data_6DAL # _model_server_result.job_id Rv7X8p3cqtdB-KtU8H5HvA _model_server_result.datetime_utc '2024-11-24 16:42:50' _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 6dal # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 6DAL # _exptl.entry_id 6DAL _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 6DAL _cell.length_a 76.558 _cell.length_b 101.62 _cell.length_c 127.13 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DAL _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _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 _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 covale ? covale1 A N CYS 38 A CYS 58 1_555 C O3 GOL . A GOL 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.307 ? metalc ? metalc1 A SG CYS 422 A CYS 442 1_555 B FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc2 B FE HEM . A HEM 601 1_555 D N29 G1D . A G1D 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? # _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 219 n n CHA C4D HEM doub 220 n n CHA HHA HEM sing 221 n n CHB C4A HEM sing 222 n n CHB C1B HEM doub 223 n n CHB HHB HEM sing 224 n n CHC C4B HEM sing 225 n n CHC C1C HEM doub 226 n n CHC HHC HEM sing 227 n n CHD C4C HEM doub 228 n n CHD C1D HEM sing 229 n n CHD HHD HEM sing 230 n n C1A C2A HEM doub 231 n y C1A NA HEM sing 232 n y C2A C3A HEM sing 233 n y C2A CAA HEM sing 234 n n C3A C4A HEM doub 235 n y C3A CMA HEM sing 236 n n C4A NA HEM sing 237 n y CMA HMA HEM sing 238 n n CMA HMAA HEM sing 239 n n CMA HMAB HEM sing 240 n n CAA CBA HEM sing 241 n n CAA HAA HEM sing 242 n n CAA HAAA HEM sing 243 n n CBA CGA HEM sing 244 n n CBA HBA HEM sing 245 n n CBA HBAA HEM sing 246 n n CGA O1A HEM doub 247 n n CGA O2A HEM sing 248 n n C1B C2B HEM sing 249 n n C1B NB HEM sing 250 n n C2B C3B HEM doub 251 n n C2B CMB HEM sing 252 n n C3B C4B HEM sing 253 n n C3B CAB HEM sing 254 n n C4B NB HEM doub 255 n n CMB HMB HEM sing 256 n n CMB HMBA HEM sing 257 n n CMB HMBB HEM sing 258 n n CAB CBB HEM doub 259 n n CAB HAB HEM sing 260 n n CBB HBB HEM sing 261 n n CBB HBBA HEM sing 262 n n C1C C2C HEM sing 263 n y C1C NC HEM sing 264 n y C2C C3C HEM doub 265 n y C2C CMC HEM sing 266 n n C3C C4C HEM sing 267 n y C3C CAC HEM sing 268 n n C4C NC HEM sing 269 n y CMC HMC HEM sing 270 n n CMC HMCA HEM sing 271 n n CMC HMCB HEM sing 272 n n CAC CBC HEM doub 273 n n CAC HAC HEM sing 274 n n CBC HBC HEM sing 275 n n CBC HBCA HEM sing 276 n n C1D C2D HEM sing 277 n n C1D ND HEM doub 278 n n C2D C3D HEM doub 279 n n C2D CMD HEM sing 280 n n C3D C4D HEM sing 281 n n C3D CAD HEM sing 282 n n C4D ND HEM sing 283 n n CMD HMD HEM sing 284 n n CMD HMDA HEM sing 285 n n CMD HMDB HEM sing 286 n n CAD CBD HEM sing 287 n n CAD HAD HEM sing 288 n n CAD HADA HEM sing 289 n n CBD CGD HEM sing 290 n n CBD HBD HEM sing 291 n n CBD HBDA HEM sing 292 n n CGD O1D HEM doub 293 n n CGD O2D HEM sing 294 n n O2A H2A HEM sing 295 n n O2D H2D HEM sing 296 n n FE NA HEM sing 297 n n FE NB HEM sing 298 n n FE NC HEM sing 299 n n FE ND HEM sing 300 n n # _atom_sites.entry_id 6DAL _atom_sites.fract_transf_matrix[1][1] 0.013062 _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] 0.009841 _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] 0.007866 _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 1 601 500 HEM HEM . C 3 GOL A 1 602 605 GOL GOL . D 4 G1D A 1 603 700 G1D 189 . # 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 -15.201 -19.856 -9.352 1 51.98 ? CHA HEM 601 A 1 HETATM 2 C CHB HEM . . . B 2 -15.83 -22.473 -13.37 1 68.37 ? CHB HEM 601 A 1 HETATM 3 C CHC HEM . . . B 2 -16.499 -26.243 -10.48 1 56.79 ? CHC HEM 601 A 1 HETATM 4 C CHD HEM . . . B 2 -15.411 -23.77 -6.498 1 48.07 ? CHD HEM 601 A 1 HETATM 5 C C1A HEM . . . B 2 -15.342 -20.254 -10.662 1 64.05 ? C1A HEM 601 A 1 HETATM 6 C C2A HEM . . . B 2 -15.236 -19.386 -11.807 1 69.57 ? C2A HEM 601 A 1 HETATM 7 C C3A HEM . . . B 2 -15.396 -20.125 -12.897 1 70.78 ? C3A HEM 601 A 1 HETATM 8 C C4A HEM . . . B 2 -15.629 -21.467 -12.492 1 59.69 ? C4A HEM 601 A 1 HETATM 9 C CMA HEM . . . B 2 -15.389 -19.711 -14.374 1 39.29 ? CMA HEM 601 A 1 HETATM 10 C CAA HEM . . . B 2 -14.957 -17.893 -11.771 1 59.51 ? CAA HEM 601 A 1 HETATM 11 C CBA HEM . . . B 2 -13.487 -17.773 -12.157 1 60.07 ? CBA HEM 601 A 1 HETATM 12 C CGA HEM . . . B 2 -13.146 -16.292 -12.212 1 73.7 ? CGA HEM 601 A 1 HETATM 13 O O1A HEM . . . B 2 -12.073 -15.973 -12.792 1 54.56 ? O1A HEM 601 A 1 HETATM 14 O O2A HEM . . . B 2 -13.941 -15.419 -11.717 1 55.59 ? O2A HEM 601 A 1 HETATM 15 C C1B HEM . . . B 2 -16.059 -23.738 -12.95 1 66.67 ? C1B HEM 601 A 1 HETATM 16 C C2B HEM . . . B 2 -16.335 -24.882 -13.795 1 70.38 ? C2B HEM 601 A 1 HETATM 17 C C3B HEM . . . B 2 -16.546 -25.934 -12.979 1 64.39 ? C3B HEM 601 A 1 HETATM 18 C C4B HEM . . . B 2 -16.376 -25.454 -11.61 1 73.84 ? C4B HEM 601 A 1 HETATM 19 C CMB HEM . . . B 2 -16.399 -24.793 -15.343 1 63.77 ? CMB HEM 601 A 1 HETATM 20 C CAB HEM . . . B 2 -16.866 -27.412 -13.302 1 54.51 ? CAB HEM 601 A 1 HETATM 21 C CBB HEM . . . B 2 -16.527 -27.975 -14.459 1 69.68 ? CBB HEM 601 A 1 HETATM 22 C C1C HEM . . . B 2 -16.191 -25.916 -9.177 1 60.48 ? C1C HEM 601 A 1 HETATM 23 C C2C HEM . . . B 2 -16.086 -26.872 -8.101 1 74.81 ? C2C HEM 601 A 1 HETATM 24 C C3C HEM . . . B 2 -15.785 -26.229 -6.974 1 70.75 ? C3C HEM 601 A 1 HETATM 25 C C4C HEM . . . B 2 -15.702 -24.819 -7.301 1 55.64 ? C4C HEM 601 A 1 HETATM 26 C CMC HEM . . . B 2 -16.268 -28.389 -8.231 1 50.89 ? CMC HEM 601 A 1 HETATM 27 C CAC HEM . . . B 2 -15.596 -26.966 -5.632 1 60.14 ? CAC HEM 601 A 1 HETATM 28 C CBC HEM . . . B 2 -15.116 -26.371 -4.549 1 67.36 ? CBC HEM 601 A 1 HETATM 29 C C1D HEM . . . B 2 -15.3 -22.468 -6.94 1 66.03 ? C1D HEM 601 A 1 HETATM 30 C C2D HEM . . . B 2 -15.088 -21.321 -6.092 1 63.94 ? C2D HEM 601 A 1 HETATM 31 C C3D HEM . . . B 2 -15.016 -20.231 -6.867 1 73.27 ? C3D HEM 601 A 1 HETATM 32 C C4D HEM . . . B 2 -15.195 -20.665 -8.25 1 49.54 ? C4D HEM 601 A 1 HETATM 33 C CMD HEM . . . B 2 -14.971 -21.377 -4.564 1 60.56 ? CMD HEM 601 A 1 HETATM 34 C CAD HEM . . . B 2 -14.802 -18.774 -6.377 1 58.37 ? CAD HEM 601 A 1 HETATM 35 C CBD HEM . . . B 2 -13.317 -18.418 -6.316 1 63.57 ? CBD HEM 601 A 1 HETATM 36 C CGD HEM . . . B 2 -12.996 -17.121 -5.571 1 83.74 ? CGD HEM 601 A 1 HETATM 37 O O1D HEM . . . B 2 -11.993 -17.084 -4.788 1 74.81 ? O1D HEM 601 A 1 HETATM 38 O O2D HEM . . . B 2 -13.722 -16.103 -5.725 1 77.26 ? O2D HEM 601 A 1 HETATM 39 N NA HEM . . . B 2 -15.597 -21.528 -11.141 1 56.86 ? NA HEM 601 A 1 HETATM 40 N NB HEM . . . B 2 -16.076 -24.106 -11.644 1 65.94 ? NB HEM 601 A 1 HETATM 41 N NC HEM . . . B 2 -15.971 -24.661 -8.632 1 63.18 ? NC HEM 601 A 1 HETATM 42 N ND HEM . . . B 2 -15.361 -22.029 -8.255 1 71.27 ? ND HEM 601 A 1 HETATM 43 FE FE HEM . . . B 2 -15.556 -23.174 -9.911 1 62.13 ? FE HEM 601 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #