data_3B4X # _model_server_result.job_id W4hWvMqGe9Em6UuLYwQZZg _model_server_result.datetime_utc '2025-03-04 09:03:02' _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 3b4x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":410}' # _entry.id 3B4X # _exptl.entry_id 3B4X _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93.85 _cell.angle_gamma 90 _cell.entry_id 3B4X _cell.length_a 135.286 _cell.length_b 55.168 _cell.length_c 51.415 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3B4X _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 SG CYS 317 A CYS 317 1_555 B FE HEM . A HEM 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc2 B FE HEM . A HEM 410 1_555 C O HOH . A HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? # _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 129 n n CHA C4D HEM doub 130 n n CHA HHA HEM sing 131 n n CHB C4A HEM sing 132 n n CHB C1B HEM doub 133 n n CHB HHB HEM sing 134 n n CHC C4B HEM sing 135 n n CHC C1C HEM doub 136 n n CHC HHC HEM sing 137 n n CHD C4C HEM doub 138 n n CHD C1D HEM sing 139 n n CHD HHD HEM sing 140 n n C1A C2A HEM doub 141 n y C1A NA HEM sing 142 n y C2A C3A HEM sing 143 n y C2A CAA HEM sing 144 n n C3A C4A HEM doub 145 n y C3A CMA HEM sing 146 n n C4A NA HEM sing 147 n y CMA HMA HEM sing 148 n n CMA HMAA HEM sing 149 n n CMA HMAB HEM sing 150 n n CAA CBA HEM sing 151 n n CAA HAA HEM sing 152 n n CAA HAAA HEM sing 153 n n CBA CGA HEM sing 154 n n CBA HBA HEM sing 155 n n CBA HBAA HEM sing 156 n n CGA O1A HEM doub 157 n n CGA O2A HEM sing 158 n n C1B C2B HEM sing 159 n n C1B NB HEM sing 160 n n C2B C3B HEM doub 161 n n C2B CMB HEM sing 162 n n C3B C4B HEM sing 163 n n C3B CAB HEM sing 164 n n C4B NB HEM doub 165 n n CMB HMB HEM sing 166 n n CMB HMBA HEM sing 167 n n CMB HMBB HEM sing 168 n n CAB CBB HEM doub 169 n n CAB HAB HEM sing 170 n n CBB HBB HEM sing 171 n n CBB HBBA HEM sing 172 n n C1C C2C HEM sing 173 n y C1C NC HEM sing 174 n y C2C C3C HEM doub 175 n y C2C CMC HEM sing 176 n n C3C C4C HEM sing 177 n y C3C CAC HEM sing 178 n n C4C NC HEM sing 179 n y CMC HMC HEM sing 180 n n CMC HMCA HEM sing 181 n n CMC HMCB HEM sing 182 n n CAC CBC HEM doub 183 n n CAC HAC HEM sing 184 n n CBC HBC HEM sing 185 n n CBC HBCA HEM sing 186 n n C1D C2D HEM sing 187 n n C1D ND HEM doub 188 n n C2D C3D HEM doub 189 n n C2D CMD HEM sing 190 n n C3D C4D HEM sing 191 n n C3D CAD HEM sing 192 n n C4D ND HEM sing 193 n n CMD HMD HEM sing 194 n n CMD HMDA HEM sing 195 n n CMD HMDB HEM sing 196 n n CAD CBD HEM sing 197 n n CAD HAD HEM sing 198 n n CAD HADA HEM sing 199 n n CBD CGD HEM sing 200 n n CBD HBD HEM sing 201 n n CBD HBDA HEM sing 202 n n CGD O1D HEM doub 203 n n CGD O2D HEM sing 204 n n O2A H2A HEM sing 205 n n O2D H2D HEM sing 206 n n FE NA HEM sing 207 n n FE NB HEM sing 208 n n FE NC HEM sing 209 n n FE ND HEM sing 210 n n # _atom_sites.entry_id 3B4X _atom_sites.fract_transf_matrix[1][1] 0.007392 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000498 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018126 _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] 0.019494 _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 HEM A 1 410 410 HEM HEM . C 3 HOH A 1 411 1 HOH HOH . C 3 HOH A 2 412 2 HOH HOH . C 3 HOH A 3 413 3 HOH HOH . C 3 HOH A 4 414 4 HOH HOH . C 3 HOH A 5 415 5 HOH HOH . C 3 HOH A 6 416 6 HOH HOH . C 3 HOH A 7 417 7 HOH HOH . C 3 HOH A 8 418 8 HOH HOH . C 3 HOH A 9 419 9 HOH HOH . C 3 HOH A 10 420 10 HOH HOH . C 3 HOH A 11 421 11 HOH HOH . C 3 HOH A 12 422 12 HOH HOH . C 3 HOH A 13 423 13 HOH HOH . C 3 HOH A 14 424 14 HOH HOH . C 3 HOH A 15 425 15 HOH HOH . C 3 HOH A 16 426 16 HOH HOH . C 3 HOH A 17 427 17 HOH HOH . C 3 HOH A 18 428 18 HOH HOH . C 3 HOH A 19 429 19 HOH HOH . C 3 HOH A 20 430 20 HOH HOH . C 3 HOH A 21 431 21 HOH HOH . C 3 HOH A 22 432 22 HOH HOH . C 3 HOH A 23 433 23 HOH HOH . C 3 HOH A 24 434 24 HOH HOH . C 3 HOH A 25 435 25 HOH HOH . C 3 HOH A 26 436 26 HOH HOH . C 3 HOH A 27 437 27 HOH HOH . C 3 HOH A 28 438 28 HOH HOH . C 3 HOH A 29 439 29 HOH HOH . C 3 HOH A 30 440 30 HOH HOH . C 3 HOH A 31 441 31 HOH HOH . C 3 HOH A 32 442 32 HOH HOH . C 3 HOH A 33 443 33 HOH HOH . C 3 HOH A 34 444 34 HOH HOH . C 3 HOH A 35 445 35 HOH HOH . C 3 HOH A 36 446 36 HOH HOH . C 3 HOH A 37 447 37 HOH HOH . C 3 HOH A 38 448 38 HOH HOH . C 3 HOH A 39 449 39 HOH HOH . C 3 HOH A 40 450 40 HOH HOH . C 3 HOH A 41 451 41 HOH HOH . C 3 HOH A 42 452 42 HOH HOH . C 3 HOH A 43 453 43 HOH HOH . C 3 HOH A 44 454 44 HOH HOH . C 3 HOH A 45 455 45 HOH HOH . C 3 HOH A 46 456 46 HOH HOH . C 3 HOH A 47 457 47 HOH HOH . C 3 HOH A 48 458 48 HOH HOH . C 3 HOH A 49 459 49 HOH HOH . C 3 HOH A 50 460 50 HOH HOH . C 3 HOH A 51 461 51 HOH HOH . C 3 HOH A 52 462 52 HOH HOH . C 3 HOH A 53 463 53 HOH HOH . C 3 HOH A 54 464 54 HOH HOH . C 3 HOH A 55 465 55 HOH HOH . C 3 HOH A 56 466 56 HOH HOH . C 3 HOH A 57 467 57 HOH HOH . C 3 HOH A 58 468 58 HOH HOH . C 3 HOH A 59 469 59 HOH HOH . C 3 HOH A 60 470 60 HOH HOH . C 3 HOH A 61 471 61 HOH HOH . C 3 HOH A 62 472 62 HOH HOH . C 3 HOH A 63 473 63 HOH HOH . C 3 HOH A 64 474 64 HOH HOH . C 3 HOH A 65 475 65 HOH HOH . C 3 HOH A 66 476 66 HOH HOH . C 3 HOH A 67 477 67 HOH HOH . C 3 HOH A 68 478 68 HOH HOH . C 3 HOH A 69 479 69 HOH HOH . C 3 HOH A 70 480 70 HOH HOH . C 3 HOH A 71 481 71 HOH HOH . C 3 HOH A 72 482 72 HOH HOH . C 3 HOH A 73 483 73 HOH HOH . C 3 HOH A 74 484 74 HOH HOH . C 3 HOH A 75 485 75 HOH HOH . C 3 HOH A 76 486 76 HOH HOH . C 3 HOH A 77 487 77 HOH HOH . C 3 HOH A 78 488 78 HOH HOH . C 3 HOH A 79 489 79 HOH HOH . C 3 HOH A 80 490 80 HOH HOH . C 3 HOH A 81 491 81 HOH HOH . C 3 HOH A 82 492 82 HOH HOH . C 3 HOH A 83 493 83 HOH HOH . C 3 HOH A 84 494 84 HOH HOH . C 3 HOH A 85 495 85 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 . . . B 2 78.058 -8.153 71.193 1 27.25 ? CHA HEM 410 A 1 HETATM 2 C CHB HEM . . . B 2 78.757 -6.139 66.608 1 26.94 ? CHB HEM 410 A 1 HETATM 3 C CHC HEM . . . B 2 80.359 -1.828 68.743 1 26.81 ? CHC HEM 410 A 1 HETATM 4 C CHD HEM . . . B 2 79.71 -3.883 73.335 1 26.85 ? CHD HEM 410 A 1 HETATM 5 C C1A HEM . . . B 2 78.114 -7.951 69.813 1 27.35 ? C1A HEM 410 A 1 HETATM 6 C C2A HEM . . . B 2 77.738 -8.85 68.8 1 26.87 ? C2A HEM 410 A 1 HETATM 7 C C3A HEM . . . B 2 77.934 -8.312 67.57 1 27.85 ? C3A HEM 410 A 1 HETATM 8 C C4A HEM . . . B 2 78.448 -7.005 67.661 1 26.41 ? C4A HEM 410 A 1 HETATM 9 C CMA HEM . . . B 2 77.628 -9.018 66.265 1 27.75 ? CMA HEM 410 A 1 HETATM 10 C CAA HEM . . . B 2 77.174 -10.23 69.063 1 27.61 ? CAA HEM 410 A 1 HETATM 11 C CBA HEM . . . B 2 78.169 -11.274 68.792 1 28.79 ? CBA HEM 410 A 1 HETATM 12 C CGA HEM . . . B 2 77.488 -12.612 69.087 1 31.4 ? CGA HEM 410 A 1 HETATM 13 O O1A HEM . . . B 2 76.235 -12.65 69.014 1 29.89 ? O1A HEM 410 A 1 HETATM 14 O O2A HEM . . . B 2 78.167 -13.61 69.394 1 32.09 ? O2A HEM 410 A 1 HETATM 15 C C1B HEM . . . B 2 79.241 -4.84 66.798 1 27.57 ? C1B HEM 410 A 1 HETATM 16 C C2B HEM . . . B 2 79.562 -3.9 65.813 1 27.81 ? C2B HEM 410 A 1 HETATM 17 C C3B HEM . . . B 2 79.991 -2.728 66.346 1 28.56 ? C3B HEM 410 A 1 HETATM 18 C C4B HEM . . . B 2 79.993 -2.806 67.786 1 27.93 ? C4B HEM 410 A 1 HETATM 19 C CMB HEM . . . B 2 79.433 -4.153 64.33 1 27.39 ? CMB HEM 410 A 1 HETATM 20 C CAB HEM . . . B 2 80.375 -1.597 65.502 1 29.48 ? CAB HEM 410 A 1 HETATM 21 C CBB HEM . . . B 2 80.79 -0.473 66.268 1 35.89 ? CBB HEM 410 A 1 HETATM 22 C C1C HEM . . . B 2 80.312 -2.028 70.14 1 27.05 ? C1C HEM 410 A 1 HETATM 23 C C2C HEM . . . B 2 80.652 -1.113 71.15 1 27.67 ? C2C HEM 410 A 1 HETATM 24 C C3C HEM . . . B 2 80.477 -1.671 72.408 1 27.52 ? C3C HEM 410 A 1 HETATM 25 C C4C HEM . . . B 2 80.012 -2.992 72.297 1 25.78 ? C4C HEM 410 A 1 HETATM 26 C CMC HEM . . . B 2 81.14 0.295 70.864 1 27.39 ? CMC HEM 410 A 1 HETATM 27 C CAC HEM . . . B 2 80.72 -1.038 73.7 1 28.81 ? CAC HEM 410 A 1 HETATM 28 C CBC HEM . . . B 2 81.181 0.308 73.552 1 32.62 ? CBC HEM 410 A 1 HETATM 29 C C1D HEM . . . B 2 79.229 -5.176 73.12 1 26.16 ? C1D HEM 410 A 1 HETATM 30 C C2D HEM . . . B 2 78.886 -6.135 74.088 1 28.02 ? C2D HEM 410 A 1 HETATM 31 C C3D HEM . . . B 2 78.442 -7.274 73.515 1 27.08 ? C3D HEM 410 A 1 HETATM 32 C C4D HEM . . . B 2 78.45 -7.182 72.114 1 26.54 ? C4D HEM 410 A 1 HETATM 33 C CMD HEM . . . B 2 78.989 -5.915 75.581 1 25.54 ? CMD HEM 410 A 1 HETATM 34 C CAD HEM . . . B 2 77.99 -8.482 74.275 1 28.77 ? CAD HEM 410 A 1 HETATM 35 C CBD HEM . . . B 2 76.465 -8.514 74.225 1 26.83 ? CBD HEM 410 A 1 HETATM 36 C CGD HEM . . . B 2 75.872 -9.692 74.956 1 27.03 ? CGD HEM 410 A 1 HETATM 37 O O1D HEM . . . B 2 76.419 -10.798 74.77 1 26.84 ? O1D HEM 410 A 1 HETATM 38 O O2D HEM . . . B 2 74.657 -9.615 75.218 1 27.06 ? O2D HEM 410 A 1 HETATM 39 N NA HEM . . . B 2 78.578 -6.725 69.115 1 25.17 ? NA HEM 410 A 1 HETATM 40 N NB HEM . . . B 2 79.508 -4.178 68.092 1 26.16 ? NB HEM 410 A 1 HETATM 41 N NC HEM . . . B 2 79.888 -3.258 70.847 1 26.64 ? NC HEM 410 A 1 HETATM 42 N ND HEM . . . B 2 78.966 -5.824 71.806 1 26.03 ? ND HEM 410 A 1 HETATM 43 FE FE HEM . . . B 2 79.252 -4.98 69.959 1 26.95 ? FE HEM 410 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #