data_8VYY # _model_server_result.job_id fgkA4ltL-EmUPCkLoEnG3w _model_server_result.datetime_utc '2025-06-27 23:28:38' _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 8vyy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 8VYY # _exptl.entry_id 8VYY _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 8VYY _cell.length_a 196.119 _cell.length_b 196.119 _cell.length_c 113.06 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VYY _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall 'I 4 2' _symmetry.space_group_name_H-M 'I 4 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_554 -y,-x,-z-1 0 -1 0 -1 0 0 0 0 -1 0 0 -113.06 # 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 E 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 203 A HIS 201 1_555 C FE HEM . A HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc2 B NE2 HIS 203 B HIS 201 1_555 E FE HEM . B HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? # _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 147 n n CHA C4D HEM doub 148 n n CHA HHA HEM sing 149 n n CHB C4A HEM sing 150 n n CHB C1B HEM doub 151 n n CHB HHB HEM sing 152 n n CHC C4B HEM sing 153 n n CHC C1C HEM doub 154 n n CHC HHC HEM sing 155 n n CHD C4C HEM doub 156 n n CHD C1D HEM sing 157 n n CHD HHD HEM sing 158 n n C1A C2A HEM doub 159 n y C1A NA HEM sing 160 n y C2A C3A HEM sing 161 n y C2A CAA HEM sing 162 n n C3A C4A HEM doub 163 n y C3A CMA HEM sing 164 n n C4A NA HEM sing 165 n y CMA HMA HEM sing 166 n n CMA HMAA HEM sing 167 n n CMA HMAB HEM sing 168 n n CAA CBA HEM sing 169 n n CAA HAA HEM sing 170 n n CAA HAAA HEM sing 171 n n CBA CGA HEM sing 172 n n CBA HBA HEM sing 173 n n CBA HBAA HEM sing 174 n n CGA O1A HEM doub 175 n n CGA O2A HEM sing 176 n n C1B C2B HEM sing 177 n n C1B NB HEM sing 178 n n C2B C3B HEM doub 179 n n C2B CMB HEM sing 180 n n C3B C4B HEM sing 181 n n C3B CAB HEM sing 182 n n C4B NB HEM doub 183 n n CMB HMB HEM sing 184 n n CMB HMBA HEM sing 185 n n CMB HMBB HEM sing 186 n n CAB CBB HEM doub 187 n n CAB HAB HEM sing 188 n n CBB HBB HEM sing 189 n n CBB HBBA HEM sing 190 n n C1C C2C HEM sing 191 n y C1C NC HEM sing 192 n y C2C C3C HEM doub 193 n y C2C CMC HEM sing 194 n n C3C C4C HEM sing 195 n y C3C CAC HEM sing 196 n n C4C NC HEM sing 197 n y CMC HMC HEM sing 198 n n CMC HMCA HEM sing 199 n n CMC HMCB HEM sing 200 n n CAC CBC HEM doub 201 n n CAC HAC HEM sing 202 n n CBC HBC HEM sing 203 n n CBC HBCA HEM sing 204 n n C1D C2D HEM sing 205 n n C1D ND HEM doub 206 n n C2D C3D HEM doub 207 n n C2D CMD HEM sing 208 n n C3D C4D HEM sing 209 n n C3D CAD HEM sing 210 n n C4D ND HEM sing 211 n n CMD HMD HEM sing 212 n n CMD HMDA HEM sing 213 n n CMD HMDB HEM sing 214 n n CAD CBD HEM sing 215 n n CAD HAD HEM sing 216 n n CAD HADA HEM sing 217 n n CBD CGD HEM sing 218 n n CBD HBD HEM sing 219 n n CBD HBDA HEM sing 220 n n CGD O1D HEM doub 221 n n CGD O2D HEM sing 222 n n O2A H2A HEM sing 223 n n O2D H2D HEM sing 224 n n FE NA HEM sing 225 n n FE NB HEM sing 226 n n FE NC HEM sing 227 n n FE ND HEM sing 228 n n # _atom_sites.entry_id 8VYY _atom_sites.fract_transf_matrix[1][1] 0.005099 _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] 0.005099 _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] 0.008845 _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 1 301 301 HEM HEM . D 3 78U A 1 302 401 78U 78U . E 2 HEM B 1 301 301 HEM HEM . F 3 78U B 1 302 401 78U 78U . G 4 HOH A 1 401 75 HOH HOH . G 4 HOH A 2 402 34 HOH HOH . G 4 HOH A 3 403 42 HOH HOH . G 4 HOH A 4 404 61 HOH HOH . G 4 HOH A 5 405 67 HOH HOH . G 4 HOH A 6 406 26 HOH HOH . G 4 HOH A 7 407 78 HOH HOH . G 4 HOH A 8 408 23 HOH HOH . G 4 HOH A 9 409 25 HOH HOH . G 4 HOH A 10 410 7 HOH HOH . G 4 HOH A 11 411 16 HOH HOH . G 4 HOH A 12 412 8 HOH HOH . G 4 HOH A 13 413 13 HOH HOH . G 4 HOH A 14 414 82 HOH HOH . G 4 HOH A 15 415 37 HOH HOH . G 4 HOH A 16 416 14 HOH HOH . G 4 HOH A 17 417 60 HOH HOH . G 4 HOH A 18 418 79 HOH HOH . G 4 HOH A 19 419 74 HOH HOH . G 4 HOH A 20 420 2 HOH HOH . G 4 HOH A 21 421 31 HOH HOH . G 4 HOH A 22 422 3 HOH HOH . G 4 HOH A 23 423 28 HOH HOH . G 4 HOH A 24 424 71 HOH HOH . G 4 HOH A 25 425 38 HOH HOH . G 4 HOH A 26 426 54 HOH HOH . G 4 HOH A 27 427 86 HOH HOH . G 4 HOH A 28 428 73 HOH HOH . G 4 HOH A 29 429 49 HOH HOH . G 4 HOH A 30 430 24 HOH HOH . G 4 HOH A 31 431 35 HOH HOH . G 4 HOH A 32 432 48 HOH HOH . G 4 HOH A 33 433 97 HOH HOH . G 4 HOH A 34 434 77 HOH HOH . G 4 HOH A 35 435 80 HOH HOH . G 4 HOH A 36 436 18 HOH HOH . G 4 HOH A 37 437 32 HOH HOH . G 4 HOH A 38 438 72 HOH HOH . G 4 HOH A 39 439 91 HOH HOH . G 4 HOH A 40 440 92 HOH HOH . G 4 HOH A 41 441 94 HOH HOH . G 4 HOH A 42 442 89 HOH HOH . G 4 HOH A 43 443 93 HOH HOH . G 4 HOH A 44 444 76 HOH HOH . G 4 HOH A 45 445 90 HOH HOH . G 4 HOH A 46 446 84 HOH HOH . G 4 HOH A 47 447 81 HOH HOH . H 4 HOH B 1 401 56 HOH HOH . H 4 HOH B 2 402 36 HOH HOH . H 4 HOH B 3 403 27 HOH HOH . H 4 HOH B 4 404 88 HOH HOH . H 4 HOH B 5 405 4 HOH HOH . H 4 HOH B 6 406 17 HOH HOH . H 4 HOH B 7 407 5 HOH HOH . H 4 HOH B 8 408 11 HOH HOH . H 4 HOH B 9 409 12 HOH HOH . H 4 HOH B 10 410 50 HOH HOH . H 4 HOH B 11 411 65 HOH HOH . H 4 HOH B 12 412 39 HOH HOH . H 4 HOH B 13 413 29 HOH HOH . H 4 HOH B 14 414 51 HOH HOH . H 4 HOH B 15 415 66 HOH HOH . H 4 HOH B 16 416 20 HOH HOH . H 4 HOH B 17 417 1 HOH HOH . H 4 HOH B 18 418 45 HOH HOH . H 4 HOH B 19 419 15 HOH HOH . H 4 HOH B 20 420 52 HOH HOH . H 4 HOH B 21 421 6 HOH HOH . H 4 HOH B 22 422 41 HOH HOH . H 4 HOH B 23 423 19 HOH HOH . H 4 HOH B 24 424 63 HOH HOH . H 4 HOH B 25 425 64 HOH HOH . H 4 HOH B 26 426 68 HOH HOH . H 4 HOH B 27 427 59 HOH HOH . H 4 HOH B 28 428 43 HOH HOH . H 4 HOH B 29 429 55 HOH HOH . H 4 HOH B 30 430 47 HOH HOH . H 4 HOH B 31 431 62 HOH HOH . H 4 HOH B 32 432 10 HOH HOH . H 4 HOH B 33 433 40 HOH HOH . H 4 HOH B 34 434 30 HOH HOH . H 4 HOH B 35 435 21 HOH HOH . H 4 HOH B 36 436 83 HOH HOH . H 4 HOH B 37 437 44 HOH HOH . H 4 HOH B 38 438 58 HOH HOH . H 4 HOH B 39 439 85 HOH HOH . H 4 HOH B 40 440 57 HOH HOH . H 4 HOH B 41 441 22 HOH HOH . H 4 HOH B 42 442 33 HOH HOH . H 4 HOH B 43 443 98 HOH HOH . H 4 HOH B 44 444 69 HOH HOH . H 4 HOH B 45 445 95 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 -10.689 31.335 -56.262 1 49.13 ? CHA HEM 301 A 1 HETATM 2 C CHB HEM . . . C 2 -13.779 34.93 -55.19 1 42.55 ? CHB HEM 301 A 1 HETATM 3 C CHC HEM . . . C 2 -14.783 35.565 -59.881 1 44.65 ? CHC HEM 301 A 1 HETATM 4 C CHD HEM . . . C 2 -11.421 32.149 -60.997 1 44.06 ? CHD HEM 301 A 1 HETATM 5 C C1A HEM . . . C 2 -11.504 32.209 -55.577 1 46.64 ? C1A HEM 301 A 1 HETATM 6 C C2A HEM . . . C 2 -11.701 32.252 -54.136 1 40.62 ? C2A HEM 301 A 1 HETATM 7 C C3A HEM . . . C 2 -12.551 33.246 -53.875 1 42.71 ? C3A HEM 301 A 1 HETATM 8 C C4A HEM . . . C 2 -12.912 33.87 -55.115 1 42.56 ? C4A HEM 301 A 1 HETATM 9 C CMA HEM . . . C 2 -13.08 33.703 -52.502 1 40.98 ? CMA HEM 301 A 1 HETATM 10 C CAA HEM . . . C 2 -11.082 31.318 -53.08 1 46.42 ? CAA HEM 301 A 1 HETATM 11 C CBA HEM . . . C 2 -11.953 30.064 -53.157 1 59.07 ? CBA HEM 301 A 1 HETATM 12 C CGA HEM . . . C 2 -11.65 29.088 -52.052 1 67.35 ? CGA HEM 301 A 1 HETATM 13 O O1A HEM . . . C 2 -12.457 28.134 -51.822 1 72.83 ? O1A HEM 301 A 1 HETATM 14 O O2A HEM . . . C 2 -10.597 29.286 -51.401 1 70.53 ? O2A HEM 301 A 1 HETATM 15 C C1B HEM . . . C 2 -14.351 35.386 -56.356 1 43.27 ? C1B HEM 301 A 1 HETATM 16 C C2B HEM . . . C 2 -15.359 36.408 -56.439 1 42.23 ? C2B HEM 301 A 1 HETATM 17 C C3B HEM . . . C 2 -15.665 36.588 -57.708 1 45.41 ? C3B HEM 301 A 1 HETATM 18 C C4B HEM . . . C 2 -14.833 35.701 -58.512 1 41.16 ? C4B HEM 301 A 1 HETATM 19 C CMB HEM . . . C 2 -16.041 37.187 -55.297 1 34.23 ? CMB HEM 301 A 1 HETATM 20 C CAB HEM . . . C 2 -16.736 37.646 -58.063 1 46.6 ? CAB HEM 301 A 1 HETATM 21 C CBB HEM . . . C 2 -17.426 37.603 -59.182 1 52.39 ? CBB HEM 301 A 1 HETATM 22 C C1C HEM . . . C 2 -13.908 34.745 -60.575 1 50.22 ? C1C HEM 301 A 1 HETATM 23 C C2C HEM . . . C 2 -13.762 34.707 -62.022 1 49.32 ? C2C HEM 301 A 1 HETATM 24 C C3C HEM . . . C 2 -12.864 33.775 -62.328 1 42.97 ? C3C HEM 301 A 1 HETATM 25 C C4C HEM . . . C 2 -12.37 33.159 -61.104 1 53.13 ? C4C HEM 301 A 1 HETATM 26 C CMC HEM . . . C 2 -14.503 35.567 -63.08 1 44.85 ? CMC HEM 301 A 1 HETATM 27 C CAC HEM . . . C 2 -12.488 33.51 -63.788 1 54.05 ? CAC HEM 301 A 1 HETATM 28 C CBC HEM . . . C 2 -11.623 32.574 -64.135 1 59.47 ? CBC HEM 301 A 1 HETATM 29 C C1D HEM . . . C 2 -10.934 31.595 -59.823 1 50.11 ? C1D HEM 301 A 1 HETATM 30 C C2D HEM . . . C 2 -10.002 30.486 -59.67 1 55.8 ? C2D HEM 301 A 1 HETATM 31 C C3D HEM . . . C 2 -9.803 30.267 -58.366 1 53.41 ? C3D HEM 301 A 1 HETATM 32 C C4D HEM . . . C 2 -10.601 31.227 -57.636 1 48.54 ? C4D HEM 301 A 1 HETATM 33 C CMD HEM . . . C 2 -9.336 29.675 -60.808 1 55.52 ? CMD HEM 301 A 1 HETATM 34 C CAD HEM . . . C 2 -8.886 29.178 -57.742 1 53.82 ? CAD HEM 301 A 1 HETATM 35 C CBD HEM . . . C 2 -7.571 29.765 -57.204 1 62.51 ? CBD HEM 301 A 1 HETATM 36 C CGD HEM . . . C 2 -6.901 30.656 -58.234 1 69.03 ? CGD HEM 301 A 1 HETATM 37 O O1D HEM . . . C 2 -6.559 30.151 -59.335 1 79.18 ? O1D HEM 301 A 1 HETATM 38 O O2D HEM . . . C 2 -6.695 31.878 -57.98 1 66.53 ? O2D HEM 301 A 1 HETATM 39 N NA HEM . . . C 2 -12.265 33.217 -56.155 1 41.51 ? NA HEM 301 A 1 HETATM 40 N NB HEM . . . C 2 -14.047 34.974 -57.643 1 41.88 ? NB HEM 301 A 1 HETATM 41 N NC HEM . . . C 2 -13.044 33.784 -60.047 1 47.5 ? NC HEM 301 A 1 HETATM 42 N ND HEM . . . C 2 -11.273 32.008 -58.55 1 53.82 ? ND HEM 301 A 1 HETATM 43 FE FE HEM . . . C 2 -12.853 33.269 -58.154 1 42.41 ? FE HEM 301 A 1 # _model_server_stats.io_time_ms 321 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #