 1 285 4 CYN CYN . F 4 HEM A 1 286 1 HEM HEM . G 4 HEM A 1 287 3 HEM HEM . H 3 CYN B 1 147 2 CYN CYN . I 4 HEM B 1 148 1 HEM HEM . J 3 CYN D 1 147 2 CYN CYN . K 4 HEM D 1 148 1 HEM HEM . L 5 HOH A 1 288 5 HOH HOH . L 5 HOH A 2 289 6 HOH HOH . L 5 HOH A 3 290 7 HOH HOH . L 5 HOH A 4 291 8 HOH HOH . L 5 HOH A 5 292 10 HOH HOH . L 5 HOH A 6 293 11 HOH HOH . L 5 HOH A 7 294 12 HOH HOH . L 5 HOH A 8 295 13 HOH HOH . L 5 HOH A 9 296 14 HOH HOH . L 5 HOH A 10 297 15 HOH HOH . L 5 HOH A 11 298 16 HOH HOH . L 5 HOH A 12 299 17 HOH HOH . L 5 HOH A 13 300 18 HOH HOH . L 5 HOH A 14 301 23 HOH HOH . L 5 HOH A 15 302 25 HOH HOH . L 5 HOH A 16 303 27 HOH HOH . L 5 HOH A 17 304 28 HOH HOH . L 5 HOH A 18 305 29 HOH HOH . L 5 HOH A 19 306 30 HOH HOH . L 5 HOH A 20 307 31 HOH HOH . L 5 HOH A 21 308 35 HOH HOH . L 5 HOH A 22 309 37 HOH HOH . L 5 HOH A 23 310 38 HOH HOH . L 5 HOH A 24 311 39 HOH HOH . L 5 HOH A 25 312 41 HOH HOH . L 5 HOH A 26 313 44 HOH HOH . L 5 HOH A 27 314 49 HOH HOH . L 5 HOH A 28 315 50 HOH HOH . L 5 HOH A 29 316 51 HOH HOH . L 5 HOH A 30 317 52 HOH HOH . L 5 HOH A 31 318 53 HOH HOH . L 5 HOH A 32 319 54 HOH HOH . L 5 HOH A 33 320 55 HOH HOH . L 5 HOH A 34 321 56 HOH HOH . L 5 HOH A 35 322 57 HOH HOH . L 5 HOH A 36 323 58 HOH HOH . L 5 HOH A 37 324 59 HOH HOH . L 5 HOH A 38 325 60 HOH HOH . L 5 HOH A 39 326 61 HOH HOH . L 5 HOH A 40 327 62 HOH HOH . L 5 HOH A 41 328 63 HOH HOH . L 5 HOH A 42 329 64 HOH HOH . L 5 HOH A 43 330 65 HOH HOH . L 5 HOH A 44 331 66 HOH HOH . L 5 HOH A 45 332 68 HOH HOH . L 5 HOH A 46 333 72 HOH HOH . L 5 HOH A 47 334 73 HOH HOH . L 5 HOH A 48 335 75 HOH HOH . L 5 HOH A 49 336 81 HOH HOH . L 5 HOH A 50 337 82 HOH HOH . L 5 HOH A 51 338 83 HOH HOH . M 5 HOH B 1 149 1 HOH HOH . M 5 HOH B 2 150 2 HOH HOH . M 5 HOH B 3 151 4 HOH HOH . M 5 HOH B 4 152 9 HOH HOH . M 5 HOH B 5 153 19 HOH HOH . M 5 HOH B 6 154 20 HOH HOH . M 5 HOH B 7 155 21 HOH HOH . M 5 HOH B 8 156 22 HOH HOH . M 5 HOH B 9 157 26 HOH HOH . M 5 HOH B 10 158 36 HOH HOH . M 5 HOH B 11 159 40 HOH HOH . M 5 HOH B 12 160 43 HOH HOH . M 5 HOH B 13 161 46 HOH HOH . M 5 HOH B 14 162 47 HOH HOH . M 5 HOH B 15 163 69 HOH HOH . M 5 HOH B 16 164 74 HOH HOH . M 5 HOH B 17 165 76 HOH HOH . M 5 HOH B 18 166 77 HOH HOH . M 5 HOH B 19 167 78 HOH HOH . M 5 HOH B 20 168 79 HOH HOH . M 5 HOH B 21 169 80 HOH HOH . N 5 HOH D 1 149 3 HOH HOH . N 5 HOH D 2 150 24 HOH HOH . N 5 HOH D 3 151 32 HOH HOH . N 5 HOH D 4 152 33 HOH HOH . N 5 HOH D 5 153 34 HOH HOH . N 5 HOH D 6 154 42 HOH HOH . N 5 HOH D 7 155 45 HOH HOH . N 5 HOH D 8 156 48 HOH HOH . N 5 HOH D 9 157 67 HOH HOH . N 5 HOH D 10 158 70 HOH HOH . N 5 HOH D 11 159 71 HOH HOH . N 5 HOH D 12 160 84 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 . . . F 4 5.12 34.971 15.598 1 22.53 ? CHA HEM 286 A 1 HETATM 2 C CHB HEM . . . F 4 6.981 35.728 20.005 1 25.97 ? CHB HEM 286 A 1 HETATM 3 C CHC HEM . . . F 4 11.443 35.124 18.262 1 16.57 ? CHC HEM 286 A 1 HETATM 4 C CHD HEM . . . F 4 9.636 34.835 13.806 1 16.17 ? CHD HEM 286 A 1 HETATM 5 C C1A HEM . . . F 4 5.225 35.23 16.961 1 23.44 ? C1A HEM 286 A 1 HETATM 6 C C2A HEM . . . F 4 4.128 35.584 17.833 1 21.1 ? C2A HEM 286 A 1 HETATM 7 C C3A HEM . . . F 4 4.659 35.84 19.053 1 21.77 ? C3A HEM 286 A 1 HETATM 8 C C4A HEM . . . F 4 6.087 35.655 18.941 1 20.75 ? C4A HEM 286 A 1 HETATM 9 C CMA HEM . . . F 4 3.903 36.179 20.346 1 19.12 ? CMA HEM 286 A 1 HETATM 10 C CAA HEM . . . F 4 2.654 35.637 17.498 1 20.32 ? CAA HEM 286 A 1 HETATM 11 C CBA HEM . . . F 4 2.256 34.226 17.112 1 31.3 ? CBA HEM 286 A 1 HETATM 12 C CGA HEM . . . F 4 0.764 34.062 16.882 1 35.84 ? CGA HEM 286 A 1 HETATM 13 O O1A HEM . . . F 4 0.019 35.062 16.994 1 32.85 ? O1A HEM 286 A 1 HETATM 14 O O2A HEM . . . F 4 0.339 32.92 16.597 1 38.39 ? O2A HEM 286 A 1 HETATM 15 C C1B HEM . . . F 4 8.36 35.53 19.944 1 24.47 ? C1B HEM 286 A 1 HETATM 16 C C2B HEM . . . F 4 9.266 35.561 21.083 1 19.58 ? C2B HEM 286 A 1 HETATM 17 C C3B HEM . . . F 4 10.516 35.351 20.589 1 20.76 ? C3B HEM 286 A 1 HETATM 18 C C4B HEM . . . F 4 10.384 35.248 19.148 1 20.62 ? C4B HEM 286 A 1 HETATM 19 C CMB HEM . . . F 4 8.853 35.721 22.556 1 10.67 ? CMB HEM 286 A 1 HETATM 20 C CAB HEM . . . F 4 11.755 35.159 21.242 1 20.21 ? CAB HEM 286 A 1 HETATM 21 C CBB HEM . . . F 4 12.263 35.899 22.389 1 12.81 ? CBB HEM 286 A 1 HETATM 22 C C1C HEM . . . F 4 11.336 34.974 16.891 1 14.36 ? C1C HEM 286 A 1 HETATM 23 C C2C HEM . . . F 4 12.447 35.005 15.987 1 10.56 ? C2C HEM 286 A 1 HETATM 24 C C3C HEM . . . F 4 11.943 34.924 14.737 1 12.57 ? C3C HEM 286 A 1 HETATM 25 C C4C HEM . . . F 4 10.518 34.86 14.859 1 14.63 ? C4C HEM 286 A 1 HETATM 26 C CMC HEM . . . F 4 13.891 35.122 16.468 1 10.13 ? CMC HEM 286 A 1 HETATM 27 C CAC HEM . . . F 4 12.623 34.961 13.57 1 12.16 ? CAC HEM 286 A 1 HETATM 28 C CBC HEM . . . F 4 13.497 36.092 13.409 1 13.72 ? CBC HEM 286 A 1 HETATM 29 C C1D HEM . . . F 4 8.255 34.846 13.915 1 20.95 ? C1D HEM 286 A 1 HETATM 30 C C2D HEM . . . F 4 7.349 34.771 12.796 1 23.48 ? C2D HEM 286 A 1 HETATM 31 C C3D HEM . . . F 4 6.09 34.816 13.298 1 22.28 ? C3D HEM 286 A 1 HETATM 32 C C4D HEM . . . F 4 6.198 34.833 14.73 1 23.18 ? C4D HEM 286 A 1 HETATM 33 C CMD HEM . . . F 4 7.826 34.59 11.358 1 17.01 ? CMD HEM 286 A 1 HETATM 34 C CAD HEM . . . F 4 4.772 34.82 12.623 1 21.13 ? CAD HEM 286 A 1 HETATM 35 C CBD HEM . . . F 4 4.542 35.897 11.598 1 25.84 ? CBD HEM 286 A 1 HETATM 36 C CGD HEM . . . F 4 3.171 35.779 10.981 1 36.31 ? CGD HEM 286 A 1 HETATM 37 O O1D HEM . . . F 4 2.164 36.022 11.698 1 37.04 ? O1D HEM 286 A 1 HETATM 38 O O2D HEM . . . F 4 3.101 35.408 9.789 1 39.58 ? O2D HEM 286 A 1 HETATM 39 N NA HEM . . . F 4 6.42 35.343 17.642 1 19.11 ? NA HEM 286 A 1 HETATM 40 N NB HEM . . . F 4 9.052 35.252 18.781 1 22.5 ? NB HEM 286 A 1 HETATM 41 N NC HEM . . . F 4 10.155 34.894 16.182 1 18.69 ? NC HEM 286 A 1 HETATM 42 N ND HEM . . . F 4 7.532 34.884 15.086 1 17.93 ? ND HEM 286 A 1 HETATM 43 FE FE HEM . . . F 4 8.238 35.025 16.897 1 19.91 ? FE HEM 286 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #