data_6BD5 # _model_server_result.job_id pTZIdLEcNBWbYYmNba-n0w _model_server_result.datetime_utc '2024-10-11 02:17:08' _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 6bd5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 6BD5 # _exptl.entry_id 6BD5 _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 6BD5 _cell.length_a 77.449 _cell.length_b 101.95 _cell.length_c 129.18 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6BD5 _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 -101.95 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 -101.95 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc2 B FE HEM . A HEM 601 1_555 C N28 D7M . A D7M 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? # _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 193 n n CHA C4D HEM doub 194 n n CHA HHA HEM sing 195 n n CHB C4A HEM sing 196 n n CHB C1B HEM doub 197 n n CHB HHB HEM sing 198 n n CHC C4B HEM sing 199 n n CHC C1C HEM doub 200 n n CHC HHC HEM sing 201 n n CHD C4C HEM doub 202 n n CHD C1D HEM sing 203 n n CHD HHD HEM sing 204 n n C1A C2A HEM doub 205 n y C1A NA HEM sing 206 n y C2A C3A HEM sing 207 n y C2A CAA HEM sing 208 n n C3A C4A HEM doub 209 n y C3A CMA HEM sing 210 n n C4A NA HEM sing 211 n y CMA HMA HEM sing 212 n n CMA HMAA HEM sing 213 n n CMA HMAB HEM sing 214 n n CAA CBA HEM sing 215 n n CAA HAA HEM sing 216 n n CAA HAAA HEM sing 217 n n CBA CGA HEM sing 218 n n CBA HBA HEM sing 219 n n CBA HBAA HEM sing 220 n n CGA O1A HEM doub 221 n n CGA O2A HEM sing 222 n n C1B C2B HEM sing 223 n n C1B NB HEM sing 224 n n C2B C3B HEM doub 225 n n C2B CMB HEM sing 226 n n C3B C4B HEM sing 227 n n C3B CAB HEM sing 228 n n C4B NB HEM doub 229 n n CMB HMB HEM sing 230 n n CMB HMBA HEM sing 231 n n CMB HMBB HEM sing 232 n n CAB CBB HEM doub 233 n n CAB HAB HEM sing 234 n n CBB HBB HEM sing 235 n n CBB HBBA HEM sing 236 n n C1C C2C HEM sing 237 n y C1C NC HEM sing 238 n y C2C C3C HEM doub 239 n y C2C CMC HEM sing 240 n n C3C C4C HEM sing 241 n y C3C CAC HEM sing 242 n n C4C NC HEM sing 243 n y CMC HMC HEM sing 244 n n CMC HMCA HEM sing 245 n n CMC HMCB HEM sing 246 n n CAC CBC HEM doub 247 n n CAC HAC HEM sing 248 n n CBC HBC HEM sing 249 n n CBC HBCA HEM sing 250 n n C1D C2D HEM sing 251 n n C1D ND HEM doub 252 n n C2D C3D HEM doub 253 n n C2D CMD HEM sing 254 n n C3D C4D HEM sing 255 n n C3D CAD HEM sing 256 n n C4D ND HEM sing 257 n n CMD HMD HEM sing 258 n n CMD HMDA HEM sing 259 n n CMD HMDB HEM sing 260 n n CAD CBD HEM sing 261 n n CAD HAD HEM sing 262 n n CAD HADA HEM sing 263 n n CBD CGD HEM sing 264 n n CBD HBD HEM sing 265 n n CBD HBDA HEM sing 266 n n CGD O1D HEM doub 267 n n CGD O2D HEM sing 268 n n O2A H2A HEM sing 269 n n O2D H2D HEM sing 270 n n FE NA HEM sing 271 n n FE NB HEM sing 272 n n FE NC HEM sing 273 n n FE ND HEM sing 274 n n # _atom_sites.entry_id 6BD5 _atom_sites.fract_transf_matrix[1][1] 0.012912 _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] 0.009809 _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] 0.007741 _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 D7M A 1 602 700 D7M 58C . # 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 -23.292 -31.051 -10.098 1 72.11 ? CHA HEM 601 A 1 HETATM 2 C CHB HEM . . . B 2 -22.831 -28.371 -14.062 1 79.71 ? CHB HEM 601 A 1 HETATM 3 C CHC HEM . . . B 2 -22.145 -24.699 -11.103 1 69.4 ? CHC HEM 601 A 1 HETATM 4 C CHD HEM . . . B 2 -23.187 -27.195 -7.181 1 77.4 ? CHD HEM 601 A 1 HETATM 5 C C1A HEM . . . B 2 -23.203 -30.633 -11.4 1 68.42 ? C1A HEM 601 A 1 HETATM 6 C C2A HEM . . . B 2 -23.324 -31.524 -12.536 1 76.08 ? C2A HEM 601 A 1 HETATM 7 C C3A HEM . . . B 2 -23.199 -30.787 -13.632 1 72.94 ? C3A HEM 601 A 1 HETATM 8 C C4A HEM . . . B 2 -22.987 -29.419 -13.211 1 72.5 ? C4A HEM 601 A 1 HETATM 9 C CMA HEM . . . B 2 -23.259 -31.285 -15.088 1 81.75 ? CMA HEM 601 A 1 HETATM 10 C CAA HEM . . . B 2 -23.579 -33.047 -12.443 1 63.6 ? CAA HEM 601 A 1 HETATM 11 C CBA HEM . . . B 2 -25.083 -33.256 -12.599 1 82.19 ? CBA HEM 601 A 1 HETATM 12 C CGA HEM . . . B 2 -25.335 -34.737 -12.67 1 89.35 ? CGA HEM 601 A 1 HETATM 13 O O1A HEM . . . B 2 -26.285 -35.14 -13.401 1 82.65 ? O1A HEM 601 A 1 HETATM 14 O O2A HEM . . . B 2 -24.58 -35.523 -12.027 1 85.58 ? O2A HEM 601 A 1 HETATM 15 C C1B HEM . . . B 2 -22.565 -27.107 -13.627 1 85.87 ? C1B HEM 601 A 1 HETATM 16 C C2B HEM . . . B 2 -22.238 -25.928 -14.437 1 93.04 ? C2B HEM 601 A 1 HETATM 17 C C3B HEM . . . B 2 -22.067 -24.938 -13.565 1 74.77 ? C3B HEM 601 A 1 HETATM 18 C C4B HEM . . . B 2 -22.279 -25.472 -12.229 1 75.21 ? C4B HEM 601 A 1 HETATM 19 C CMB HEM . . . B 2 -22.113 -25.88 -15.987 1 72.66 ? CMB HEM 601 A 1 HETATM 20 C CAB HEM . . . B 2 -21.687 -23.458 -13.754 1 80.02 ? CAB HEM 601 A 1 HETATM 21 C CBB HEM . . . B 2 -21.422 -22.892 -14.931 1 85.94 ? CBB HEM 601 A 1 HETATM 22 C C1C HEM . . . B 2 -22.434 -25.033 -9.815 1 79.74 ? C1C HEM 601 A 1 HETATM 23 C C2C HEM . . . B 2 -22.501 -24.07 -8.727 1 83.81 ? C2C HEM 601 A 1 HETATM 24 C C3C HEM . . . B 2 -22.792 -24.724 -7.635 1 82.04 ? C3C HEM 601 A 1 HETATM 25 C C4C HEM . . . B 2 -22.92 -26.136 -7.999 1 82.85 ? C4C HEM 601 A 1 HETATM 26 C CMC HEM . . . B 2 -22.297 -22.56 -8.779 1 65.51 ? CMC HEM 601 A 1 HETATM 27 C CAC HEM . . . B 2 -22.957 -24.021 -6.279 1 69.06 ? CAC HEM 601 A 1 HETATM 28 C CBC HEM . . . B 2 -23.172 -24.756 -5.191 1 93.68 ? CBC HEM 601 A 1 HETATM 29 C C1D HEM . . . B 2 -23.279 -28.503 -7.568 1 81.72 ? C1D HEM 601 A 1 HETATM 30 C C2D HEM . . . B 2 -23.513 -29.62 -6.679 1 76.69 ? C2D HEM 601 A 1 HETATM 31 C C3D HEM . . . B 2 -23.533 -30.831 -7.612 1 73.31 ? C3D HEM 601 A 1 HETATM 32 C C4D HEM . . . B 2 -23.335 -30.294 -8.948 1 79.81 ? C4D HEM 601 A 1 HETATM 33 C CMD HEM . . . B 2 -23.65 -29.587 -5.14 1 80.83 ? CMD HEM 601 A 1 HETATM 34 C CAD HEM . . . B 2 -23.745 -32.317 -7.263 1 88.62 ? CAD HEM 601 A 1 HETATM 35 C CBD HEM . . . B 2 -25.214 -32.426 -6.862 1 92.5 ? CBD HEM 601 A 1 HETATM 36 C CGD HEM . . . B 2 -25.424 -33.703 -6.104 1 98.57 ? CGD HEM 601 A 1 HETATM 37 O O1D HEM . . . B 2 -26.435 -33.809 -5.346 1 74.7 ? O1D HEM 601 A 1 HETATM 38 O O2D HEM . . . B 2 -24.553 -34.605 -6.257 1 113.95 ? O2D HEM 601 A 1 HETATM 39 N NA HEM . . . B 2 -23 -29.352 -11.845 1 74.33 ? NA HEM 601 A 1 HETATM 40 N NB HEM . . . B 2 -22.594 -26.792 -12.29 1 68.16 ? NB HEM 601 A 1 HETATM 41 N NC HEM . . . B 2 -22.69 -26.287 -9.339 1 79.07 ? NC HEM 601 A 1 HETATM 42 N ND HEM . . . B 2 -23.181 -28.935 -8.878 1 84.95 ? ND HEM 601 A 1 HETATM 43 FE FE HEM . . . B 2 -22.873 -27.853 -10.511 1 76.45 ? FE HEM 601 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 43 #