data_3SDN # _model_server_result.job_id VDWZHpsa0t5dxZpEMV0iZg _model_server_result.datetime_utc '2024-11-27 13:17:57' _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 3sdn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":160}' # _entry.id 3SDN # _exptl.entry_id 3SDN _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 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 90 _cell.entry_id 3SDN _cell.length_a 40.036 _cell.length_b 48.011 _cell.length_c 77.557 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SDN _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 94 A HIS 93 1_555 B FE HEM . A HEM 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc2 B FE HEM . A HEM 160 1_555 C O ACT . A ACT 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? # _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 131 n n CHA C4D HEM doub 132 n n CHA HHA HEM sing 133 n n CHB C4A HEM sing 134 n n CHB C1B HEM doub 135 n n CHB HHB HEM sing 136 n n CHC C4B HEM sing 137 n n CHC C1C HEM doub 138 n n CHC HHC HEM sing 139 n n CHD C4C HEM doub 140 n n CHD C1D HEM sing 141 n n CHD HHD HEM sing 142 n n C1A C2A HEM doub 143 n y C1A NA HEM sing 144 n y C2A C3A HEM sing 145 n y C2A CAA HEM sing 146 n n C3A C4A HEM doub 147 n y C3A CMA HEM sing 148 n n C4A NA HEM sing 149 n y CMA HMA HEM sing 150 n n CMA HMAA HEM sing 151 n n CMA HMAB HEM sing 152 n n CAA CBA HEM sing 153 n n CAA HAA HEM sing 154 n n CAA HAAA HEM sing 155 n n CBA CGA HEM sing 156 n n CBA HBA HEM sing 157 n n CBA HBAA HEM sing 158 n n CGA O1A HEM doub 159 n n CGA O2A HEM sing 160 n n C1B C2B HEM sing 161 n n C1B NB HEM sing 162 n n C2B C3B HEM doub 163 n n C2B CMB HEM sing 164 n n C3B C4B HEM sing 165 n n C3B CAB HEM sing 166 n n C4B NB HEM doub 167 n n CMB HMB HEM sing 168 n n CMB HMBA HEM sing 169 n n CMB HMBB HEM sing 170 n n CAB CBB HEM doub 171 n n CAB HAB HEM sing 172 n n CBB HBB HEM sing 173 n n CBB HBBA HEM sing 174 n n C1C C2C HEM sing 175 n y C1C NC HEM sing 176 n y C2C C3C HEM doub 177 n y C2C CMC HEM sing 178 n n C3C C4C HEM sing 179 n y C3C CAC HEM sing 180 n n C4C NC HEM sing 181 n y CMC HMC HEM sing 182 n n CMC HMCA HEM sing 183 n n CMC HMCB HEM sing 184 n n CAC CBC HEM doub 185 n n CAC HAC HEM sing 186 n n CBC HBC HEM sing 187 n n CBC HBCA HEM sing 188 n n C1D C2D HEM sing 189 n n C1D ND HEM doub 190 n n C2D C3D HEM doub 191 n n C2D CMD HEM sing 192 n n C3D C4D HEM sing 193 n n C3D CAD HEM sing 194 n n C4D ND HEM sing 195 n n CMD HMD HEM sing 196 n n CMD HMDA HEM sing 197 n n CMD HMDB HEM sing 198 n n CAD CBD HEM sing 199 n n CAD HAD HEM sing 200 n n CAD HADA HEM sing 201 n n CBD CGD HEM sing 202 n n CBD HBD HEM sing 203 n n CBD HBDA HEM sing 204 n n CGD O1D HEM doub 205 n n CGD O2D HEM sing 206 n n O2A H2A HEM sing 207 n n O2D H2D HEM sing 208 n n FE NA HEM sing 209 n n FE NB HEM sing 210 n n FE NC HEM sing 211 n n FE ND HEM sing 212 n n # _atom_sites.entry_id 3SDN _atom_sites.fract_transf_matrix[1][1] 0.024978 _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] 0.020829 _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] 0.012894 _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 HEM A 1 160 160 HEM HEM . C 3 ACT A 1 165 165 ACT ACT . D 4 EDO A 1 167 167 EDO EDO . E 4 EDO A 1 168 168 EDO EDO . F 5 HOH A 1 154 64 HOH HOH . F 5 HOH A 2 301 301 HOH HOH . F 5 HOH A 3 302 302 HOH HOH . F 5 HOH A 4 303 303 HOH HOH . F 5 HOH A 5 304 304 HOH HOH . F 5 HOH A 6 305 305 HOH HOH . F 5 HOH A 7 306 306 HOH HOH . F 5 HOH A 8 307 307 HOH HOH . F 5 HOH A 9 308 308 HOH HOH . F 5 HOH A 10 310 310 HOH HOH . F 5 HOH A 11 311 311 HOH HOH . F 5 HOH A 12 312 312 HOH HOH . F 5 HOH A 13 313 313 HOH HOH . F 5 HOH A 14 314 314 HOH HOH . F 5 HOH A 15 315 315 HOH HOH . F 5 HOH A 16 316 316 HOH HOH . F 5 HOH A 17 318 318 HOH HOH . F 5 HOH A 18 319 319 HOH HOH . F 5 HOH A 19 320 320 HOH HOH . F 5 HOH A 20 321 321 HOH HOH . F 5 HOH A 21 322 322 HOH HOH . F 5 HOH A 22 323 323 HOH HOH . F 5 HOH A 23 324 324 HOH HOH . F 5 HOH A 24 326 326 HOH HOH . F 5 HOH A 25 327 327 HOH HOH . F 5 HOH A 26 328 328 HOH HOH . F 5 HOH A 27 329 329 HOH HOH . F 5 HOH A 28 331 331 HOH HOH . F 5 HOH A 29 333 333 HOH HOH . F 5 HOH A 30 334 334 HOH HOH . F 5 HOH A 31 335 335 HOH HOH . F 5 HOH A 32 337 337 HOH HOH . F 5 HOH A 33 339 339 HOH HOH . F 5 HOH A 34 340 340 HOH HOH . F 5 HOH A 35 341 341 HOH HOH . F 5 HOH A 36 370 370 HOH HOH . F 5 HOH A 37 371 371 HOH HOH . F 5 HOH A 38 372 372 HOH HOH . F 5 HOH A 39 373 373 HOH HOH . F 5 HOH A 40 375 375 HOH HOH . F 5 HOH A 41 376 376 HOH HOH . F 5 HOH A 42 377 377 HOH HOH . F 5 HOH A 43 378 378 HOH HOH . F 5 HOH A 44 379 379 HOH HOH . F 5 HOH A 45 382 382 HOH HOH . F 5 HOH A 46 383 383 HOH HOH . F 5 HOH A 47 385 385 HOH HOH . F 5 HOH A 48 386 386 HOH HOH . F 5 HOH A 49 387 387 HOH HOH . F 5 HOH A 50 388 388 HOH HOH . F 5 HOH A 51 389 389 HOH HOH . F 5 HOH A 52 390 390 HOH HOH . F 5 HOH A 53 393 393 HOH HOH . F 5 HOH A 54 394 394 HOH HOH . F 5 HOH A 55 396 396 HOH HOH . F 5 HOH A 56 397 397 HOH HOH . F 5 HOH A 57 398 398 HOH HOH . F 5 HOH A 58 399 399 HOH HOH . F 5 HOH A 59 400 400 HOH HOH . F 5 HOH A 60 401 401 HOH HOH . F 5 HOH A 61 402 402 HOH HOH . F 5 HOH A 62 403 403 HOH HOH . F 5 HOH A 63 406 406 HOH HOH . F 5 HOH A 64 407 407 HOH HOH . F 5 HOH A 65 408 408 HOH HOH . F 5 HOH A 66 409 409 HOH HOH . F 5 HOH A 67 410 410 HOH HOH . F 5 HOH A 68 411 411 HOH HOH . F 5 HOH A 69 414 414 HOH HOH . F 5 HOH A 70 415 415 HOH HOH . F 5 HOH A 71 416 416 HOH HOH . F 5 HOH A 72 417 417 HOH HOH . F 5 HOH A 73 418 418 HOH HOH . F 5 HOH A 74 420 420 HOH HOH . F 5 HOH A 75 421 421 HOH HOH . F 5 HOH A 76 422 422 HOH HOH . F 5 HOH A 77 423 423 HOH HOH . F 5 HOH A 78 424 424 HOH HOH . F 5 HOH A 79 425 425 HOH HOH . F 5 HOH A 80 426 426 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 . . . B 2 -5.978 -8.897 9.236 1 15.88 ? CHA HEM 160 A 1 HETATM 2 C CHB HEM . . . B 2 -4.708 -6.637 5.195 1 13.43 ? CHB HEM 160 A 1 HETATM 3 C CHC HEM . . . B 2 -4.875 -2.392 7.412 1 14.13 ? CHC HEM 160 A 1 HETATM 4 C CHD HEM . . . B 2 -5.933 -4.652 11.575 1 13.83 ? CHD HEM 160 A 1 HETATM 5 C C1A HEM . . . B 2 -5.614 -8.634 7.922 1 16.01 ? C1A HEM 160 A 1 HETATM 6 C C2A HEM . . . B 2 -5.407 -9.667 6.894 1 14.81 ? C2A HEM 160 A 1 HETATM 7 C C3A HEM . . . B 2 -5.112 -9.014 5.757 1 15.87 ? C3A HEM 160 A 1 HETATM 8 C C4A HEM . . . B 2 -4.992 -7.635 6.076 1 12.39 ? C4A HEM 160 A 1 HETATM 9 C CMA HEM . . . B 2 -4.794 -9.691 4.39 1 16.79 ? CMA HEM 160 A 1 HETATM 10 C CAA HEM . . . B 2 -5.745 -11.141 7.148 1 16.9 ? CAA HEM 160 A 1 HETATM 11 C CBA HEM . . . B 2 -7.131 -11.448 6.608 0.5 14.26 ? CBA HEM 160 A 1 HETATM 12 C CGA HEM . . . B 2 -8.258 -10.635 7.155 0.5 11.11 ? CGA HEM 160 A 1 HETATM 13 O O1A HEM . . . B 2 -8.818 -9.811 6.396 0.5 14.9 ? O1A HEM 160 A 1 HETATM 14 O O2A HEM . . . B 2 -8.612 -10.892 8.307 0.5 14.83 ? O2A HEM 160 A 1 HETATM 15 C C1B HEM . . . B 2 -4.674 -5.288 5.455 1 12.28 ? C1B HEM 160 A 1 HETATM 16 C C2B HEM . . . B 2 -4.278 -4.344 4.418 1 12.74 ? C2B HEM 160 A 1 HETATM 17 C C3B HEM . . . B 2 -4.264 -3.13 5.075 1 14.08 ? C3B HEM 160 A 1 HETATM 18 C C4B HEM . . . B 2 -4.742 -3.33 6.402 1 13.4 ? C4B HEM 160 A 1 HETATM 19 C CMB HEM . . . B 2 -3.877 -4.714 2.952 1 16.13 ? CMB HEM 160 A 1 HETATM 20 C CAB HEM . . . B 2 -3.985 -1.723 4.571 1 17.95 ? CAB HEM 160 A 1 HETATM 21 C CBB HEM . . . B 2 -2.943 -1.609 3.768 1 21.32 ? CBB HEM 160 A 1 HETATM 22 C C1C HEM . . . B 2 -5.105 -2.697 8.735 1 13.8 ? C1C HEM 160 A 1 HETATM 23 C C2C HEM . . . B 2 -5.031 -1.694 9.791 1 14.16 ? C2C HEM 160 A 1 HETATM 24 C C3C HEM . . . B 2 -5.283 -2.28 10.941 1 14.68 ? C3C HEM 160 A 1 HETATM 25 C C4C HEM . . . B 2 -5.635 -3.653 10.63 1 12.42 ? C4C HEM 160 A 1 HETATM 26 C CMC HEM . . . B 2 -4.676 -0.229 9.529 1 15.97 ? CMC HEM 160 A 1 HETATM 27 C CAC HEM . . . B 2 -5.318 -1.701 12.346 1 14.33 ? CAC HEM 160 A 1 HETATM 28 C CBC HEM . . . B 2 -5.012 -0.471 12.783 1 15.83 ? CBC HEM 160 A 1 HETATM 29 C C1D HEM . . . B 2 -6.038 -5.952 11.26 1 14.8 ? C1D HEM 160 A 1 HETATM 30 C C2D HEM . . . B 2 -6.272 -6.921 12.322 1 14.61 ? C2D HEM 160 A 1 HETATM 31 C C3D HEM . . . B 2 -6.311 -8.234 11.635 1 16.42 ? C3D HEM 160 A 1 HETATM 32 C C4D HEM . . . B 2 -5.99 -7.962 10.292 1 14.61 ? C4D HEM 160 A 1 HETATM 33 C CMD HEM . . . B 2 -6.485 -6.568 13.795 1 19.45 ? CMD HEM 160 A 1 HETATM 34 C CAD HEM . . . B 2 -6.471 -9.647 12.225 1 16.32 ? CAD HEM 160 A 1 HETATM 35 C CBD HEM . . . B 2 -5.131 -10.079 12.722 1 21.49 ? CBD HEM 160 A 1 HETATM 36 C CGD HEM . . . B 2 -5.283 -11.433 13.372 1 27.97 ? CGD HEM 160 A 1 HETATM 37 O O1D HEM . . . B 2 -5.586 -11.409 14.569 1 31.44 ? O1D HEM 160 A 1 HETATM 38 O O2D HEM . . . B 2 -5.038 -12.53 12.741 1 30.34 ? O2D HEM 160 A 1 HETATM 39 N NA HEM . . . B 2 -5.337 -7.386 7.331 1 13.35 ? NA HEM 160 A 1 HETATM 40 N NB HEM . . . B 2 -4.93 -4.656 6.651 1 13.08 ? NB HEM 160 A 1 HETATM 41 N NC HEM . . . B 2 -5.483 -3.922 9.279 1 11.14 ? NC HEM 160 A 1 HETATM 42 N ND HEM . . . B 2 -5.94 -6.645 10.014 1 13.93 ? ND HEM 160 A 1 HETATM 43 FE FE HEM . . . B 2 -5.494 -5.613 8.31 1 14.56 ? FE HEM 160 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 43 #