data_6NEF # _model_server_result.job_id DW7H1C5pyCd4NoejCiBayw _model_server_result.datetime_utc '2025-09-04 08:16:09' _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 6nef # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 6NEF # _exptl.entry_id 6NEF _exptl.method 'ELECTRON MICROSCOPY' # _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 6 _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 6NEF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6NEF _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? nonameric 9 'representative helical assembly' 1 ? monomeric 1 'helical asymmetric unit' 2 # 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,F,G,H 1 (1-9) A,B,C,D,E,F,G,H 2 1 # 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 'helical symmetry operation' ? ? 0.110978 0.993822 -0.001637 -0.993812 0.110984 0.00453 0.004684 0.001124 0.999988 -0.27569 0.14616 47.68607 3 'helical symmetry operation' ? ? 0.114483 -0.993425 0.000923 0.993424 0.114484 0.001357 -0.001454 0.000762 0.999999 -0.16191 0.52867 -47.68451 4 'helical symmetry operation' ? ? -0.975364 0.220589 0.002683 -0.220567 -0.97535 0.00666 0.004087 0.005904 0.999973 -0.23909 0.65238 95.37044 5 'helical symmetry operation' ? ? -0.973787 -0.227461 -0.000319 0.227459 -0.973785 0.002429 -0.000863 0.002294 0.999998 -0.74965 0.36364 -95.36833 6 'helical symmetry operation' ? ? -0.327455 -0.944853 0.005279 0.944867 -0.327445 0.002602 -0.00073 0.005841 0.999982 0.19001 0.8882 143.05498 7 'helical symmetry operation' ? ? -0.337447 0.941344 -0.001527 -0.941344 -0.337445 0.001318 0.000726 0.001882 0.999999 -0.69701 -0.30384 -143.05138 8 'helical symmetry operation' ? ? 0.902691 -0.43029 0.001535 0.430291 0.902692 -0.000428 -0.001202 0.001047 0.999997 0.39393 0.70394 190.74121 9 'helical symmetry operation' ? ? 0.896524 0.442996 -0.000561 -0.442996 0.896524 -0.000009 0.000499 0.000257 1.000001 -0.0719 -0.39266 -190.73496 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G 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 covale ? covale1 A SG CYS 9 A CYS 34 1_555 B CAB HEC . A HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.832 ? covale ? covale2 A SG CYS 47 A CYS 72 1_555 C CAB HEC . A HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.835 ? covale ? covale3 A SG CYS 140 A CYS 165 1_555 D CAB HEC . A HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.78 ? covale ? covale4 A SG CYS 239 A CYS 264 1_555 E CAB HEC . A HEC 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.784 ? covale ? covale5 A SG CYS 328 A CYS 353 1_555 F CAB HEC . A HEC 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? covale ? covale6 A SG CYS 400 A CYS 425 1_555 G CAB HEC . A HEC 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.819 ? metalc ? metalc1 A NE2 HIS 13 A HIS 38 1_555 B FE HEC . A HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc2 A NE2 HIS 51 A HIS 76 1_555 C FE HEC . A HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? metalc ? metalc3 A O GLU 106 A GLU 131 1_555 H MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? metalc ? metalc4 A O GLY 109 A GLY 134 1_555 H MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.916 ? metalc ? metalc5 A NE2 HIS 110 A HIS 135 1_555 E FE HEC . A HEC 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc6 A OD1 ASN 111 A ASN 136 1_555 H MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc7 A OD2 ASP 122 A ASP 147 1_555 H MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc8 A NE2 HIS 147 A HIS 172 1_555 B FE HEC . A HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? metalc ? metalc9 A NE2 HIS 243 A HIS 268 1_555 E FE HEC . A HEC 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc10 A NE2 HIS 257 A HIS 282 1_555 G FE HEC . A HEC 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc11 A NE2 HIS 332 A HIS 357 1_555 F FE HEC . A HEC 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc12 A NE2 HIS 404 A HIS 429 1_555 G FE HEC . A HEC 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc13 E O1A HEC . A HEC 504 1_555 H MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc14 E O1D HEC . A HEC 504 1_555 H MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? metalc ? metalc15 E O2D HEC . A HEC 504 1_555 H MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? # _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 6NEF _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 HEC A 1 501 501 HEC HEM . C 2 HEC A 1 502 502 HEC HEM . D 2 HEC A 1 503 503 HEC HEM . E 2 HEC A 1 504 504 HEC HEM . F 2 HEC A 1 505 505 HEC HEM . G 2 HEC A 1 506 506 HEC HEM . H 3 MG A 1 507 507 MG MG . # 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 . . . C 2 8.927 0.935 -10.996 1 76.17 ? FE HEC 502 A 1 HETATM 2 C CHA HEC . . . C 2 11.884 1.887 -9.862 1 41.16 ? CHA HEC 502 A 1 HETATM 3 C CHB HEC . . . C 2 7.35 2.267 -8.267 1 34.66 ? CHB HEC 502 A 1 HETATM 4 C CHC HEC . . . C 2 5.75 0.336 -12.431 1 27.89 ? CHC HEC 502 A 1 HETATM 5 C CHD HEC . . . C 2 10.265 -1.062 -13.331 1 55.41 ? CHD HEC 502 A 1 HETATM 6 N NA HEC . . . C 2 9.508 1.854 -9.329 1 60.71 ? NA HEC 502 A 1 HETATM 7 C C1A HEC . . . C 2 10.798 2.247 -9.101 1 72.92 ? C1A HEC 502 A 1 HETATM 8 C C2A HEC . . . C 2 10.818 3.106 -7.942 1 23.48 ? C2A HEC 502 A 1 HETATM 9 C C3A HEC . . . C 2 9.589 3.22 -7.474 1 49.4 ? C3A HEC 502 A 1 HETATM 10 C C4A HEC . . . C 2 8.731 2.435 -8.342 1 17.25 ? C4A HEC 502 A 1 HETATM 11 C CMA HEC . . . C 2 9.175 4.053 -6.25 1 75.12 ? CMA HEC 502 A 1 HETATM 12 C CAA HEC . . . C 2 12.074 3.778 -7.391 1 39.97 ? CAA HEC 502 A 1 HETATM 13 C CBA HEC . . . C 2 12.602 4.691 -8.493 1 41.84 ? CBA HEC 502 A 1 HETATM 14 C CGA HEC . . . C 2 13.152 6.008 -7.984 1 178.36 ? CGA HEC 502 A 1 HETATM 15 O O1A HEC . . . C 2 14.124 6.527 -8.596 1 77.13 ? O1A HEC 502 A 1 HETATM 16 O O2A HEC . . . C 2 12.634 6.552 -6.974 1 67.89 ? O2A HEC 502 A 1 HETATM 17 N NB HEC . . . C 2 6.933 1.226 -10.438 1 70.62 ? NB HEC 502 A 1 HETATM 18 C C1B HEC . . . C 2 6.514 1.858 -9.292 1 91.53 ? C1B HEC 502 A 1 HETATM 19 C C2B HEC . . . C 2 5.082 1.989 -9.371 1 2.32 ? C2B HEC 502 A 1 HETATM 20 C C3B HEC . . . C 2 4.695 1.434 -10.483 1 59.96 ? C3B HEC 502 A 1 HETATM 21 C C4B HEC . . . C 2 5.821 0.98 -11.201 1 32.38 ? C4B HEC 502 A 1 HETATM 22 C CMB HEC . . . C 2 4.152 2.632 -8.342 1 157.96 ? CMB HEC 502 A 1 HETATM 23 C CAB HEC . . . C 2 3.304 1.404 -11.053 1 15 ? CAB HEC 502 A 1 HETATM 24 C CBB HEC . . . C 2 2.628 2.542 -10.89 1 65.31 ? CBB HEC 502 A 1 HETATM 25 N NC HEC . . . C 2 8.097 -0.243 -12.564 1 91.83 ? NC HEC 502 A 1 HETATM 26 C C1C HEC . . . C 2 6.809 -0.292 -13.052 1 69.58 ? C1C HEC 502 A 1 HETATM 27 C C2C HEC . . . C 2 6.828 -1.099 -14.259 1 23.79 ? C2C HEC 502 A 1 HETATM 28 C C3C HEC . . . C 2 8.091 -1.48 -14.458 1 32.46 ? C3C HEC 502 A 1 HETATM 29 C C4C HEC . . . C 2 8.908 -0.91 -13.433 1 71.23 ? C4C HEC 502 A 1 HETATM 30 C CMC HEC . . . C 2 5.626 -1.47 -15.134 1 47.15 ? CMC HEC 502 A 1 HETATM 31 C CAC HEC . . . C 2 8.707 -2.279 -15.603 1 29.78 ? CAC HEC 502 A 1 HETATM 32 C CBC HEC . . . C 2 8.171 -2.06 -16.803 1 58.26 ? CBC HEC 502 A 1 HETATM 33 N ND HEC . . . C 2 10.705 0.46 -11.461 1 77.46 ? ND HEC 502 A 1 HETATM 34 C C1D HEC . . . C 2 11.096 -0.293 -12.55 1 43.01 ? C1D HEC 502 A 1 HETATM 35 C C2D HEC . . . C 2 12.533 -0.17 -12.691 1 29.34 ? C2D HEC 502 A 1 HETATM 36 C C3D HEC . . . C 2 12.965 0.617 -11.753 1 40.58 ? C3D HEC 502 A 1 HETATM 37 C C4D HEC . . . C 2 11.841 1.047 -10.951 1 67.23 ? C4D HEC 502 A 1 HETATM 38 C CMD HEC . . . C 2 13.454 -0.821 -13.73 1 35.61 ? CMD HEC 502 A 1 HETATM 39 C CAD HEC . . . C 2 14.436 0.997 -11.642 1 27.87 ? CAD HEC 502 A 1 HETATM 40 C CBD HEC . . . C 2 14.759 1.855 -12.867 1 68.69 ? CBD HEC 502 A 1 HETATM 41 C CGD HEC . . . C 2 14.252 3.273 -12.758 1 127.85 ? CGD HEC 502 A 1 HETATM 42 O O1D HEC . . . C 2 13.668 3.639 -11.711 1 117.41 ? O1D HEC 502 A 1 HETATM 43 O O2D HEC . . . C 2 14.442 4.051 -13.73 1 125.81 ? O2D HEC 502 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #