data_4ZFA # _model_server_result.job_id 0Pwt7xdk1Sp37-QQ7-6jhg _model_server_result.datetime_utc '2024-11-12 21:03:44' _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 4zfa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4ZFA # _exptl.entry_id 4ZFA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 2 _entity.src_method nat _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 90 _cell.angle_gamma 120 _cell.entry_id 4ZFA _cell.length_a 55.503 _cell.length_b 55.503 _cell.length_c 717.749 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZFA _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # _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,D,E,F,G,H,I _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 N THR 2 A THR 1 1_555 E NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc2 A OG1 THR 2 A THR 1 1_555 E NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc3 A NE2 HIS 139 A HIS 138 1_555 F NI NI . A NI 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc4 A NE2 HIS 237 A HIS 236 1_555 H NI NI . A NI 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc5 A OD2 ASP 339 A ASP 338 1_555 E NI NI . A NI 504 10_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc6 A OE2 GLU 349 A GLU 348 1_555 E NI NI . A NI 504 10_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc7 A SG CYS 401 A CYS 400 1_555 B FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc8 A NE2 HIS 427 A HIS 426 1_555 F NI NI . A NI 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc9 B FE HEM . A HEM 501 1_555 D O2 EDO . A EDO 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? metalc ? metalc10 G NI NI . A NI 506 1_555 I O HOH . A HOH 650 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? # _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 175 n n CHA C4D HEM doub 176 n n CHA HHA HEM sing 177 n n CHB C4A HEM sing 178 n n CHB C1B HEM doub 179 n n CHB HHB HEM sing 180 n n CHC C4B HEM sing 181 n n CHC C1C HEM doub 182 n n CHC HHC HEM sing 183 n n CHD C4C HEM doub 184 n n CHD C1D HEM sing 185 n n CHD HHD HEM sing 186 n n C1A C2A HEM doub 187 n y C1A NA HEM sing 188 n y C2A C3A HEM sing 189 n y C2A CAA HEM sing 190 n n C3A C4A HEM doub 191 n y C3A CMA HEM sing 192 n n C4A NA HEM sing 193 n y CMA HMA HEM sing 194 n n CMA HMAA HEM sing 195 n n CMA HMAB HEM sing 196 n n CAA CBA HEM sing 197 n n CAA HAA HEM sing 198 n n CAA HAAA HEM sing 199 n n CBA CGA HEM sing 200 n n CBA HBA HEM sing 201 n n CBA HBAA HEM sing 202 n n CGA O1A HEM doub 203 n n CGA O2A HEM sing 204 n n C1B C2B HEM sing 205 n n C1B NB HEM sing 206 n n C2B C3B HEM doub 207 n n C2B CMB HEM sing 208 n n C3B C4B HEM sing 209 n n C3B CAB HEM sing 210 n n C4B NB HEM doub 211 n n CMB HMB HEM sing 212 n n CMB HMBA HEM sing 213 n n CMB HMBB HEM sing 214 n n CAB CBB HEM doub 215 n n CAB HAB HEM sing 216 n n CBB HBB HEM sing 217 n n CBB HBBA HEM sing 218 n n C1C C2C HEM sing 219 n y C1C NC HEM sing 220 n y C2C C3C HEM doub 221 n y C2C CMC HEM sing 222 n n C3C C4C HEM sing 223 n y C3C CAC HEM sing 224 n n C4C NC HEM sing 225 n y CMC HMC HEM sing 226 n n CMC HMCA HEM sing 227 n n CMC HMCB HEM sing 228 n n CAC CBC HEM doub 229 n n CAC HAC HEM sing 230 n n CBC HBC HEM sing 231 n n CBC HBCA HEM sing 232 n n C1D C2D HEM sing 233 n n C1D ND HEM doub 234 n n C2D C3D HEM doub 235 n n C2D CMD HEM sing 236 n n C3D C4D HEM sing 237 n n C3D CAD HEM sing 238 n n C4D ND HEM sing 239 n n CMD HMD HEM sing 240 n n CMD HMDA HEM sing 241 n n CMD HMDB HEM sing 242 n n CAD CBD HEM sing 243 n n CAD HAD HEM sing 244 n n CAD HADA HEM sing 245 n n CBD CGD HEM sing 246 n n CBD HBD HEM sing 247 n n CBD HBDA HEM sing 248 n n CGD O1D HEM doub 249 n n CGD O2D HEM sing 250 n n O2A H2A HEM sing 251 n n O2D H2D HEM sing 252 n n FE NA HEM sing 253 n n FE NB HEM sing 254 n n FE NC HEM sing 255 n n FE ND HEM sing 256 n n # _atom_sites.entry_id 4ZFA _atom_sites.fract_transf_matrix[1][1] 0.018017 _atom_sites.fract_transf_matrix[1][2] 0.010402 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020804 _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] 0.001393 _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 1 501 500 HEM HEM . C 3 1PE A 1 502 501 1PE 1PE . D 4 EDO A 1 503 502 EDO EDO . E 5 NI A 1 504 601 NI NI . F 5 NI A 1 505 602 NI NI . G 5 NI A 1 506 603 NI NI . H 5 NI A 1 507 604 NI NI . I 6 HOH A 1 601 740 HOH HOH . I 6 HOH A 2 602 726 HOH HOH . I 6 HOH A 3 603 705 HOH HOH . I 6 HOH A 4 604 706 HOH HOH . I 6 HOH A 5 605 731 HOH HOH . I 6 HOH A 6 606 712 HOH HOH . I 6 HOH A 7 607 743 HOH HOH . I 6 HOH A 8 608 728 HOH HOH . I 6 HOH A 9 609 732 HOH HOH . I 6 HOH A 10 610 733 HOH HOH . I 6 HOH A 11 611 714 HOH HOH . I 6 HOH A 12 612 709 HOH HOH . I 6 HOH A 13 613 727 HOH HOH . I 6 HOH A 14 614 739 HOH HOH . I 6 HOH A 15 615 718 HOH HOH . I 6 HOH A 16 616 721 HOH HOH . I 6 HOH A 17 617 744 HOH HOH . I 6 HOH A 18 618 746 HOH HOH . I 6 HOH A 19 619 730 HOH HOH . I 6 HOH A 20 620 702 HOH HOH . I 6 HOH A 21 621 738 HOH HOH . I 6 HOH A 22 622 748 HOH HOH . I 6 HOH A 23 623 711 HOH HOH . I 6 HOH A 24 624 749 HOH HOH . I 6 HOH A 25 625 720 HOH HOH . I 6 HOH A 26 626 704 HOH HOH . I 6 HOH A 27 627 719 HOH HOH . I 6 HOH A 28 628 701 HOH HOH . I 6 HOH A 29 629 757 HOH HOH . I 6 HOH A 30 630 715 HOH HOH . I 6 HOH A 31 631 703 HOH HOH . I 6 HOH A 32 632 717 HOH HOH . I 6 HOH A 33 633 729 HOH HOH . I 6 HOH A 34 634 707 HOH HOH . I 6 HOH A 35 635 710 HOH HOH . I 6 HOH A 36 636 736 HOH HOH . I 6 HOH A 37 637 747 HOH HOH . I 6 HOH A 38 638 751 HOH HOH . I 6 HOH A 39 639 723 HOH HOH . I 6 HOH A 40 640 750 HOH HOH . I 6 HOH A 41 641 742 HOH HOH . I 6 HOH A 42 642 741 HOH HOH . I 6 HOH A 43 643 745 HOH HOH . I 6 HOH A 44 644 725 HOH HOH . I 6 HOH A 45 645 737 HOH HOH . I 6 HOH A 46 646 752 HOH HOH . I 6 HOH A 47 647 724 HOH HOH . I 6 HOH A 48 648 754 HOH HOH . I 6 HOH A 49 649 722 HOH HOH . I 6 HOH A 50 650 735 HOH HOH . I 6 HOH A 51 651 713 HOH HOH . I 6 HOH A 52 652 755 HOH HOH . I 6 HOH A 53 653 734 HOH HOH . I 6 HOH A 54 654 716 HOH HOH . I 6 HOH A 55 655 708 HOH HOH . I 6 HOH A 56 656 753 HOH HOH . I 6 HOH A 57 657 756 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 -10.599 5.931 30.451 1 43.33 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . B 2 -10.789 1.204 29.391 1 43.87 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . B 2 -13.09 2.217 25.237 1 43.27 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . B 2 -12.007 6.914 25.864 1 44.51 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . B 2 -10.467 4.564 30.541 1 43.12 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . B 2 -9.895 3.827 31.65 1 43.01 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . B 2 -9.946 2.528 31.355 1 42.72 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . B 2 -10.556 2.388 30.05 1 43.32 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . B 2 -9.446 1.373 32.249 1 42.18 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . B 2 -9.316 4.431 32.947 1 43.59 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . B 2 -7.85 4.772 32.71 1 43.62 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . B 2 -7.114 4.814 34.023 1 44.35 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . B 2 -5.858 4.87 34 1 45.07 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . B 2 -7.781 4.782 35.089 1 44.34 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . B 2 -11.446 1.06 28.19 1 43.85 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . B 2 -11.773 -0.197 27.559 1 43.95 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . B 2 -12.408 0.056 26.415 1 43.85 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . B 2 -12.511 1.504 26.269 1 43.53 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . B 2 -11.446 -1.6 28.114 1 44.99 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . B 2 -12.909 -1.064 25.473 1 43.5 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . B 2 -13.575 -0.817 24.345 1 44.61 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . B 2 -13.06 3.589 25.073 1 43.71 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . B 2 -13.786 4.354 24.078 1 44.61 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . B 2 -13.5 5.646 24.239 1 44.02 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . B 2 -12.57 5.762 25.353 1 44.32 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . B 2 -14.737 3.792 23.001 1 45.31 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . B 2 -14.099 6.763 23.35 1 44.8 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . B 2 -13.834 8.059 23.532 1 45.24 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . B 2 -11.547 7.11 27.149 1 43.74 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . B 2 -11.18 8.386 27.726 1 43.26 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . B 2 -10.737 8.072 29.161 1 43.58 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . B 2 -10.886 6.643 29.306 1 43.75 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . B 2 -11.217 9.771 27.045 1 45.17 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . B 2 -10.248 9.064 30.236 1 45.92 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . B 2 -11.465 9.747 30.853 1 45.89 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . B 2 -11.068 10.492 32.1 1 45.92 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . B 2 -11.862 11.352 32.56 1 46.62 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . B 2 -9.958 10.23 32.632 1 45.39 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . B 2 -10.863 3.652 29.581 1 43.69 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . B 2 -11.91 2.078 27.377 1 43.65 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . B 2 -12.33 4.485 25.832 1 44.2 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . B 2 -11.361 6.118 28.107 1 43.33 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . B 2 -11.767 4.112 27.772 1 41.7 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #