data_8DYC # _model_server_result.job_id X-jx7fkhvz9VM3mlBnX9Gg _model_server_result.datetime_utc '2024-11-14 19:41:33' _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 8dyc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 8DYC # _exptl.entry_id 8DYC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 2 _entity.src_method man _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 8DYC _cell.length_a 78.069 _cell.length_b 101.239 _cell.length_c 130.16 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DYC _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E 1 1 A,B,C,D,E 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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc2 B FE HEM . A HEM 601 1_555 E O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? # _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 142 n n CHA C4D HEM doub 143 n n CHA HHA HEM sing 144 n n CHB C4A HEM sing 145 n n CHB C1B HEM doub 146 n n CHB HHB HEM sing 147 n n CHC C4B HEM sing 148 n n CHC C1C HEM doub 149 n n CHC HHC HEM sing 150 n n CHD C4C HEM doub 151 n n CHD C1D HEM sing 152 n n CHD HHD HEM sing 153 n n C1A C2A HEM doub 154 n y C1A NA HEM sing 155 n y C2A C3A HEM sing 156 n y C2A CAA HEM sing 157 n n C3A C4A HEM doub 158 n y C3A CMA HEM sing 159 n n C4A NA HEM sing 160 n y CMA HMA HEM sing 161 n n CMA HMAA HEM sing 162 n n CMA HMAB HEM sing 163 n n CAA CBA HEM sing 164 n n CAA HAA HEM sing 165 n n CAA HAAA HEM sing 166 n n CBA CGA HEM sing 167 n n CBA HBA HEM sing 168 n n CBA HBAA HEM sing 169 n n CGA O1A HEM doub 170 n n CGA O2A HEM sing 171 n n C1B C2B HEM sing 172 n n C1B NB HEM sing 173 n n C2B C3B HEM doub 174 n n C2B CMB HEM sing 175 n n C3B C4B HEM sing 176 n n C3B CAB HEM sing 177 n n C4B NB HEM doub 178 n n CMB HMB HEM sing 179 n n CMB HMBA HEM sing 180 n n CMB HMBB HEM sing 181 n n CAB CBB HEM doub 182 n n CAB HAB HEM sing 183 n n CBB HBB HEM sing 184 n n CBB HBBA HEM sing 185 n n C1C C2C HEM sing 186 n y C1C NC HEM sing 187 n y C2C C3C HEM doub 188 n y C2C CMC HEM sing 189 n n C3C C4C HEM sing 190 n y C3C CAC HEM sing 191 n n C4C NC HEM sing 192 n y CMC HMC HEM sing 193 n n CMC HMCA HEM sing 194 n n CMC HMCB HEM sing 195 n n CAC CBC HEM doub 196 n n CAC HAC HEM sing 197 n n CBC HBC HEM sing 198 n n CBC HBCA HEM sing 199 n n C1D C2D HEM sing 200 n n C1D ND HEM doub 201 n n C2D C3D HEM doub 202 n n C2D CMD HEM sing 203 n n C3D C4D HEM sing 204 n n C3D CAD HEM sing 205 n n C4D ND HEM sing 206 n n CMD HMD HEM sing 207 n n CMD HMDA HEM sing 208 n n CMD HMDB HEM sing 209 n n CAD CBD HEM sing 210 n n CAD HAD HEM sing 211 n n CAD HADA HEM sing 212 n n CBD CGD HEM sing 213 n n CBD HBD HEM sing 214 n n CBD HBDA HEM sing 215 n n CGD O1D HEM doub 216 n n CGD O2D HEM sing 217 n n O2A H2A HEM sing 218 n n O2D H2D HEM sing 219 n n FE NA HEM sing 220 n n FE NB HEM sing 221 n n FE NC HEM sing 222 n n FE ND HEM sing 223 n n # _atom_sites.entry_id 8DYC _atom_sites.fract_transf_matrix[1][1] 0.012809 _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] 0.009878 _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] 0.007683 _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 UC7 A 1 602 600 UC7 FLO . D 4 GOL A 1 603 700 GOL GOL . E 5 HOH A 1 701 3 HOH HOH . E 5 HOH A 2 702 8 HOH HOH . E 5 HOH A 3 703 2 HOH HOH . E 5 HOH A 4 704 1 HOH HOH . E 5 HOH A 5 705 6 HOH HOH . E 5 HOH A 6 706 5 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 . . . B 2 -15.619 -19.593 -10.092 1 65.02 ? CHA HEM 601 A 1 HETATM 2 C CHB HEM . . . B 2 -16.513 -22.331 -13.977 1 47.52 ? CHB HEM 601 A 1 HETATM 3 C CHC HEM . . . B 2 -16.93 -26.206 -11.057 1 52.27 ? CHC HEM 601 A 1 HETATM 4 C CHD HEM . . . B 2 -15.8 -23.539 -7.247 1 52.41 ? CHD HEM 601 A 1 HETATM 5 C C1A HEM . . . B 2 -15.836 -19.962 -11.406 1 54.09 ? C1A HEM 601 A 1 HETATM 6 C C2A HEM . . . B 2 -15.767 -19.111 -12.583 1 56.38 ? C2A HEM 601 A 1 HETATM 7 C C3A HEM . . . B 2 -16.042 -19.873 -13.638 1 51.43 ? C3A HEM 601 A 1 HETATM 8 C C4A HEM . . . B 2 -16.243 -21.236 -13.184 1 48.17 ? C4A HEM 601 A 1 HETATM 9 C CMA HEM . . . B 2 -16.096 -19.383 -15.104 1 49.67 ? CMA HEM 601 A 1 HETATM 10 C CAA HEM . . . B 2 -15.499 -17.582 -12.638 1 51.99 ? CAA HEM 601 A 1 HETATM 11 C CBA HEM . . . B 2 -14.041 -17.264 -12.381 1 57.02 ? CBA HEM 601 A 1 HETATM 12 C CGA HEM . . . B 2 -13.791 -15.871 -12.868 1 61.45 ? CGA HEM 601 A 1 HETATM 13 O O1A HEM . . . B 2 -12.757 -15.659 -13.559 1 54.78 ? O1A HEM 601 A 1 HETATM 14 O O2A HEM . . . B 2 -14.643 -14.995 -12.572 1 62.51 ? O2A HEM 601 A 1 HETATM 15 C C1B HEM . . . B 2 -16.683 -23.62 -13.504 1 59.32 ? C1B HEM 601 A 1 HETATM 16 C C2B HEM . . . B 2 -16.939 -24.782 -14.345 1 62.81 ? C2B HEM 601 A 1 HETATM 17 C C3B HEM . . . B 2 -17.074 -25.846 -13.541 1 60.67 ? C3B HEM 601 A 1 HETATM 18 C C4B HEM . . . B 2 -16.882 -25.387 -12.171 1 57.91 ? C4B HEM 601 A 1 HETATM 19 C CMB HEM . . . B 2 -17.04 -24.7 -15.889 1 62.28 ? CMB HEM 601 A 1 HETATM 20 C CAB HEM . . . B 2 -17.331 -27.335 -13.894 1 66.13 ? CAB HEM 601 A 1 HETATM 21 C CBB HEM . . . B 2 -17.199 -27.846 -15.124 1 61.93 ? CBB HEM 601 A 1 HETATM 22 C C1C HEM . . . B 2 -16.573 -25.844 -9.785 1 58.82 ? C1C HEM 601 A 1 HETATM 23 C C2C HEM . . . B 2 -16.335 -26.737 -8.662 1 61.12 ? C2C HEM 601 A 1 HETATM 24 C C3C HEM . . . B 2 -15.996 -25.976 -7.61 1 62.01 ? C3C HEM 601 A 1 HETATM 25 C C4C HEM . . . B 2 -16.047 -24.607 -8.046 1 64.22 ? C4C HEM 601 A 1 HETATM 26 C CMC HEM . . . B 2 -16.423 -28.28 -8.746 1 51.1 ? CMC HEM 601 A 1 HETATM 27 C CAC HEM . . . B 2 -15.645 -26.343 -6.159 1 50.18 ? CAC HEM 601 A 1 HETATM 28 C CBC HEM . . . B 2 -15.918 -27.526 -5.633 1 63.52 ? CBC HEM 601 A 1 HETATM 29 C C1D HEM . . . B 2 -15.735 -22.256 -7.718 1 58.36 ? C1D HEM 601 A 1 HETATM 30 C C2D HEM . . . B 2 -15.633 -21.118 -6.848 1 63.75 ? C2D HEM 601 A 1 HETATM 31 C C3D HEM . . . B 2 -15.588 -20.032 -7.615 1 58.97 ? C3D HEM 601 A 1 HETATM 32 C C4D HEM . . . B 2 -15.639 -20.448 -9.002 1 62.18 ? C4D HEM 601 A 1 HETATM 33 C CMD HEM . . . B 2 -15.603 -21.216 -5.308 1 61.44 ? CMD HEM 601 A 1 HETATM 34 C CAD HEM . . . B 2 -15.44 -18.587 -7.117 1 46.55 ? CAD HEM 601 A 1 HETATM 35 C CBD HEM . . . B 2 -13.925 -18.423 -6.953 1 59.65 ? CBD HEM 601 A 1 HETATM 36 C CGD HEM . . . B 2 -13.538 -17.09 -6.338 1 70.33 ? CGD HEM 601 A 1 HETATM 37 O O1D HEM . . . B 2 -12.426 -17.011 -5.702 1 53.83 ? O1D HEM 601 A 1 HETATM 38 O O2D HEM . . . B 2 -14.348 -16.121 -6.476 1 68.51 ? O2D HEM 601 A 1 HETATM 39 N NA HEM . . . B 2 -16.144 -21.25 -11.811 1 47.67 ? NA HEM 601 A 1 HETATM 40 N NB HEM . . . B 2 -16.668 -24.018 -12.171 1 54.76 ? NB HEM 601 A 1 HETATM 41 N NC HEM . . . B 2 -16.377 -24.545 -9.381 1 57.79 ? NC HEM 601 A 1 HETATM 42 N ND HEM . . . B 2 -15.748 -21.827 -9.037 1 51.56 ? ND HEM 601 A 1 HETATM 43 FE FE HEM . . . B 2 -16.016 -23.015 -10.647 1 57.03 ? 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 8 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #