data_2YIU # _model_server_result.job_id m77kxXRRAh8ElzqO4wc0Mg _model_server_result.datetime_utc '2024-11-13 20:58:25' _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 2yiu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":500}' # _entry.id 2YIU # _exptl.entry_id 2YIU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _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 103.18 _cell.angle_gamma 90 _cell.entry_id 2YIU _cell.length_a 85.3 _cell.length_b 164.91 _cell.length_c 100.61 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YIU _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 J N N ? 6 O 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 disulf ? disulf1 C SG CYS 137 C CYS 137 1_555 C SG CYS 154 C CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf2 F SG CYS 137 F CYS 137 1_555 F SG CYS 154 F CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 B SG CYS 58 B CYS 82 1_555 J CAB HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.63 ? covale ? covale2 B SG CYS 61 B CYS 85 1_555 J CAC HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.673 ? covale ? covale3 E SG CYS 58 E CYS 82 1_555 O CAB HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.627 ? covale ? covale4 E SG CYS 61 E CYS 85 1_555 O CAC HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.664 ? metalc ? metalc1 A NE2 HIS 97 A HIS 97 1_555 G FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? metalc ? metalc2 A NE2 HIS 111 A HIS 111 1_555 H FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc3 A NE2 HIS 198 A HIS 198 1_555 G FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.829 ? metalc ? metalc4 A NE2 HIS 212 A HIS 212 1_555 H FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc5 B NE2 HIS 62 B HIS 86 1_555 J FE HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc6 B SD MET 186 B MET 210 1_555 J FE HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc7 C SG CYS 132 C CYS 132 1_555 K FE2 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc8 C ND1 HIS 134 C HIS 134 1_555 K FE1 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc9 C SG CYS 152 C CYS 152 1_555 K FE2 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc10 C ND1 HIS 155 C HIS 155 1_555 K FE1 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc11 D NE2 HIS 97 D HIS 97 1_555 L FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc12 D NE2 HIS 111 D HIS 111 1_555 M FE HEM . D HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc13 D NE2 HIS 198 D HIS 198 1_555 L FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc14 D NE2 HIS 212 D HIS 212 1_555 M FE HEM . D HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc15 E NE2 HIS 62 E HIS 86 1_555 O FE HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc16 E SD MET 186 E MET 210 1_555 O FE HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc17 F SG CYS 132 F CYS 132 1_555 P FE2 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc18 F ND1 HIS 134 F HIS 134 1_555 P FE1 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc19 F SG CYS 152 F CYS 152 1_555 P FE2 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc20 F ND1 HIS 155 F HIS 155 1_555 P FE1 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? # _chem_comp.formula 'C34 H34 Fe N4 O4' _chem_comp.formula_weight 618.503 _chem_comp.id HEC _chem_comp.mon_nstd_flag . _chem_comp.name 'HEME C' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 FE NA HEC sing 133 n n FE NB HEC sing 134 n n FE NC HEC sing 135 n n FE ND HEC sing 136 n n CHA C1A HEC doub 137 n n CHA C4D HEC sing 138 n n CHA HHA HEC sing 139 n n CHB C4A HEC doub 140 n n CHB C1B HEC sing 141 n n CHB HHB HEC sing 142 n n CHC C4B HEC doub 143 n n CHC C1C HEC sing 144 n n CHC HHC HEC sing 145 n n CHD C4C HEC doub 146 n n CHD C1D HEC sing 147 n n CHD HHD HEC sing 148 n n NA C1A HEC sing 149 n y NA C4A HEC sing 150 n y C1A C2A HEC sing 151 n y C2A C3A HEC doub 152 n y C2A CAA HEC sing 153 n n C3A C4A HEC sing 154 n y C3A CMA HEC sing 155 n n CMA HMA1 HEC sing 156 n n CMA HMA2 HEC sing 157 n n CMA HMA3 HEC sing 158 n n CAA CBA HEC sing 159 n n CAA HAA1 HEC sing 160 n n CAA HAA2 HEC sing 161 n n CBA CGA HEC sing 162 n n CBA HBA1 HEC sing 163 n n CBA HBA2 HEC sing 164 n n CGA O1A HEC doub 165 n n CGA O2A HEC sing 166 n n O2A H2A HEC sing 167 n n NB C1B HEC sing 168 n y NB C4B HEC sing 169 n y C1B C2B HEC doub 170 n y C2B C3B HEC sing 171 n y C2B CMB HEC sing 172 n n C3B C4B HEC sing 173 n y C3B CAB HEC doub 174 e n CMB HMB1 HEC sing 175 n n CMB HMB2 HEC sing 176 n n CMB HMB3 HEC sing 177 n n CAB CBB HEC sing 178 n n CAB HAB HEC sing 179 n n CBB HBB1 HEC sing 180 n n CBB HBB2 HEC sing 181 n n CBB HBB3 HEC sing 182 n n NC C1C HEC sing 183 n y NC C4C HEC sing 184 n y C1C C2C HEC doub 185 n y C2C C3C HEC sing 186 n y C2C CMC HEC sing 187 n n C3C C4C HEC sing 188 n y C3C CAC HEC doub 189 e n CMC HMC1 HEC sing 190 n n CMC HMC2 HEC sing 191 n n CMC HMC3 HEC sing 192 n n CAC CBC HEC sing 193 n n CAC HAC HEC sing 194 n n CBC HBC1 HEC sing 195 n n CBC HBC2 HEC sing 196 n n CBC HBC3 HEC sing 197 n n ND C1D HEC sing 198 n y ND C4D HEC sing 199 n y C1D C2D HEC doub 200 n y C2D C3D HEC sing 201 n y C2D CMD HEC sing 202 n n C3D C4D HEC doub 203 n y C3D CAD HEC sing 204 n n CMD HMD1 HEC sing 205 n n CMD HMD2 HEC sing 206 n n CMD HMD3 HEC sing 207 n n CAD CBD HEC sing 208 n n CAD HAD1 HEC sing 209 n n CAD HAD2 HEC sing 210 n n CBD CGD HEC sing 211 n n CBD HBD1 HEC sing 212 n n CBD HBD2 HEC sing 213 n n CGD O1D HEC doub 214 n n CGD O2D HEC sing 215 n n O2D H2D HEC sing 216 n n # _atom_sites.entry_id 2YIU _atom_sites.fract_transf_matrix[1][1] 0.011723 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002745 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006064 _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] 0.010208 _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 G 4 HEM A 1 500 500 HEM HEM . H 4 HEM A 1 501 501 HEM HEM . I 5 SMA A 1 502 502 SMA SMA . J 6 HEC B 1 500 500 HEC HEC . K 7 FES C 1 500 500 FES FES . L 4 HEM D 1 500 500 HEM HEM . M 4 HEM D 1 501 501 HEM HEM . N 5 SMA D 1 502 502 SMA SMA . O 6 HEC E 1 500 500 HEC HEC . P 7 FES F 1 500 500 FES FES . Q 8 HOH A 1 2001 2001 HOH HOH . Q 8 HOH A 2 2002 2002 HOH HOH . Q 8 HOH A 3 2003 2003 HOH HOH . R 8 HOH B 1 2001 2001 HOH HOH . S 8 HOH D 1 2001 2001 HOH HOH . T 8 HOH F 1 2001 2001 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 FE FE HEC . . . J 6 17.817 -10.662 -32.44 1 28.18 ? FE HEC 500 B 1 HETATM 2 C CHA HEC . . . J 6 16.154 -12.849 -34.442 1 26.29 ? CHA HEC 500 B 1 HETATM 3 C CHB HEC . . . J 6 20.034 -13.197 -31.64 1 26.24 ? CHB HEC 500 B 1 HETATM 4 C CHC HEC . . . J 6 19.796 -8.558 -30.514 1 25.47 ? CHC HEC 500 B 1 HETATM 5 C CHD HEC . . . J 6 15.715 -8.134 -33.097 1 27.95 ? CHD HEC 500 B 1 HETATM 6 N NA HEC . . . J 6 18.006 -12.607 -32.925 1 25.31 ? NA HEC 500 B 1 HETATM 7 C C1A HEC . . . J 6 17.245 -13.338 -33.81 1 26.63 ? C1A HEC 500 B 1 HETATM 8 C C2A HEC . . . J 6 17.789 -14.689 -33.914 1 27.73 ? C2A HEC 500 B 1 HETATM 9 C C3A HEC . . . J 6 18.838 -14.74 -33.123 1 26.96 ? C3A HEC 500 B 1 HETATM 10 C C4A HEC . . . J 6 18.999 -13.457 -32.495 1 26.81 ? C4A HEC 500 B 1 HETATM 11 C CMA HEC . . . J 6 19.734 -15.96 -32.904 1 25.98 ? CMA HEC 500 B 1 HETATM 12 C CAA HEC . . . J 6 17.359 -15.923 -34.723 1 27.29 ? CAA HEC 500 B 1 HETATM 13 C CBA HEC . . . J 6 16.094 -15.752 -35.55 1 26.97 ? CBA HEC 500 B 1 HETATM 14 C CGA HEC . . . J 6 15.846 -17.114 -36.199 1 27.51 ? CGA HEC 500 B 1 HETATM 15 O O1A HEC . . . J 6 14.648 -17.319 -36.591 1 27.15 ? O1A HEC 500 B 1 HETATM 16 O O2A HEC . . . J 6 16.821 -17.965 -36.325 1 20.22 ? O2A HEC 500 B 1 HETATM 17 N NB HEC . . . J 6 19.628 -10.832 -31.366 1 25.57 ? NB HEC 500 B 1 HETATM 18 C C1B HEC . . . J 6 20.315 -11.993 -31.087 1 24.25 ? C1B HEC 500 B 1 HETATM 19 C C2B HEC . . . J 6 21.383 -11.735 -30.155 1 22.61 ? C2B HEC 500 B 1 HETATM 20 C C3B HEC . . . J 6 21.29 -10.455 -29.815 1 24.51 ? C3B HEC 500 B 1 HETATM 21 C C4B HEC . . . J 6 20.205 -9.857 -30.577 1 25.79 ? C4B HEC 500 B 1 HETATM 22 C CMB HEC . . . J 6 22.367 -12.745 -29.53 1 19.49 ? CMB HEC 500 B 1 HETATM 23 C CAB HEC . . . J 6 22.2 -9.753 -28.795 1 24.88 ? CAB HEC 500 B 1 HETATM 24 C CBB HEC . . . J 6 23.529 -9.418 -29.469 1 24 ? CBB HEC 500 B 1 HETATM 25 N NC HEC . . . J 6 17.76 -8.736 -31.922 1 26.23 ? NC HEC 500 B 1 HETATM 26 C C1C HEC . . . J 6 18.667 -8.06 -31.127 1 26.53 ? C1C HEC 500 B 1 HETATM 27 C C2C HEC . . . J 6 18.253 -6.678 -31.029 1 25.39 ? C2C HEC 500 B 1 HETATM 28 C C3C HEC . . . J 6 17.144 -6.529 -31.764 1 26.18 ? C3C HEC 500 B 1 HETATM 29 C C4C HEC . . . J 6 16.802 -7.824 -32.313 1 27.1 ? C4C HEC 500 B 1 HETATM 30 C CMC HEC . . . J 6 19.081 -5.637 -30.254 1 19.91 ? CMC HEC 500 B 1 HETATM 31 C CAC HEC . . . J 6 16.314 -5.242 -31.937 1 32.06 ? CAC HEC 500 B 1 HETATM 32 C CBC HEC . . . J 6 17.181 -4.13 -32.557 1 31.86 ? CBC HEC 500 B 1 HETATM 33 N ND HEC . . . J 6 16.205 -10.534 -33.537 1 25.94 ? ND HEC 500 B 1 HETATM 34 C C1D HEC . . . J 6 15.489 -9.362 -33.703 1 27.87 ? C1D HEC 500 B 1 HETATM 35 C C2D HEC . . . J 6 14.442 -9.624 -34.66 1 29.75 ? C2D HEC 500 B 1 HETATM 36 C C3D HEC . . . J 6 14.562 -11.09 -35.045 1 30.45 ? C3D HEC 500 B 1 HETATM 37 C C4D HEC . . . J 6 15.702 -11.565 -34.324 1 27.53 ? C4D HEC 500 B 1 HETATM 38 C CMD HEC . . . J 6 13.378 -8.649 -35.186 1 32.27 ? CMD HEC 500 B 1 HETATM 39 C CAD HEC . . . J 6 13.701 -11.877 -36.053 1 33.18 ? CAD HEC 500 B 1 HETATM 40 C CBD HEC . . . J 6 14.547 -11.976 -37.318 1 37.07 ? CBD HEC 500 B 1 HETATM 41 C CGD HEC . . . J 6 13.633 -12.35 -38.44 1 40.63 ? CGD HEC 500 B 1 HETATM 42 O O1D HEC . . . J 6 13.265 -13.56 -38.478 1 42.35 ? O1D HEC 500 B 1 HETATM 43 O O2D HEC . . . J 6 13.277 -11.445 -39.267 1 42.93 ? O2D HEC 500 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 220 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 43 #