data_6DYB # _model_server_result.job_id xa5CLrU0Vvz-_vWxDvXKSA _model_server_result.datetime_utc '2024-12-15 05:32:56' _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 6dyb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":201}' # _entry.id 6DYB # _exptl.entry_id 6DYB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 2 _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 90 _cell.angle_gamma 120 _cell.entry_id 6DYB _cell.length_a 73.008 _cell.length_b 73.008 _cell.length_c 143.994 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DYB _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,K 1 1 B,H,I,J,L 2 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 ? 2 C N N ? 2 H 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 A SG CYS 96 A CYS 96 1_555 B SG CYS 96 C CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 A SG CYS 98 A CYS 98 1_555 C CAB HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.774 ? covale ? covale2 A SG CYS 101 A CYS 101 1_555 C CAC HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.771 ? covale ? covale3 B SG CYS 98 C CYS 98 1_555 H CAB HEC . C HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.764 ? covale ? covale4 B SG CYS 101 C CYS 101 1_555 H CAC HEC . C HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.772 ? metalc ? metalc1 A OE1 GLU 4 A GLU 4 1_555 D CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc2 A OE1 GLU 4 A GLU 4 1_555 D CA CA . A CA 202 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? metalc ? metalc3 A OE2 GLU 4 A GLU 4 1_555 D CA CA . A CA 202 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? metalc ? metalc4 A OE2 GLU 4 A GLU 4 1_555 F CA CA . A CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc5 A OD1 ASP 5 A ASP 5 1_555 E CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc6 A OD1 ASP 5 A ASP 5 1_555 E CA CA . A CA 203 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? metalc ? metalc7 A OD2 ASP 5 A ASP 5 1_555 E CA CA . A CA 203 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc8 A SD MET 7 A MET 7 1_555 C FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc9 A OE2 GLU 8 A GLU 8 1_555 D CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc10 A OE1 GLU 8 A GLU 8 1_555 E CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc11 A OD2 ASP 50 A ASP 50 1_555 D CA CA . A CA 202 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc12 A OD2 ASP 50 A ASP 50 1_555 F CA CA . A CA 204 10_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.989 ? metalc ? metalc13 A OD1 ASP 50 A ASP 50 1_555 G CA CA . A CA 205 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? metalc ? metalc14 A NE2 HIS 102 A HIS 102 1_555 C FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc15 C O1A HEC . A HEC 201 1_555 D CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc16 E CA CA . A CA 203 1_555 K O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc17 E CA CA . A CA 203 1_555 K O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc18 E CA CA . A CA 203 1_555 K O HOH . A HOH 304 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc19 F CA CA . A CA 204 1_555 K O HOH . A HOH 306 10_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? metalc ? metalc20 G CA CA . A CA 205 1_555 K O HOH . A HOH 306 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.803 ? metalc ? metalc21 B OE2 GLU 4 C GLU 4 1_555 I CA CA . C CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? metalc ? metalc22 B OE2 GLU 4 C GLU 4 1_555 I CA CA . C CA 202 10_444 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc23 B OE1 GLU 4 C GLU 4 1_555 J CA CA . C CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? metalc ? metalc24 B SD MET 7 C MET 7 1_555 H FE HEC . C HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? metalc ? metalc25 B OE1 GLU 8 C GLU 8 1_555 J CA CA . C CA 203 10_444 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc26 B OE2 GLU 8 C GLU 8 1_555 J CA CA . C CA 203 10_444 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc27 B NE2 HIS 102 C HIS 102 1_555 H FE HEC . C HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc28 H O1A HEC . C HEC 201 1_555 I CA CA . C CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc29 H O1A HEC . C HEC 201 1_555 I CA CA . C CA 202 10_444 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? # _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 129 n n FE NB HEC sing 130 n n FE NC HEC sing 131 n n FE ND HEC sing 132 n n CHA C1A HEC doub 133 n n CHA C4D HEC sing 134 n n CHA HHA HEC sing 135 n n CHB C4A HEC doub 136 n n CHB C1B HEC sing 137 n n CHB HHB HEC sing 138 n n CHC C4B HEC doub 139 n n CHC C1C HEC sing 140 n n CHC HHC HEC sing 141 n n CHD C4C HEC doub 142 n n CHD C1D HEC sing 143 n n CHD HHD HEC sing 144 n n NA C1A HEC sing 145 n y NA C4A HEC sing 146 n y C1A C2A HEC sing 147 n y C2A C3A HEC doub 148 n y C2A CAA HEC sing 149 n n C3A C4A HEC sing 150 n y C3A CMA HEC sing 151 n n CMA HMA1 HEC sing 152 n n CMA HMA2 HEC sing 153 n n CMA HMA3 HEC sing 154 n n CAA CBA HEC sing 155 n n CAA HAA1 HEC sing 156 n n CAA HAA2 HEC sing 157 n n CBA CGA HEC sing 158 n n CBA HBA1 HEC sing 159 n n CBA HBA2 HEC sing 160 n n CGA O1A HEC doub 161 n n CGA O2A HEC sing 162 n n O2A H2A HEC sing 163 n n NB C1B HEC sing 164 n y NB C4B HEC sing 165 n y C1B C2B HEC doub 166 n y C2B C3B HEC sing 167 n y C2B CMB HEC sing 168 n n C3B C4B HEC sing 169 n y C3B CAB HEC doub 170 e n CMB HMB1 HEC sing 171 n n CMB HMB2 HEC sing 172 n n CMB HMB3 HEC sing 173 n n CAB CBB HEC sing 174 n n CAB HAB HEC sing 175 n n CBB HBB1 HEC sing 176 n n CBB HBB2 HEC sing 177 n n CBB HBB3 HEC sing 178 n n NC C1C HEC sing 179 n y NC C4C HEC sing 180 n y C1C C2C HEC doub 181 n y C2C C3C HEC sing 182 n y C2C CMC HEC sing 183 n n C3C C4C HEC sing 184 n y C3C CAC HEC doub 185 e n CMC HMC1 HEC sing 186 n n CMC HMC2 HEC sing 187 n n CMC HMC3 HEC sing 188 n n CAC CBC HEC sing 189 n n CAC HAC HEC sing 190 n n CBC HBC1 HEC sing 191 n n CBC HBC2 HEC sing 192 n n CBC HBC3 HEC sing 193 n n ND C1D HEC sing 194 n y ND C4D HEC sing 195 n y C1D C2D HEC doub 196 n y C2D C3D HEC sing 197 n y C2D CMD HEC sing 198 n n C3D C4D HEC doub 199 n y C3D CAD HEC sing 200 n n CMD HMD1 HEC sing 201 n n CMD HMD2 HEC sing 202 n n CMD HMD3 HEC sing 203 n n CAD CBD HEC sing 204 n n CAD HAD1 HEC sing 205 n n CAD HAD2 HEC sing 206 n n CBD CGD HEC sing 207 n n CBD HBD1 HEC sing 208 n n CBD HBD2 HEC sing 209 n n CGD O1D HEC doub 210 n n CGD O2D HEC sing 211 n n O2D H2D HEC sing 212 n n # _atom_sites.entry_id 6DYB _atom_sites.fract_transf_matrix[1][1] 0.013697 _atom_sites.fract_transf_matrix[1][2] 0.007908 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015816 _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] 0.006945 _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 C 2 HEC A 1 201 1 HEC HEC . D 3 CA A 1 202 3 CA CA . E 3 CA A 1 203 4 CA CA . F 3 CA A 1 204 6 CA CA . G 3 CA A 1 205 7 CA CA . H 2 HEC C 1 201 2 HEC HEC . I 3 CA C 1 202 2 CA CA . J 3 CA C 1 203 5 CA CA . K 4 HOH A 1 301 15 HOH HOH . K 4 HOH A 2 302 13 HOH HOH . K 4 HOH A 3 303 4 HOH HOH . K 4 HOH A 4 304 5 HOH HOH . K 4 HOH A 5 305 7 HOH HOH . K 4 HOH A 6 306 8 HOH HOH . K 4 HOH A 7 307 6 HOH HOH . K 4 HOH A 8 308 9 HOH HOH . L 4 HOH C 1 301 12 HOH HOH . L 4 HOH C 2 302 11 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 . . . H 2 0.457 -34.494 -14.453 1 96.27 ? FE HEC 201 C 1 HETATM 2 C CHA HEC . . . H 2 0.319 -38.035 -13.958 1 93 ? CHA HEC 201 C 1 HETATM 3 C CHB HEC . . . H 2 2.073 -34.304 -11.457 1 84.92 ? CHB HEC 201 C 1 HETATM 4 C CHC HEC . . . H 2 0.358 -31.178 -14.784 1 84.06 ? CHC HEC 201 C 1 HETATM 5 C CHD HEC . . . H 2 -1.089 -34.908 -17.474 1 92.33 ? CHD HEC 201 C 1 HETATM 6 N NA HEC . . . H 2 1.077 -35.936 -12.976 1 88.95 ? NA HEC 201 C 1 HETATM 7 C C1A HEC . . . H 2 0.931 -37.311 -12.962 1 91.14 ? C1A HEC 201 C 1 HETATM 8 C C2A HEC . . . H 2 1.524 -37.833 -11.736 1 88.69 ? C2A HEC 201 C 1 HETATM 9 C C3A HEC . . . H 2 2.007 -36.802 -11.056 1 84.26 ? C3A HEC 201 C 1 HETATM 10 C C4A HEC . . . H 2 1.736 -35.59 -11.813 1 87.67 ? C4A HEC 201 C 1 HETATM 11 C CMA HEC . . . H 2 2.718 -36.903 -9.696 1 81.49 ? CMA HEC 201 C 1 HETATM 12 C CAA HEC . . . H 2 1.625 -39.306 -11.263 1 94.99 ? CAA HEC 201 C 1 HETATM 13 C CBA HEC . . . H 2 2.479 -40.135 -12.23 1 91.69 ? CBA HEC 201 C 1 HETATM 14 C CGA HEC . . . H 2 2.891 -41.474 -11.649 1 96.22 ? CGA HEC 201 C 1 HETATM 15 O O1A HEC . . . H 2 3.006 -42.444 -12.449 1 93.54 ? O1A HEC 201 C 1 HETATM 16 O O2A HEC . . . H 2 3.106 -41.579 -10.405 1 92.4 ? O2A HEC 201 C 1 HETATM 17 N NB HEC . . . H 2 1.097 -33.053 -13.36 1 87.64 ? NB HEC 201 C 1 HETATM 18 C C1B HEC . . . H 2 1.721 -33.151 -12.131 1 85.52 ? C1B HEC 201 C 1 HETATM 19 C C2B HEC . . . H 2 1.955 -31.801 -11.665 1 79.99 ? C2B HEC 201 C 1 HETATM 20 C C3B HEC . . . H 2 1.479 -30.931 -12.581 1 82.9 ? C3B HEC 201 C 1 HETATM 21 C C4B HEC . . . H 2 0.931 -31.71 -13.66 1 84.69 ? C4B HEC 201 C 1 HETATM 22 C CMB HEC . . . H 2 2.627 -31.488 -10.314 1 76.51 ? CMB HEC 201 C 1 HETATM 23 C CAB HEC . . . H 2 1.449 -29.373 -12.568 1 81.38 ? CAB HEC 201 C 1 HETATM 24 C CBB HEC . . . H 2 2.819 -28.677 -12.39 1 72.96 ? CBB HEC 201 C 1 HETATM 25 N NC HEC . . . H 2 -0.249 -33.281 -15.876 1 84.09 ? NC HEC 201 C 1 HETATM 26 C C1C HEC . . . H 2 -0.19 -31.912 -15.803 1 91.02 ? C1C HEC 201 C 1 HETATM 27 C C2C HEC . . . H 2 -0.948 -31.354 -16.895 1 94.93 ? C2C HEC 201 C 1 HETATM 28 C C3C HEC . . . H 2 -1.184 -32.375 -17.756 1 92.99 ? C3C HEC 201 C 1 HETATM 29 C C4C HEC . . . H 2 -0.867 -33.612 -17.052 1 84.36 ? C4C HEC 201 C 1 HETATM 30 C CMC HEC . . . H 2 -0.852 -29.825 -17.146 1 92.79 ? CMC HEC 201 C 1 HETATM 31 C CAC HEC . . . H 2 -1.938 -32.402 -19.11 1 95.31 ? CAC HEC 201 C 1 HETATM 32 C CBC HEC . . . H 2 -1.957 -31.113 -19.953 1 98.59 ? CBC HEC 201 C 1 HETATM 33 N ND HEC . . . H 2 -0.295 -36.22 -15.524 1 89.85 ? ND HEC 201 C 1 HETATM 34 C C1D HEC . . . H 2 -0.84 -36.091 -16.797 1 90.78 ? C1D HEC 201 C 1 HETATM 35 C C2D HEC . . . H 2 -1.13 -37.415 -17.309 1 91.71 ? C2D HEC 201 C 1 HETATM 36 C C3D HEC . . . H 2 -0.685 -38.396 -16.214 1 96.45 ? C3D HEC 201 C 1 HETATM 37 C C4D HEC . . . H 2 -0.182 -37.557 -15.148 1 91.18 ? C4D HEC 201 C 1 HETATM 38 C CMD HEC . . . H 2 -1.751 -37.765 -18.678 1 96.77 ? CMD HEC 201 C 1 HETATM 39 C CAD HEC . . . H 2 -0.763 -39.95 -16.224 1 104.01 ? CAD HEC 201 C 1 HETATM 40 C CBD HEC . . . H 2 0.625 -40.593 -16.369 1 101.92 ? CBD HEC 201 C 1 HETATM 41 C CGD HEC . . . H 2 0.692 -41.968 -15.726 1 105.48 ? CGD HEC 201 C 1 HETATM 42 O O1D HEC . . . H 2 1.261 -42.078 -14.602 1 103.94 ? O1D HEC 201 C 1 HETATM 43 O O2D HEC . . . H 2 0.189 -42.963 -16.322 1 104.51 ? O2D HEC 201 C 1 # _model_server_stats.io_time_ms 135 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 43 #