data_2PBJ # _model_server_result.job_id fG-lJHJ4SYf4bIvtTm0LpQ _model_server_result.datetime_utc '2024-11-05 00:29:31' _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 2pbj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":476}' # _entry.id 2PBJ # _exptl.entry_id 2PBJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 111 _cell.angle_gamma 90 _cell.entry_id 2PBJ _cell.length_a 127 _cell.length_b 122.49 _cell.length_c 110.97 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PBJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 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,B,E,F,G,H,I,J,Q,R 1 1 C,D,K,L,M,N,O,P,S,T 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 ? 3 F N N ? 3 I N N ? 3 L N N ? 3 O N N # _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 165 n n CHA C4D HEM doub 166 n n CHA HHA HEM sing 167 n n CHB C4A HEM sing 168 n n CHB C1B HEM doub 169 n n CHB HHB HEM sing 170 n n CHC C4B HEM sing 171 n n CHC C1C HEM doub 172 n n CHC HHC HEM sing 173 n n CHD C4C HEM doub 174 n n CHD C1D HEM sing 175 n n CHD HHD HEM sing 176 n n C1A C2A HEM doub 177 n y C1A NA HEM sing 178 n y C2A C3A HEM sing 179 n y C2A CAA HEM sing 180 n n C3A C4A HEM doub 181 n y C3A CMA HEM sing 182 n n C4A NA HEM sing 183 n y CMA HMA HEM sing 184 n n CMA HMAA HEM sing 185 n n CMA HMAB HEM sing 186 n n CAA CBA HEM sing 187 n n CAA HAA HEM sing 188 n n CAA HAAA HEM sing 189 n n CBA CGA HEM sing 190 n n CBA HBA HEM sing 191 n n CBA HBAA HEM sing 192 n n CGA O1A HEM doub 193 n n CGA O2A HEM sing 194 n n C1B C2B HEM sing 195 n n C1B NB HEM sing 196 n n C2B C3B HEM doub 197 n n C2B CMB HEM sing 198 n n C3B C4B HEM sing 199 n n C3B CAB HEM sing 200 n n C4B NB HEM doub 201 n n CMB HMB HEM sing 202 n n CMB HMBA HEM sing 203 n n CMB HMBB HEM sing 204 n n CAB CBB HEM doub 205 n n CAB HAB HEM sing 206 n n CBB HBB HEM sing 207 n n CBB HBBA HEM sing 208 n n C1C C2C HEM sing 209 n y C1C NC HEM sing 210 n y C2C C3C HEM doub 211 n y C2C CMC HEM sing 212 n n C3C C4C HEM sing 213 n y C3C CAC HEM sing 214 n n C4C NC HEM sing 215 n y CMC HMC HEM sing 216 n n CMC HMCA HEM sing 217 n n CMC HMCB HEM sing 218 n n CAC CBC HEM doub 219 n n CAC HAC HEM sing 220 n n CBC HBC HEM sing 221 n n CBC HBCA HEM sing 222 n n C1D C2D HEM sing 223 n n C1D ND HEM doub 224 n n C2D C3D HEM doub 225 n n C2D CMD HEM sing 226 n n C3D C4D HEM sing 227 n n C3D CAD HEM sing 228 n