data_6NEF # _model_server_result.job_id CcK3MD4GZFL97T79QaOqdQ _model_server_result.datetime_utc '2024-11-09 02:39:33' _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 6nef # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":504}' # _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 . . . E 2 -1.172 3.469 6.287 1 80.32 ? FE HEC 504 A 1 HETATM 2 C CHA HEC . . . E 2 -3.289 1.204 7.717 1 64.1 ? CHA HEC 504 A 1 HETATM 3 C CHB HEC . . . E 2 1.187 2.927 8.71 1 57.62 ? CHB HEC 504 A 1 HETATM 4 C CHC HEC . . . E 2 0.644 5.954 4.987 1 34.48 ? CHC HEC 504 A 1 HETATM 5 C CHD HEC . . . E 2 -3.854 4.33 4.006 1 2.32 ? CHD HEC 504 A 1 HETATM 6 N NA HEC . . . E 2 -1.115 2.384 7.993 1 42 ? NA HEC 504 A 1 HETATM 7 C C1A HEC . . . E 2 -2.06 1.432 8.311 1 68.06 ? C1A HEC 504 A 1 HETATM 8 C C2A HEC . . . E 2 -1.521 0.679 9.408 1 37.19 ? C2A HEC 504 A 1 HETATM 9 C C3A HEC . . . E 2 -0.302 1.104 9.685 1 44.13 ? C3A HEC 504 A 1 HETATM 10 C C4A HEC . . . E 2 -0.002 2.207 8.79 1 51.25 ? C4A HEC 504 A 1 HETATM 11 C CMA HEC . . . E 2 0.61 0.523 10.788 1 204.89 ? CMA HEC 504 A 1 HETATM 12 C CAA HEC . . . E 2 -2.242 -0.508 10.027 1 64.84 ? CAA HEC 504 A 1 HETATM 13 C CBA HEC . . . E 2 -2.143 -1.456 8.849 1 70.66 ? CBA HEC 504 A 1 HETATM 14 C CGA HEC . . . E 2 -2.845 -2.74 9.139 1 54.13 ? CGA HEC 504 A 1 HETATM 15 O O1A HEC . . . E 2 -2.721 -3.719 8.323 1 39.21 ? O1A HEC 504 A 1 HETATM 16 O O2A HEC . . . E 2 -3.552 -2.775 10.183 1 134.6 ? O2A HEC 504 A 1 HETATM 17 N NB HEC . . . E 2 0.618 4.288 6.795 1 73.92 ? NB HEC 504 A 1 HETATM 18 C C1B HEC . . . E 2 1.525 3.86 7.742 1 9.99 ? C1B HEC 504 A 1 HETATM 19 C C2B HEC . . . E 2 2.737 4.659 7.575 1 10.31 ? C2B HEC 504 A 1 HETATM 20 C C3B HEC . . . E 2 2.522 5.476 6.567 1 20.05 ? C3B HEC 504 A 1 HETATM 21 C C4B HEC . . . E 2 1.209 5.257 6.027 1 39.87 ? C4B HEC 504 A 1 HETATM 22 C CMB HEC . . . E 2 4.084 4.638 8.336 1 50.74 ? CMB HEC 504 A 1 HETATM 23 C CAB HEC . . . E 2 3.589 6.379 5.959 1 17.26 ? CAB HEC 504 A 1 HETATM 24 C CBB HEC . . . E 2 4.782 5.814 5.695 1 30.23 ? CBB HEC 504 A 1 HETATM 25 N NC HEC . . . E 2 -1.577 4.915 4.813 1 17.26 ? NC HEC 504 A 1 HETATM 26 C C1C HEC . . . E 2 -0.612 5.816 4.452 1 29.07 ? C1C HEC 504 A 1 HETATM 27 C C2C HEC . . . E 2 -1.121 6.583 3.357 1 45.25 ? C2C HEC 504 A 1 HETATM 28 C C3C HEC . . . E 2 -2.348 6.138 3.09 1 13.7 ? C3C HEC 504 A 1 HETATM 29 C C4C HEC . . . E 2 -2.673 5.056 3.981 1 160.17 ? C4C HEC 504 A 1 HETATM 30 C CMC HEC . . . E 2 -0.34 7.723 2.679 1 15.39 ? CMC HEC 504 A 1 HETATM 31 C CAC HEC . . . E 2 -3.312 6.628 1.99 1 11.82 ? CAC HEC 504 A 1 HETATM 32 C CBC HEC . . . E 2 -2.882 7.376 0.967 1 63.2 ? CBC HEC 504 A 1 HETATM 33 N ND HEC . . . E 2 -3.212 2.914 5.953 1 81.24 ? ND HEC 504 A 1 HETATM 34 C C1D HEC . . . E 2 -4.067 3.331 4.932 1 91.2 ? C1D HEC 504 A 1 HETATM 35 C C2D HEC . . . E 2 -5.224 2.491 4.996 1 54.56 ? C2D HEC 504 A 1 HETATM 36 C C3D HEC . . . E 2 -5.072 1.644 5.998 1 45.68 ? C3D HEC 504 A 1 HETATM 37 C C4D HEC . . . E 2 -3.793 1.852 6.62 1 2.55 ? C4D HEC 504 A 1 HETATM 38 C CMD HEC . . . E 2 -6.455 2.55 4.091 1 29.47 ? CMD HEC 504 A 1 HETATM 39 C CAD HEC . . . E 2 -6.095 0.562 6.305 1 99.29 ? CAD HEC 504 A 1 HETATM 40 C CBD HEC . . . E 2 -5.794 -0.394 5.134 1 25.01 ? CBD HEC 504 A 1 HETATM 41 C CGD HEC . . . E 2 -5.213 -1.704 5.633 1 83.21 ? CGD HEC 504 A 1 HETATM 42 O O1D HEC . . . E 2 -5.425 -2.035 6.812 1 102.15 ? O1D HEC 504 A 1 HETATM 43 O O2D HEC . . . E 2 -4.55 -2.477 4.896 1 29.83 ? O2D HEC 504 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #