data_1KYO # _model_server_result.job_id hoRbNmylGRnWAOtizDAQdA _model_server_result.datetime_utc '2024-12-21 14:57:11' _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 1kyo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"AA","auth_seq_id":503}' # _entry.id 1KYO # _exptl.entry_id 1KYO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 13 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _entity.pdbx_number_of_molecules 7 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 104.19 _cell.angle_gamma 90 _cell.entry_id 1KYO _cell.length_a 147.224 _cell.length_b 165.531 _cell.length_c 195.889 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KYO _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 ? _pdbx_struct_assembly.oligomeric_details 23-meric _pdbx_struct_assembly.oligomeric_count 23 _pdbx_struct_assembly.details author_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,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA _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 ? 13 X N N ? 13 Y N N ? 13 AA N N ? 13 CA N N ? 13 DA N N ? 13 FA N N ? 13 HA 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 E SG CYS 134 E CYS 164 1_555 E SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf2 F SG CYS 28 F CYS 101 1_555 F SG CYS 50 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 J SG CYS 22 J CYS 22 1_555 J SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 K SG CYS 23 K CYS 23 1_555 K SG CYS 88 K CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 P SG CYS 134 P CYS 164 1_555 P SG CYS 150 P CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 Q SG CYS 28 Q CYS 101 1_555 Q SG CYS 50 Q CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf7 U SG CYS 22 U CYS 22 1_555 U SG CYS 96 U CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 V SG CYS 23 V CYS 23 1_555 V SG CYS 88 V CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 D SG CYS 40 D CYS 101 1_555 AA CAB HEC . D HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.806 ? covale ? covale2 D SG CYS 43 D CYS 104 1_555 AA CAC HEC . D HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale3 O SG CYS 40 O CYS 101 1_555 FA CAB HEC . O HEC 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? covale ? covale4 O SG CYS 43 O CYS 104 1_555 FA CAC HEC . O HEC 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.832 ? covale ? covale5 W SG CYS 19 W CYS 19 1_555 HA CAB HEC . W HEC 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.803 ? covale ? covale6 W SG CYS 22 W CYS 22 1_555 HA CAC HEC . W HEC 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.817 ? covale ? covale7 W C PRO 76 W PRO 76 1_555 W N M3L 77 W M3L 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale8 W C M3L 77 W M3L 77 1_555 W N LYS 78 W LYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 C NE2 HIS 82 C HIS 82 1_555 X FE HEC . C HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc2 C NE2 HIS 96 C HIS 96 1_555 Y FE HEC . C HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc3 C NE2 HIS 183 C HIS 183 1_555 X FE HEC . C HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc4 C NE2 HIS 197 C HIS 197 1_555 Y FE HEC . C HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc5 D NE2 HIS 44 D HIS 105 1_555 AA FE HEC . D HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? metalc ? metalc6 D SD MET 164 D MET 225 1_555 AA FE HEC . D HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc7 E SG CYS 129 E CYS 159 1_555 BA FE1 FES . E FES 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc8 E ND1 HIS 131 E HIS 161 1_555 BA FE2 FES . E FES 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc9 E SG CYS 148 E CYS 178 1_555 BA FE1 FES . E FES 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc10 E ND1 HIS 151 E HIS 181 1_555 BA FE2 FES . E FES 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc11 N NE2 HIS 82 N HIS 82 1_555 CA FE HEC . N HEC 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc12 N NE2 HIS 96 N HIS 96 1_555 DA FE HEC . N HEC 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc13 N NE2 HIS 183 N HIS 183 1_555 CA FE HEC . N HEC 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc14 N NE2 HIS 197 N HIS 197 1_555 DA FE HEC . N HEC 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc15 O NE2 HIS 44 O HIS 105 1_555 FA FE HEC . O HEC 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc16 O SD MET 164 O MET 225 1_555 FA FE HEC . O HEC 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc17 P SG CYS 129 P CYS 159 1_555 GA FE1 FES . P FES 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc18 P ND1 HIS 131 P HIS 161 1_555 GA FE2 FES . P FES 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc19 P SG CYS 148 P CYS 178 1_555 GA FE1 FES . P FES 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc20 P ND1 HIS 151 P HIS 181 1_555 GA FE2 FES . P FES 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc21 W NE2 HIS 23 W HIS 23 1_555 HA FE HEC . W HEC 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc22 W SD MET 85 W MET 85 1_555 HA FE HEC . W HEC 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? # _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 1KYO _atom_sites.fract_transf_matrix[1][1] 0.006792 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001718 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006041 _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] 0.005266 _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 X 13 HEC C 1 501 1 HEC HEM . Y 13 HEC C 1 502 2 HEC HEM . Z 14 SMA C 1 505 5 SMA STG . AA 13 HEC D 1 503 3 HEC HEM . BA 15 FES E 1 504 4 FES FES . CA 13 HEC N 1 521 21 HEC HEM . DA 13 HEC N 1 522 22 HEC HEM . EA 14 SMA N 1 525 25 SMA STG . FA 13 HEC O 1 523 23 HEC HEM . GA 15 FES P 1 524 24 FES FES . HA 13 HEC W 1 526 26 HEC HEM . # 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 . . . AA 13 34.763 -50.859 74.388 1 32.25 ? FE HEC 503 D 1 HETATM 2 C CHA HEC . . . AA 13 32.11 -48.648 74.893 1 32.12 ? CHA HEC 503 D 1 HETATM 3 C CHB HEC . . . AA 13 36.917 -48.24 74.747 1 32.57 ? CHB HEC 503 D 1 HETATM 4 C CHC HEC . . . AA 13 37.386 -52.998 74.204 1 35.89 ? CHC HEC 503 D 1 HETATM 5 C CHD HEC . . . AA 13 32.536 -53.39 74.112 1 35.31 ? CHD HEC 503 D 1 HETATM 6 N NA HEC . . . AA 13 34.539 -48.842 74.668 1 32.9 ? NA HEC 503 D 1 HETATM 7 C C1A HEC . . . AA 13 33.383 -48.119 74.868 1 30.85 ? C1A HEC 503 D 1 HETATM 8 C C2A HEC . . . AA 13 33.689 -46.733 75.031 1 29.18 ? C2A HEC 503 D 1 HETATM 9 C C3A HEC . . . AA 13 35.029 -46.613 74.992 1 30.48 ? C3A HEC 503 D 1 HETATM 10 C C4A HEC . . . AA 13 35.565 -47.935 74.801 1 32.02 ? C4A HEC 503 D 1 HETATM 11 C CMA HEC . . . AA 13 35.906 -45.374 75.106 1 30.33 ? CMA HEC 503 D 1 HETATM 12 C CAA HEC . . . AA 13 32.645 -45.701 75.185 1 28.92 ? CAA HEC 503 D 1 HETATM 13 C CBA HEC . . . AA 13 32.376 -45.299 76.608 1 29.33 ? CBA HEC 503 D 1 HETATM 14 C CGA HEC . . . AA 13 31.246 -44.3 76.709 1 30.56 ? CGA HEC 503 D 1 HETATM 15 O O1A HEC . . . AA 13 30.134 -44.637 76.229 1 32.07 ? O1A HEC 503 D 1 HETATM 16 O O2A HEC . . . AA 13 31.469 -43.189 77.256 1 28.04 ? O2A HEC 503 D 1 HETATM 17 N NB HEC . . . AA 13 36.752 -50.653 74.416 1 33.74 ? NB HEC 503 D 1 HETATM 18 C C1B HEC . . . AA 13 37.467 -49.492 74.552 1 33.16 ? C1B HEC 503 D 1 HETATM 19 C C2B HEC . . . AA 13 38.86 -49.747 74.297 1 34.84 ? C2B HEC 503 D 1 HETATM 20 C C3B HEC . . . AA 13 39.004 -51.084 74.203 1 35.3 ? C3B HEC 503 D 1 HETATM 21 C C4B HEC . . . AA 13 37.689 -51.653 74.324 1 34.79 ? C4B HEC 503 D 1 HETATM 22 C CMB HEC . . . AA 13 39.952 -48.688 74.112 1 33.4 ? CMB HEC 503 D 1 HETATM 23 C CAB HEC . . . AA 13 40.232 -51.974 73.989 1 37.5 ? CAB HEC 503 D 1 HETATM 24 C CBB HEC . . . AA 13 41.159 -51.949 75.199 1 40.16 ? CBB HEC 503 D 1 HETATM 25 N NC HEC . . . AA 13 34.933 -52.778 74.153 1 35.59 ? NC HEC 503 D 1 HETATM 26 C C1C HEC . . . AA 13 36.098 -53.522 74.118 1 36.48 ? C1C HEC 503 D 1 HETATM 27 C C2C HEC . . . AA 13 35.783 -54.904 73.832 1 36.04 ? C2C HEC 503 D 1 HETATM 28 C C3C HEC . . . AA 13 34.444 -54.969 73.653 1 37.12 ? C3C HEC 503 D 1 HETATM 29 C C4C HEC . . . AA 13 33.895 -53.675 74.01 1 36.45 ? C4C HEC 503 D 1 HETATM 30 C CMC HEC . . . AA 13 36.779 -56.036 73.688 1 32.99 ? CMC HEC 503 D 1 HETATM 31 C CAC HEC . . . AA 13 33.461 -55.98 73.168 1 36.4 ? CAC HEC 503 D 1 HETATM 32 C CBC HEC . . . AA 13 33.398 -57.073 74.214 1 34.92 ? CBC HEC 503 D 1 HETATM 33 N ND HEC . . . AA 13 32.722 -50.981 74.44 1 34.49 ? ND HEC 503 D 1 HETATM 34 C C1D HEC . . . AA 13 31.989 -52.14 74.338 1 34.86 ? C1D HEC 503 D 1 HETATM 35 C C2D HEC . . . AA 13 30.614 -51.883 74.697 1 35.37 ? C2D HEC 503 D 1 HETATM 36 C C3D HEC . . . AA 13 30.48 -50.548 74.827 1 36.09 ? C3D HEC 503 D 1 HETATM 37 C C4D HEC . . . AA 13 31.801 -49.984 74.702 1 34.46 ? C4D HEC 503 D 1 HETATM 38 C CMD HEC . . . AA 13 29.534 -52.88 75.025 1 35.32 ? CMD HEC 503 D 1 HETATM 39 C CAD HEC . . . AA 13 29.163 -49.799 75.164 1 39.78 ? CAD HEC 503 D 1 HETATM 40 C CBD HEC . . . AA 13 29.156 -49.001 76.483 1 43.36 ? CBD HEC 503 D 1 HETATM 41 C CGD HEC . . . AA 13 27.783 -48.441 76.867 1 44.13 ? CGD HEC 503 D 1 HETATM 42 O O1D HEC . . . AA 13 27.352 -47.451 76.231 1 45.22 ? O1D HEC 503 D 1 HETATM 43 O O2D HEC . . . AA 13 27.161 -48.971 77.825 1 43.51 ? O2D HEC 503 D 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 43 #