data_6BDK # _model_server_result.job_id LDLIwouaSn3xaVXhW5eMDA _model_server_result.datetime_utc '2024-11-29 01:47:30' _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 6bdk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 6BDK # _exptl.entry_id 6BDK _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 6BDK _cell.length_a 77.479 _cell.length_b 102.39 _cell.length_c 127.76 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6BDK _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 2_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -102.39 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_545 x,-y-1,-z 1 0 0 0 -1 0 0 0 -1 0 -102.39 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 SG CYS 422 A CYS 442 1_555 B FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc2 B FE HEM . A HEM 601 1_555 C N28 DJ1 . A DJ1 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? # _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 212 n n CHA C4D HEM doub 213 n n CHA HHA HEM sing 214 n n CHB C4A HEM sing 215 n n CHB C1B HEM doub 216 n n CHB HHB HEM sing 217 n n CHC C4B HEM sing 218 n n CHC C1C HEM doub 219 n n CHC HHC HEM sing 220 n n CHD C4C HEM doub 221 n n CHD C1D HEM sing 222 n n CHD HHD HEM sing 223 n n C1A C2A HEM doub 224 n y C1A NA HEM sing 225 n y C2A C3A HEM sing 226 n y C2A CAA HEM sing 227 n n C3A C4A HEM doub 228 n y C3A CMA HEM sing 229 n n C4A NA HEM sing 230 n y CMA HMA HEM sing 231 n n CMA HMAA HEM sing 232 n n CMA HMAB HEM sing 233 n n CAA CBA HEM sing 234 n n CAA HAA HEM sing 235 n n CAA HAAA HEM sing 236 n n CBA CGA HEM sing 237 n n CBA HBA HEM sing 238 n n CBA HBAA HEM sing 239 n n CGA O1A HEM doub 240 n n CGA O2A HEM sing 241 n n C1B C2B HEM sing 242 n n C1B NB HEM sing 243 n n C2B C3B HEM doub 244 n n C2B CMB HEM sing 245 n n C3B C4B HEM sing 246 n n C3B CAB HEM sing 247 n n C4B NB HEM doub 248 n n CMB HMB HEM sing 249 n n CMB HMBA HEM sing 250 n n CMB HMBB HEM sing 251 n n CAB CBB HEM doub 252 n n CAB HAB HEM sing 253 n n CBB HBB HEM sing 254 n n CBB HBBA HEM sing 255 n n C1C C2C HEM sing 256 n y C1C NC HEM sing 257 n y C2C C3C HEM doub 258 n y C2C CMC HEM sing 259 n n C3C C4C HEM sing 260 n y C3C CAC HEM sing 261 n n C4C NC HEM sing 262 n y CMC HMC HEM sing 263 n n CMC HMCA HEM sing 264 n n CMC HMCB HEM sing 265 n n CAC CBC HEM doub 266 n n CAC HAC HEM sing 267 n n CBC HBC HEM sing 268 n n CBC HBCA HEM sing 269 n n C1D C2D HEM sing 270 n n C1D ND HEM doub 271 n n C2D C3D HEM doub 272 n n C2D CMD HEM sing 273 n n C3D C4D HEM sing 274 n n C3D CAD HEM sing 275 n n C4D ND HEM sing 276 n n CMD HMD HEM sing 277 n n CMD HMDA HEM sing 278 n n CMD HMDB HEM sing 279 n n CAD CBD HEM sing 280 n n CAD HAD HEM sing 281 n n CAD HADA HEM sing 282 n n CBD CGD HEM sing 283 n n CBD HBD HEM sing 284 n n CBD HBDA HEM sing 285 n n CGD O1D HEM doub 286 n n CGD O2D HEM sing 287 n n O2A H2A HEM sing 288 n n O2D H2D HEM sing 289 n n FE NA HEM sing 290 n n FE NB HEM sing 291 n n FE NC HEM sing 292 n n FE ND HEM sing 293 n n # _atom_sites.entry_id 6BDK _atom_sites.fract_transf_matrix[1][1] 0.012907 _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] 0.009767 _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] 0.007827 _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 DJ1 A 1 602 700 DJ1 68D . # 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 -23.325 -31.289 -9.591 1 59.5 ? CHA HEM 601 A 1 HETATM 2 C CHB HEM . . . B 2 -22.38 -28.652 -13.528 1 64.76 ? CHB HEM 601 A 1 HETATM 3 C CHC HEM . . . B 2 -22.015 -24.799 -10.653 1 73.66 ? CHC HEM 601 A 1 HETATM 4 C CHD HEM . . . B 2 -23.029 -27.424 -6.721 1 59.76 ? CHD HEM 601 A 1 HETATM 5 C C1A HEM . . . B 2 -23.084 -30.883 -10.873 1 56.16 ? C1A HEM 601 A 1 HETATM 6 C C2A HEM . . . B 2 -23.155 -31.77 -11.997 1 54.27 ? C2A HEM 601 A 1 HETATM 7 C C3A HEM . . . B 2 -22.91 -31.052 -13.088 1 59.11 ? C3A HEM 601 A 1 HETATM 8 C C4A HEM . . . B 2 -22.661 -29.69 -12.692 1 65 ? C4A HEM 601 A 1 HETATM 9 C CMA HEM . . . B 2 -22.878 -31.611 -14.512 1 39.09 ? CMA HEM 601 A 1 HETATM 10 C CAA HEM . . . B 2 -23.48 -33.274 -11.943 1 50.09 ? CAA HEM 601 A 1 HETATM 11 C CBA HEM . . . B 2 -24.994 -33.368 -12.223 1 54.65 ? CBA HEM 601 A 1 HETATM 12 C CGA HEM . . . B 2 -25.392 -34.806 -12.413 1 66.26 ? CGA HEM 601 A 1 HETATM 13 O O1A HEM . . . B 2 -26.458 -35.06 -13.024 1 66.12 ? O1A HEM 601 A 1 HETATM 14 O O2A HEM . . . B 2 -24.62 -35.702 -11.959 1 70.18 ? O2A HEM 601 A 1 HETATM 15 C C1B HEM . . . B 2 -22.225 -27.359 -13.094 1 65.9 ? C1B HEM 601 A 1 HETATM 16 C C2B HEM . . . B 2 -21.933 -26.2 -13.913 1 66.9 ? C2B HEM 601 A 1 HETATM 17 C C3B HEM . . . B 2 -21.813 -25.157 -13.089 1 66.54 ? C3B HEM 601 A 1 HETATM 18 C C4B HEM . . . B 2 -22.043 -25.621 -11.751 1 73.14 ? C4B HEM 601 A 1 HETATM 19 C CMB HEM . . . B 2 -21.793 -26.262 -15.455 1 64.39 ? CMB HEM 601 A 1 HETATM 20 C CAB HEM . . . B 2 -21.531 -23.658 -13.357 1 64.73 ? CAB HEM 601 A 1 HETATM 21 C CBB HEM . . . B 2 -21.427 -23.108 -14.579 1 50.79 ? CBB HEM 601 A 1 HETATM 22 C C1C HEM . . . B 2 -22.28 -25.163 -9.358 1 72.47 ? C1C HEM 601 A 1 HETATM 23 C C2C HEM . . . B 2 -22.327 -24.263 -8.212 1 73.45 ? C2C HEM 601 A 1 HETATM 24 C C3C HEM . . . B 2 -22.619 -24.969 -7.142 1 66.87 ? C3C HEM 601 A 1 HETATM 25 C C4C HEM . . . B 2 -22.76 -26.363 -7.535 1 55.5 ? C4C HEM 601 A 1 HETATM 26 C CMC HEM . . . B 2 -22.143 -22.739 -8.112 1 65.38 ? CMC HEM 601 A 1 HETATM 27 C CAC HEM . . . B 2 -22.718 -24.25 -5.792 1 48.43 ? CAC HEM 601 A 1 HETATM 28 C CBC HEM . . . B 2 -23.508 -24.718 -4.861 1 58.95 ? CBC HEM 601 A 1 HETATM 29 C C1D HEM . . . B 2 -23.155 -28.718 -7.176 1 65.49 ? C1D HEM 601 A 1 HETATM 30 C C2D HEM . . . B 2 -23.34 -29.88 -6.345 1 58.65 ? C2D HEM 601 A 1 HETATM 31 C C3D HEM . . . B 2 -23.426 -30.959 -7.125 1 64.42 ? C3D HEM 601 A 1 HETATM 32 C C4D HEM . . . B 2 -23.303 -30.492 -8.49 1 59.32 ? C4D HEM 601 A 1 HETATM 33 C CMD HEM . . . B 2 -23.407 -29.84 -4.817 1 48.17 ? CMD HEM 601 A 1 HETATM 34 C CAD HEM . . . B 2 -23.652 -32.432 -6.68 1 62.08 ? CAD HEM 601 A 1 HETATM 35 C CBD HEM . . . B 2 -25.148 -32.546 -6.376 1 71.07 ? CBD HEM 601 A 1 HETATM 36 C CGD HEM . . . B 2 -25.57 -33.929 -5.901 1 74.75 ? CGD HEM 601 A 1 HETATM 37 O O1D HEM . . . B 2 -26.681 -34.046 -5.315 1 64.23 ? O1D HEM 601 A 1 HETATM 38 O O2D HEM . . . B 2 -24.803 -34.919 -6.068 1 71.16 ? O2D HEM 601 A 1 HETATM 39 N NA HEM . . . B 2 -22.771 -29.618 -11.323 1 54.84 ? NA HEM 601 A 1 HETATM 40 N NB HEM . . . B 2 -22.287 -26.971 -11.782 1 67.61 ? NB HEM 601 A 1 HETATM 41 N NC HEM . . . B 2 -22.551 -26.445 -8.9 1 62.92 ? NC HEM 601 A 1 HETATM 42 N ND HEM . . . B 2 -23.161 -29.13 -8.493 1 67.32 ? ND HEM 601 A 1 HETATM 43 FE FE HEM . . . B 2 -22.708 -28.029 -10.136 1 62.4 ? FE HEM 601 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #