data_5EM4 # _model_server_result.job_id KDnBkHM_Sdht0X_gg45CPg _model_server_result.datetime_utc '2025-03-11 04:58:33' _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 5em4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5EM4 # _exptl.entry_id 5EM4 _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 120 _cell.entry_id 5EM4 _cell.length_a 92.03 _cell.length_b 92.03 _cell.length_c 151.85 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EM4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31' # 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 SG CYS 436 A CYS 436 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc2 B SG CYS 436 B CYS 436 1_555 F FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? # _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 207 n n CHA C4D HEM doub 208 n n CHA HHA HEM sing 209 n n CHB C4A HEM sing 210 n n CHB C1B HEM doub 211 n n CHB HHB HEM sing 212 n n CHC C4B HEM sing 213 n n CHC C1C HEM doub 214 n n CHC HHC HEM sing 215 n n CHD C4C HEM doub 216 n n CHD C1D HEM sing 217 n n CHD HHD HEM sing 218 n n C1A C2A HEM doub 219 n y C1A NA HEM sing 220 n y C2A C3A HEM sing 221 n y C2A CAA HEM sing 222 n n C3A C4A HEM doub 223 n y C3A CMA HEM sing 224 n n C4A NA HEM sing 225 n y CMA HMA HEM sing 226 n n CMA HMAA HEM sing 227 n n CMA HMAB HEM sing 228 n n CAA CBA HEM sing 229 n n CAA HAA HEM sing 230 n n CAA HAAA HEM sing 231 n n CBA CGA HEM sing 232 n n CBA HBA HEM sing 233 n n CBA HBAA HEM sing 234 n n CGA O1A HEM doub 235 n n CGA O2A HEM sing 236 n n C1B C2B HEM sing 237 n n C1B NB HEM sing 238 n n C2B C3B HEM doub 239 n n C2B CMB HEM sing 240 n n C3B C4B HEM sing 241 n n C3B CAB HEM sing 242 n n C4B NB HEM doub 243 n n CMB HMB HEM sing 244 n n CMB HMBA HEM sing 245 n n CMB HMBB HEM sing 246 n n CAB CBB HEM doub 247 n n CAB HAB HEM sing 248 n n CBB HBB HEM sing 249 n n CBB HBBA HEM sing 250 n n C1C C2C HEM sing 251 n y C1C NC HEM sing 252 n y C2C C3C HEM doub 253 n y C2C CMC HEM sing 254 n n C3C C4C HEM sing 255 n y C3C CAC HEM sing 256 n n C4C NC HEM sing 257 n y CMC HMC HEM sing 258 n n CMC HMCA HEM sing 259 n n CMC HMCB HEM sing 260 n n CAC CBC HEM doub 261 n n CAC HAC HEM sing 262 n n CBC HBC HEM sing 263 n n CBC HBCA HEM sing 264 n n C1D C2D HEM sing 265 n n C1D ND HEM doub 266 n n C2D C3D HEM doub 267 n n C2D CMD HEM sing 268 n n C3D C4D HEM sing 269 n n C3D CAD HEM sing 270 n n C4D ND HEM sing 271 n n CMD HMD HEM sing 272 n n CMD HMDA HEM sing 273 n n CMD HMDB HEM sing 274 n n CAD CBD HEM sing 275 n n CAD HAD HEM sing 276 n n CAD HADA HEM sing 277 n n CBD CGD HEM sing 278 n n CBD HBD HEM sing 279 n n CBD HBDA HEM sing 280 n n CGD O1D HEM doub 281 n n CGD O2D HEM sing 282 n n O2A H2A HEM sing 283 n n O2D H2D HEM sing 284 n n FE NA HEM sing 285 n n FE NB HEM sing 286 n n FE NC HEM sing 287 n n FE ND HEM sing 288 n n # _atom_sites.entry_id 5EM4 _atom_sites.fract_transf_matrix[1][1] 0.010866 _atom_sites.fract_transf_matrix[1][2] 0.006274 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012547 _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] 0.006585 _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 1 501 501 HEM HEM . D 3 CM5 A 1 502 502 CM5 CM5 . E 3 CM5 A 1 503 503 CM5 CM5 . F 2 HEM B 1 501 501 HEM HEM . G 3 CM5 B 1 502 502 CM5 CM5 . H 3 CM5 B 1 503 503 CM5 CM5 . I 4 HOH A 1 601 601 HOH HOH . I 4 HOH A 2 602 602 HOH HOH . I 4 HOH A 3 603 603 HOH HOH . J 4 HOH B 1 601 601 HOH HOH . J 4 HOH B 2 602 602 HOH HOH . J 4 HOH B 3 603 603 HOH HOH . J 4 HOH B 4 604 604 HOH HOH . J 4 HOH B 5 605 605 HOH HOH . J 4 HOH B 6 606 606 HOH HOH . J 4 HOH B 7 607 607 HOH HOH . J 4 HOH B 8 608 608 HOH HOH . J 4 HOH B 9 609 609 HOH HOH . J 4 HOH B 10 610 610 HOH HOH . J 4 HOH B 11 611 611 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 -21.247 72.999 36.466 1 70.6 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . C 2 -23.221 71.323 32.437 1 63.85 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . C 2 -27.554 71.9 34.409 1 64.76 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . C 2 -25.515 72.816 38.657 1 71.74 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . C 2 -21.433 72.517 35.217 1 66.6 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . C 2 -20.373 72.187 34.362 1 73.75 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . C 2 -20.923 71.71 33.209 1 76.74 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . C 2 -22.323 71.748 33.369 1 72.08 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . C 2 -20.202 71.229 31.974 1 69.55 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . C 2 -18.906 72.358 34.645 1 72.63 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . C 2 -18.263 70.992 34.769 1 72.69 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . C 2 -16.816 71.306 34.986 1 76.69 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . C 2 -16.482 71.667 36.125 1 80.6 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . C 2 -15.979 71.267 34.048 1 77.6 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . C 2 -24.585 71.352 32.643 1 60.18 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . C 2 -25.51 71.022 31.636 1 64.94 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . C 2 -26.741 71.181 32.164 1 65.47 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . C 2 -26.517 71.647 33.537 1 63.95 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . C 2 -25.196 70.563 30.24 1 70.71 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . C 2 -28.075 70.98 31.562 1 65.85 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . C 2 -28.297 70.604 30.314 1 71.51 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . C 2 -27.405 72.159 35.744 1 66.39 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . C 2 -28.443 72.269 36.682 1 64.34 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . C 2 -27.855 72.551 37.914 1 62.24 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . C 2 -26.451 72.554 37.689 1 66.64 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . C 2 -29.901 72.123 36.339 1 62.03 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . C 2 -28.445 72.695 39.251 1 60.19 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . C 2 -29.691 72.379 39.555 1 62.47 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . C 2 -24.158 72.957 38.367 1 73 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . C 2 -23.171 73.362 39.39 1 65.8 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . C 2 -21.989 73.41 38.779 1 68.6 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . C 2 -22.266 73.058 37.378 1 73.11 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . C 2 -23.388 73.664 40.847 1 65.83 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . C 2 -20.656 73.773 39.411 1 71.59 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . C 2 -19.667 72.594 39.4 1 68.2 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . C 2 -18.689 72.726 40.53 1 70.06 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . C 2 -18.522 71.742 41.248 1 74 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . C 2 -18.042 73.774 40.771 1 68.2 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . C 2 -22.614 72.223 34.6 1 67.04 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . C 2 -25.225 71.695 33.731 1 62.37 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . C 2 -26.23 72.352 36.357 1 64.48 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . C 2 -23.561 72.771 37.171 1 76.7 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . C 2 -24.351 72.303 35.513 1 70.41 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 43 #