n C4D ND HEM sing 229 n n CMD HMD HEM sing 230 n n CMD HMDA HEM sing 231 n n CMD HMDB HEM sing 232 n n CAD CBD HEM sing 233 n n CAD HAD HEM sing 234 n n CAD HADA HEM sing 235 n n CBD CGD HEM sing 236 n n CBD HBD HEM sing 237 n n CBD HBDA HEM sing 238 n n CGD O1D HEM doub 239 n n CGD O2D HEM sing 240 n n O2A H2A HEM sing 241 n n O2D H2D HEM sing 242 n n FE NA HEM sing 243 n n FE NB HEM sing 244 n n FE NC HEM sing 245 n n FE ND HEM sing 246 n n # _atom_sites.entry_id 2PBJ _atom_sites.fract_transf_matrix[1][1] 0.007874 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003023 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008164 _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] 0.009653 _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 E 2 CL A 1 475 475 CL CL . F 3 HEM A 1 476 476 HEM HEM . G 4 GSH A 1 477 477 GSH GSH . H 2 CL B 1 475 475 CL CL . I 3 HEM B 1 476 476 HEM HEM . J 4 GSH B 1 477 477 GSH GSH . K 2 CL C 1 475 475 CL CL . L 3 HEM C 1 476 476 HEM HEM . M 4 GSH C 1 477 477 GSH GSH . N 2 CL D 1 475 475 CL CL . O 3 HEM D 1 476 476 HEM HEM . P 4 GSH D 1 477 477 GSH GSH . Q 5 HOH A 1 478 1 HOH HOH . Q 5 HOH A 2 479 8 HOH HOH . Q 5 HOH A 3 480 9 HOH HOH . Q 5 HOH A 4 481 16 HOH HOH . Q 5 HOH A 5 482 18 HOH HOH . Q 5 HOH A 6 483 25 HOH HOH . Q 5 HOH A 7 484 29 HOH HOH . Q 5 HOH A 8 485 30 HOH HOH . Q 5 HOH A 9 486 33 HOH HOH . Q 5 HOH A 10 487 35 HOH HOH . Q 5 HOH A 11 488 37 HOH HOH . Q 5 HOH A 12 489 38 HOH HOH . Q 5 HOH A 13 490 40 HOH HOH . Q 5 HOH A 14 491 42 HOH HOH . Q 5 HOH A 15 492 46 HOH HOH . Q 5 HOH A 16 493 49 HOH HOH . Q 5 HOH A 17 494 53 HOH HOH . Q 5 HOH A 18 495 59 HOH HOH . Q 5 HOH A 19 496 63 HOH HOH . Q 5 HOH A 20 497 66 HOH HOH . Q 5 HOH A 21 498 69 HOH HOH . Q 5 HOH A 22 499 71 HOH HOH . Q 5 HOH A 23 500 72 HOH HOH . Q 5 HOH A 24 501 73 HOH HOH . Q 5 HOH A 25 502 86 HOH HOH . Q 5 HOH A 26 503 90 HOH HOH . Q 5 HOH A 27 504 95 HOH HOH . Q 5 HOH A 28 505 97 HOH HOH . Q 5 HOH A 29 506 103 HOH HOH . Q 5 HOH A 30 507 104 HOH HOH . Q 5 HOH A 31 508 105 HOH HOH . Q 5 HOH A 32 509 107 HOH HOH . Q 5 HOH A 33 510 112 HOH HOH . Q 5 HOH A 34 511 115 HOH HOH . Q 5 HOH A 35 512 118 HOH HOH . Q 5 HOH A 36 513 123 HOH HOH . Q 5 HOH A 37 514 124 HOH HOH . Q 5 HOH A 38 515 127 HOH HOH . Q 5 HOH A 39 516 128 HOH HOH . Q 5 HOH A 40 517 129 HOH HOH . Q 5 HOH A 41 518 133 HOH HOH . Q 5 HOH A 42 519 134 HOH HOH . Q 5 HOH A 43 520 139 HOH HOH . Q 5 HOH A 44 521 140 HOH HOH . Q 5 HOH A 45 522 142 HOH HOH . Q 5 HOH A 46 523 147 HOH HOH . Q 5 HOH A 47 524 152 HOH HOH . Q 5 HOH A 48 525 154 HOH HOH . Q 5 HOH A 49 526 156 HOH HOH . Q 5 HOH A 50 527 160 HOH HOH . Q 5 HOH A 51 528 161 HOH HOH . Q 5 HOH A 52 529 164 HOH HOH . R 5 HOH B 1 478 2 HOH HOH . R 5 HOH B 2 479 4 HOH HOH . R 5 HOH B 3 480 10 HOH HOH . R 5 HOH B 4 481 11 HOH HOH . R 5 HOH B 5 482 12 HOH HOH . R 5 HOH B 6 483 19 HOH HOH . R 5 HOH B 7 484 20 HOH HOH . R 5 HOH B 8 485 21 HOH HOH . R 5 HOH B 9 486 22 HOH HOH . R 5 HOH B 10 487 28 HOH HOH . R 5 HOH B 11 488 34 HOH HOH . R 5 HOH B 12 489 39 HOH HOH . R 5 HOH B 13 490 41 HOH HOH . R 5 HOH B 14 491 43 HOH HOH . R 5 HOH B 15 492 44 HOH HOH . R 5 HOH B 16 493 45 HOH HOH . R 5 HOH B 17 494 47 HOH HOH . R 5 HOH B 18 495 52 HOH HOH . R 5 HOH B 19 496 57 HOH HOH . R 5 HOH B 20 497 58 HOH HOH . R 5 HOH B 21 498 61 HOH HOH . R 5 HOH B 22 499 68 HOH HOH . R 5 HOH B 23 500 70 HOH HOH . R 5 HOH B 24 501 76 HOH HOH . R 5 HOH B 25 502 83 HOH HOH . R 5 HOH B 26 503 84 HOH HOH . R 5 HOH B 27 504 88 HOH HOH . R 5 HOH B 28 505 96 HOH HOH . R 5 HOH B 29 506 100 HOH HOH . R 5 HOH B 30 507 109 HOH HOH . R 5 HOH B 31 508 114 HOH HOH . R 5 HOH B 32 509 120 HOH HOH . R 5 HOH B 33 510 135 HOH HOH . R 5 HOH B 34 511 138 HOH HOH . R 5 HOH B 35 512 143 HOH HOH . R 5 HOH B 36 513 151 HOH HOH . R 5 HOH B 37 514 155 HOH HOH . R 5 HOH B 38 515 158 HOH HOH . R 5 HOH B 39 516 163 HOH HOH . S 5 HOH C 1 478 3 HOH HOH . S 5 HOH C 2 479 5 HOH HOH . S 5 HOH C 3 480 7 HOH HOH . S 5 HOH C 4 481 13 HOH HOH . S 5 HOH C 5 482 14 HOH HOH . S 5 HOH C 6 483 15 HOH HOH . S 5 HOH C 7 484 17 HOH HOH . S 5 HOH C 8 485 23 HOH HOH . S 5 HOH C 9 486 24 HOH HOH . S 5 HOH C 10 487 31 HOH HOH . S 5 HOH C 11 488 32 HOH HOH . S 5 HOH C 12 489 36 HOH HOH . S 5 HOH C 13 490 48 HOH HOH . S 5 HOH C 14 491 50 HOH HOH . S 5 HOH C 15 492 60 HOH HOH . S 5 HOH C 16 493 64 HOH HOH . S 5 HOH C 17 494 65 HOH HOH . S 5 HOH C 18 495 67 HOH HOH . S 5 HOH C 19 496 74 HOH HOH . S 5 HOH C 20 497 78 HOH HOH . S 5 HOH C 21 498 91 HOH HOH . S 5 HOH C 22 499 94 HOH HOH . S 5 HOH C 23 500 99 HOH HOH . S 5 HOH C 24 501 113 HOH HOH . S 5 HOH C 25 502 116 HOH HOH . S 5 HOH C 26 503 119 HOH HOH . S 5 HOH C 27 504 121 HOH HOH . S 5 HOH C 28 505 125 HOH HOH . S 5 HOH C 29 506 126 HOH HOH . S 5 HOH C 30 507 130 HOH HOH . S 5 HOH C 31 508 131 HOH HOH . S 5 HOH C 32 509 137 HOH HOH . S 5 HOH C 33 510 141 HOH HOH . S 5 HOH C 34 511 146 HOH HOH . S 5 HOH C 35 512 150 HOH HOH . S 5 HOH C 36 513 153 HOH HOH . S 5 HOH C 37 514 157 HOH HOH . S 5 HOH C 38 515 159 HOH HOH . S 5 HOH C 39 516 166 HOH HOH . S 5 HOH C 40 517 167 HOH HOH . T 5 HOH D 1 478 6 HOH HOH . T 5 HOH D 2 479 26 HOH HOH . T 5 HOH D 3 480 27 HOH HOH . T 5 HOH D 4 481 51 HOH HOH . T 5 HOH D 5 482 54 HOH HOH . T 5 HOH D 6 483 55 HOH HOH . T 5 HOH D 7 484 56 HOH HOH . T 5 HOH D 8 485 62 HOH HOH . T 5 HOH D 9 486 75 HOH HOH . T 5 HOH D 10 487 77 HOH HOH . T 5 HOH D 11 488 79 HOH HOH . T 5 HOH D 12 489 80 HOH HOH . T 5 HOH D 13 490 81 HOH HOH . T 5 HOH D 14 491 82 HOH HOH . T 5 HOH D 15 492 85 HOH HOH . T 5 HOH D 16 493 87 HOH HOH . T 5 HOH D 17 494 89 HOH HOH . T 5 HOH D 18 495 92 HOH HOH . T 5 HOH D 19 496 93 HOH HOH . T 5 HOH D 20 497 98 HOH HOH . T 5 HOH D 21 498 101 HOH HOH . T 5 HOH D 22 499 102 HOH HOH . T 5 HOH D 23 500 106 HOH HOH . T 5 HOH D 24 501 108 HOH HOH . T 5 HOH D 25 502 110 HOH HOH . T 5 HOH D 26 503 111 HOH HOH . T 5 HOH D 27 504 117 HOH HOH . T 5 HOH D 28 505 122 HOH HOH . T 5 HOH D 29 506 132 HOH HOH . T 5 HOH D 30 507 136 HOH HOH . T 5 HOH D 31 508 144 HOH HOH . T 5 HOH D 32 509 145 HOH HOH . T 5 HOH D 33 510 148 HOH HOH . T 5 HOH D 34 511 149 HOH HOH . T 5 HOH D 35 512 162 HOH HOH . T 5 HOH D 36 513 165 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 . . . F 3 -19.789 48.93 12.446 1 45.03 ? CHA HEM 476 A 1 HETATM 2 C CHB HEM . . . F 3 -20.983 53.452 11.668 1 41.39 ? CHB HEM 476 A 1 HETATM 3 C CHC HEM . . . F 3 -17.094 54.91 13.968 1 42.33 ? CHC HEM 476 A 1 HETATM 4 C CHD HEM . . . F 3 -15.725 50.362 14.52 1 44.73 ? CHD HEM 476 A 1 HETATM 5 C C1A HEM . . . F 3 -20.423 50.03 12.004 1 44.53 ? C1A HEM 476 A 1 HETATM 6 C C2A HEM . . . F 3 -21.584 50.024 11.185 1 44.64 ? C2A HEM 476 A 1 HETATM 7 C C3A HEM . . . F 3 -21.935 51.313 10.976 1 44.3 ? C3A HEM 476 A 1 HETATM 8 C C4A HEM . . . F 3 -20.987 52.112 11.67 1 43.56 ? C4A HEM 476 A 1 HETATM 9 C CMA HEM . . . F 3 -23.11 51.82 10.155 1 44.36 ? CMA HEM 476 A 1 HETATM 10 C CAA HEM . . . F 3 -22.295 48.786 10.643 1 46.85 ? CAA HEM 476 A 1 HETATM 11 C CBA HEM . . . F 3 -21.846 48.513 9.18 1 48.72 ? CBA HEM 476 A 1 HETATM 12 C CGA HEM . . . F 3 -21.221 47.13 9.019 1 50.16 ? CGA HEM 476 A 1 HETATM 13 O O1A HEM . . . F 3 -20.897 46.46 9.983 1 49.68 ? O1A HEM 476 A 1 HETATM 14 O O2A HEM . . . F 3 -21.022 46.643 7.782 1 52.13 ? O2A HEM 476 A 1 HETATM 15 C C1B HEM . . . F 3 -20.059 54.23 12.315 1 41.86 ? C1B HEM 476 A 1 HETATM 16 C C2B HEM . . . F 3 -20.187 55.667 12.38 1 42.14 ? C2B HEM 476 A 1 HETATM 17 C C3B HEM . . . F 3 -19.125 56.132 13.042 1 40.91 ? C3B HEM 476 A 1 HETATM 18 C C4B HEM . . . F 3 -18.318 54.896 13.383 1 41.53 ? C4B HEM 476 A 1 HETATM 19 C CMB HEM . . . F 3 -21.33 56.503 11.806 1 39.79 ? CMB HEM 476 A 1 HETATM 20 C CAB HEM . . . F 3 -18.872 57.582 13.334 1 38.88 ? CAB HEM 476 A 1 HETATM 21 C CBB HEM . . . F 3 -17.829 58.049 13.984 1 37.54 ? CBB HEM 476 A 1 HETATM 22 C C1C HEM . . . F 3 -16.36 53.807 14.27 1 43.23 ? C1C HEM 476 A 1 HETATM 23 C C2C HEM . . . F 3 -15.044 53.848 14.81 1 42.84 ? C2C HEM 476 A 1 HETATM 24 C C3C HEM . . . F 3 -14.637 52.549 14.99 1 44.29 ? C3C HEM 476 A 1 HETATM 25 C C4C HEM . . . F 3 -15.739 51.719 14.545 1 44.42 ? C4C HEM 476 A 1 HETATM 26 C CMC HEM . . . F 3 -14.248 55.11 15.124 1 42.1 ? CMC HEM 476 A 1 HETATM 27 C CAC HEM . . . F 3 -13.318 52.057 15.527 1 45.51 ? CAC HEM 476 A 1 HETATM 28 C CBC HEM . . . F 3 -12.808 52.479 16.696 1 45.67 ? CBC HEM 476 A 1 HETATM 29 C C1D HEM . . . F 3 -16.791 49.596 14.07 1 45.22 ? C1D HEM 476 A 1 HETATM 30 C C2D HEM . . . F 3 -16.812 48.102 14.188 1 45.39 ? C2D HEM 476 A 1 HETATM 31 C C3D HEM . . . F 3 -17.962 47.706 13.655 1 45.97 ? C3D HEM 476 A 1 HETATM 32 C C4D HEM . . . F 3 -18.643 48.946 13.185 1 45.41 ? C4D HEM 476 A 1 HETATM 33 C CMD HEM . . . F 3 -15.738 47.232 14.808 1 44.21 ? CMD HEM 476 A 1 HETATM 34 C CAD HEM . . . F 3 -18.492 46.284 13.53 1 47.77 ? CAD HEM 476 A 1 HETATM 35 C CBD HEM . . . F 3 -19.244 45.888 14.82 1 50.33 ? CBD HEM 476 A 1 HETATM 36 C CGD HEM . . . F 3 -19.942 44.554 14.662 1 51.56 ? CGD HEM 476 A 1 HETATM 37 O O1D HEM . . . F 3 -19.326 43.574 14.282 1 52.43 ? O1D HEM 476 A 1 HETATM 38 O O2D HEM . . . F 3 -21.252 44.451 14.956 1 53.19 ? O2D HEM 476 A 1 HETATM 39 N NA HEM . . . F 3 -20.038 51.326 12.318 1 44.76 ? NA HEM 476 A 1 HETATM 40 N NB HEM . . . F 3 -18.992 53.782 12.998 1 42.4 ? NB HEM 476 A 1 HETATM 41 N NC HEM . . . F 3 -16.79 52.506 14.109 1 44.02 ? NC HEM 476 A 1 HETATM 42 N ND HEM . . . F 3 -17.954 50.051 13.551 1 44.36 ? ND HEM 476 A 1 HETATM 43 FE FE HEM . . . F 3 -18.501 51.911 13.374 1 43.23 ? FE HEM 476 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #