data_3NC3 # _model_server_result.job_id ky2c12OMHG-aQcBoKnuQQA _model_server_result.datetime_utc '2024-11-05 01:21:23' _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 3nc3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":406}' # _entry.id 3NC3 # _exptl.entry_id 3NC3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _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 90 _cell.entry_id 3NC3 _cell.length_a 63.8 _cell.length_b 105.4 _cell.length_c 143.9 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NC3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_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,H,M 1 1 B,I,J,K,L,N 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 I 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 metalc ? metalc1 A O PRO 208 A PRO 172 1_555 G MG MG . A MG 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? metalc ? metalc2 A SG CYS 389 A CYS 353 1_555 C FE HEM . A HEM 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc3 C FE HEM . A HEM 406 1_555 M O HOH . A HOH 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc4 B OG SER 99 B SER 63 1_555 L MG MG . B MG 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.751 ? metalc ? metalc5 B SG CYS 389 B CYS 353 1_555 I FE HEM . B HEM 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc6 I FE HEM . B HEM 406 1_555 N O HOH . B HOH 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? # _chem_comp.formula 'C34 H32 Fe N4 O4' _chem_comp.formula_weight 616.487 _chem_comp.id HEM _chem_comp.mon_nstd_flag . _chem_comp.name 'PROTOPORPHYRIN IX CONTAINING FE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms HEME # 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 CHA C1A HEM sing 142 n n CHA C4D HEM doub 143 n n CHA HHA HEM sing 144 n n CHB C4A HEM sing 145 n n CHB C1B HEM doub 146 n n CHB HHB HEM sing 147 n n CHC C4B HEM sing 148 n n CHC C1C HEM doub 149 n n CHC HHC HEM sing 150 n n CHD C4C HEM doub 151 n n CHD C1D HEM sing 152 n n CHD HHD HEM sing 153 n n C1A C2A HEM doub 154 n y C1A NA HEM sing 155 n y C2A C3A HEM sing 156 n y C2A CAA HEM sing 157 n n C3A C4A HEM doub 158 n y C3A CMA HEM sing 159 n n C4A NA HEM sing 160 n y CMA HMA HEM sing 161 n n CMA HMAA HEM sing 162 n n CMA HMAB HEM sing 163 n n CAA CBA HEM sing 164 n n CAA HAA HEM sing 165 n n CAA HAAA HEM sing 166 n n CBA CGA HEM sing 167 n n CBA HBA HEM sing 168 n n CBA HBAA HEM sing 169 n n CGA O1A HEM doub 170 n n CGA O2A HEM sing 171 n n C1B C2B HEM sing 172 n n C1B NB HEM sing 173 n n C2B C3B HEM doub 174 n n C2B CMB HEM sing 175 n n C3B C4B HEM sing 176 n n C3B CAB HEM sing 177 n n C4B NB HEM doub 178 n n CMB HMB HEM sing 179 n n CMB HMBA HEM sing 180 n n CMB HMBB HEM sing 181 n n CAB CBB HEM doub 182 n n CAB HAB HEM sing 183 n n CBB HBB HEM sing 184 n n CBB HBBA HEM sing 185 n n C1C C2C HEM sing 186 n y C1C NC HEM sing 187 n y C2C C3C HEM doub 188 n y C2C CMC HEM sing 189 n n C3C C4C HEM sing 190 n y C3C CAC HEM sing 191 n n C4C NC HEM sing 192 n y CMC HMC HEM sing 193 n n CMC HMCA HEM sing 194 n n CMC HMCB HEM sing 195 n n CAC CBC HEM doub 196 n n CAC HAC HEM sing 197 n n CBC HBC HEM sing 198 n n CBC HBCA HEM sing 199 n n C1D C2D HEM sing 200 n n C1D ND HEM doub 201 n n C2D C3D HEM doub 202 n n C2D CMD HEM sing 203 n n C3D C4D HEM sing 204 n n C3D CAD HEM sing 205 n n C4D ND HEM sing 206 n n CMD HMD HEM sing 207 n n CMD HMDA HEM sing 208 n n CMD HMDB HEM sing 209 n n CAD CBD HEM sing 210 n n CAD HAD HEM sing 211 n n CAD HADA HEM sing 212 n n CBD CGD HEM sing 213 n n CBD HBD HEM sing 214 n n CBD HBDA HEM sing 215 n n CGD O1D HEM doub 216 n n CGD O2D HEM sing 217 n n O2A H2A HEM sing 218 n n O2D H2D HEM sing 219 n n FE NA HEM sing 220 n n FE NB HEM sing 221 n n FE NC HEM sing 222 n n FE ND HEM sing 223 n n # _atom_sites.entry_id 3NC3 _atom_sites.fract_transf_matrix[1][1] 0.015674 _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] 0.009488 _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] 0.006949 _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 HEM A 1 406 1 HEM HEM . D 3 GOL A 1 407 2 GOL GOL . E 4 MG A 1 408 2 MG MG . F 4 MG A 1 409 4 MG MG . G 4 MG A 1 410 5 MG MG . H 4 MG A 1 411 6 MG MG . I 2 HEM B 1 406 1 HEM HEM . J 3 GOL B 1 407 1 GOL GOL . K 4 MG B 1 408 1 MG MG . L 4 MG B 1 409 3 MG MG . M 5 HOH A 1 412 3 HOH HOH . M 5 HOH A 2 413 4 HOH HOH . M 5 HOH A 3 414 5 HOH HOH . M 5 HOH A 4 415 7 HOH HOH . M 5 HOH A 5 416 29 HOH HOH . M 5 HOH A 6 417 31 HOH HOH . M 5 HOH A 7 418 33 HOH HOH . M 5 HOH A 8 419 42 HOH HOH . M 5 HOH A 9 420 56 HOH HOH . M 5 HOH A 10 421 69 HOH HOH . M 5 HOH A 11 422 70 HOH HOH . M 5 HOH A 12 423 73 HOH HOH . M 5 HOH A 13 424 74 HOH HOH . M 5 HOH A 14 425 75 HOH HOH . M 5 HOH A 15 426 86 HOH HOH . M 5 HOH A 16 427 89 HOH HOH . M 5 HOH A 17 428 98 HOH HOH . M 5 HOH A 18 429 99 HOH HOH . M 5 HOH A 19 430 105 HOH HOH . M 5 HOH A 20 431 106 HOH HOH . M 5 HOH A 21 432 107 HOH HOH . M 5 HOH A 22 433 108 HOH HOH . N 5 HOH B 1 410 9 HOH HOH . N 5 HOH B 2 411 23 HOH HOH . N 5 HOH B 3 412 30 HOH HOH . N 5 HOH B 4 413 35 HOH HOH . N 5 HOH B 5 414 45 HOH HOH . N 5 HOH B 6 415 51 HOH HOH . N 5 HOH B 7 416 52 HOH HOH . N 5 HOH B 8 417 54 HOH HOH . N 5 HOH B 9 418 78 HOH HOH . N 5 HOH B 10 419 79 HOH HOH . N 5 HOH B 11 420 80 HOH HOH . N 5 HOH B 12 421 81 HOH HOH . N 5 HOH B 13 422 82 HOH HOH . N 5 HOH B 14 423 83 HOH HOH . N 5 HOH B 15 424 84 HOH HOH . N 5 HOH B 16 425 90 HOH HOH . N 5 HOH B 17 426 91 HOH HOH . N 5 HOH B 18 427 92 HOH HOH . N 5 HOH B 19 428 93 HOH HOH . N 5 HOH B 20 429 94 HOH HOH . N 5 HOH B 21 430 95 HOH HOH . N 5 HOH B 22 431 96 HOH HOH . N 5 HOH B 23 432 97 HOH HOH . N 5 HOH B 24 433 104 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 C CHA HEM . . . C 2 28.775 -21.241 -11.313 1 27.51 ? CHA HEM 406 A 1 HETATM 2 C CHB HEM . . . C 2 29.778 -16.754 -9.78 1 25.92 ? CHB HEM 406 A 1 HETATM 3 C CHC HEM . . . C 2 34.375 -17.187 -11.13 1 25.08 ? CHC HEM 406 A 1 HETATM 4 C CHD HEM . . . C 2 33.487 -21.769 -12.397 1 25.06 ? CHD HEM 406 A 1 HETATM 5 C C1A HEM . . . C 2 28.66 -19.999 -10.743 1 26.95 ? C1A HEM 406 A 1 HETATM 6 C C2A HEM . . . C 2 27.467 -19.413 -10.144 1 27.71 ? C2A HEM 406 A 1 HETATM 7 C C3A HEM . . . C 2 27.754 -18.189 -9.723 1 27.79 ? C3A HEM 406 A 1 HETATM 8 C C4A HEM . . . C 2 29.14 -17.943 -10.045 1 27.68 ? C4A HEM 406 A 1 HETATM 9 C CMA HEM . . . C 2 26.803 -17.195 -9.028 1 26.47 ? CMA HEM 406 A 1 HETATM 10 C CAA HEM . . . C 2 26.089 -20.05 -9.996 1 29.06 ? CAA HEM 406 A 1 HETATM 11 C CBA HEM . . . C 2 26.151 -21.256 -9.058 1 33.61 ? CBA HEM 406 A 1 HETATM 12 C CGA HEM . . . C 2 24.704 -21.59 -8.746 1 36.42 ? CGA HEM 406 A 1 HETATM 13 O O1A HEM . . . C 2 24.252 -21.367 -7.584 1 36.11 ? O1A HEM 406 A 1 HETATM 14 O O2A HEM . . . C 2 23.978 -22.056 -9.676 1 39.15 ? O2A HEM 406 A 1 HETATM 15 C C1B HEM . . . C 2 31.103 -16.507 -9.955 1 25.14 ? C1B HEM 406 A 1 HETATM 16 C C2B HEM . . . C 2 31.787 -15.335 -9.442 1 25.84 ? C2B HEM 406 A 1 HETATM 17 C C3B HEM . . . C 2 33.081 -15.448 -9.813 1 25.89 ? C3B HEM 406 A 1 HETATM 18 C C4B HEM . . . C 2 33.218 -16.697 -10.559 1 25.56 ? C4B HEM 406 A 1 HETATM 19 C CMB HEM . . . C 2 31.099 -14.203 -8.629 1 22.43 ? CMB HEM 406 A 1 HETATM 20 C CAB HEM . . . C 2 34.248 -14.477 -9.488 1 26.64 ? CAB HEM 406 A 1 HETATM 21 C CBB HEM . . . C 2 34.356 -13.216 -9.924 1 28.31 ? CBB HEM 406 A 1 HETATM 22 C C1C HEM . . . C 2 34.517 -18.469 -11.602 1 23.6 ? C1C HEM 406 A 1 HETATM 23 C C2C HEM . . . C 2 35.729 -19.06 -12.108 1 22.55 ? C2C HEM 406 A 1 HETATM 24 C C3C HEM . . . C 2 35.466 -20.323 -12.435 1 22.68 ? C3C HEM 406 A 1 HETATM 25 C C4C HEM . . . C 2 34.093 -20.57 -12.15 1 24.4 ? C4C HEM 406 A 1 HETATM 26 C CMC HEM . . . C 2 37.063 -18.314 -12.218 1 22.74 ? CMC HEM 406 A 1 HETATM 27 C CAC HEM . . . C 2 36.372 -21.402 -13.017 1 23.38 ? CAC HEM 406 A 1 HETATM 28 C CBC HEM . . . C 2 37.636 -21.485 -12.593 1 27.05 ? CBC HEM 406 A 1 HETATM 29 C C1D HEM . . . C 2 32.141 -21.999 -12.36 1 26.53 ? C1D HEM 406 A 1 HETATM 30 C C2D HEM . . . C 2 31.492 -23.111 -12.997 1 27.06 ? C2D HEM 406 A 1 HETATM 31 C C3D HEM . . . C 2 30.004 -22.954 -12.674 1 28.52 ? C3D HEM 406 A 1 HETATM 32 C C4D HEM . . . C 2 29.917 -21.76 -11.861 1 28.19 ? C4D HEM 406 A 1 HETATM 33 C CMD HEM . . . C 2 32.166 -24.206 -13.838 1 26.63 ? CMD HEM 406 A 1 HETATM 34 C CAD HEM . . . C 2 28.872 -23.894 -13.127 1 32.09 ? CAD HEM 406 A 1 HETATM 35 C CBD HEM . . . C 2 27.881 -23.211 -14.073 1 35.67 ? CBD HEM 406 A 1 HETATM 36 C CGD HEM . . . C 2 27.386 -24.214 -15.1 1 37.81 ? CGD HEM 406 A 1 HETATM 37 O O1D HEM . . . C 2 26.648 -25.174 -14.705 1 39.63 ? O1D HEM 406 A 1 HETATM 38 O O2D HEM . . . C 2 27.724 -24.052 -16.311 1 37.36 ? O2D HEM 406 A 1 HETATM 39 N NA HEM . . . C 2 29.66 -19.072 -10.669 1 25.67 ? NA HEM 406 A 1 HETATM 40 N NB HEM . . . C 2 31.987 -17.316 -10.628 1 24.18 ? NB HEM 406 A 1 HETATM 41 N NC HEM . . . C 2 33.53 -19.42 -11.642 1 23.75 ? NC HEM 406 A 1 HETATM 42 N ND HEM . . . C 2 31.193 -21.23 -11.696 1 26.72 ? ND HEM 406 A 1 HETATM 43 FE FE HEM . . . C 2 31.582 -19.304 -11.054 1 29.14 ? FE HEM 406 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 43 #