data_5L92 # _model_server_result.job_id YrQZXJLCEecdJnMLc-vCPA _model_server_result.datetime_utc '2024-12-01 12:08:02' _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 5l92 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5L92 # _exptl.entry_id 5L92 _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 114.42 _cell.angle_gamma 90 _cell.entry_id 5L92 _cell.length_a 60.495 _cell.length_b 135.701 _cell.length_c 61.567 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5L92 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 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,G 1 1 B,F,H 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 F 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 SG CYS 352 A CYS 352 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc2 C FE HEM . A HEM 501 1_555 D O1 C0R . A C0R 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? metalc ? metalc3 B SG CYS 352 B CYS 352 1_555 F FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? # _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 187 n n CHA C4D HEM doub 188 n n CHA HHA HEM sing 189 n n CHB C4A HEM sing 190 n n CHB C1B HEM doub 191 n n CHB HHB HEM sing 192 n n CHC C4B HEM sing 193 n n CHC C1C HEM doub 194 n n CHC HHC HEM sing 195 n n CHD C4C HEM doub 196 n n CHD C1D HEM sing 197 n n CHD HHD HEM sing 198 n n C1A C2A HEM doub 199 n y C1A NA HEM sing 200 n y C2A C3A HEM sing 201 n y C2A CAA HEM sing 202 n n C3A C4A HEM doub 203 n y C3A CMA HEM sing 204 n n C4A NA HEM sing 205 n y CMA HMA HEM sing 206 n n CMA HMAA HEM sing 207 n n CMA HMAB HEM sing 208 n n CAA CBA HEM sing 209 n n CAA HAA HEM sing 210 n n CAA HAAA HEM sing 211 n n CBA CGA HEM sing 212 n n CBA HBA HEM sing 213 n n CBA HBAA HEM sing 214 n n CGA O1A HEM doub 215 n n CGA O2A HEM sing 216 n n C1B C2B HEM sing 217 n n C1B NB HEM sing 218 n n C2B C3B HEM doub 219 n n C2B CMB HEM sing 220 n n C3B C4B HEM sing 221 n n C3B CAB HEM sing 222 n n C4B NB HEM doub 223 n n CMB HMB HEM sing 224 n n CMB HMBA HEM sing 225 n n CMB HMBB HEM sing 226 n n CAB CBB HEM doub 227 n n CAB HAB HEM sing 228 n n CBB HBB HEM sing 229 n n CBB HBBA HEM sing 230 n n C1C C2C HEM sing 231 n y C1C NC HEM sing 232 n y C2C C3C HEM doub 233 n y C2C CMC HEM sing 234 n n C3C C4C HEM sing 235 n y C3C CAC HEM sing 236 n n C4C NC HEM sing 237 n y CMC HMC HEM sing 238 n n CMC HMCA HEM sing 239 n n CMC HMCB HEM sing 240 n n CAC CBC HEM doub 241 n n CAC HAC HEM sing 242 n n CBC HBC HEM sing 243 n n CBC HBCA HEM sing 244 n n C1D C2D HEM sing 245 n n C1D ND HEM doub 246 n n C2D C3D HEM doub 247 n n C2D CMD HEM sing 248 n n C3D C4D HEM sing 249 n n C3D CAD HEM sing 250 n n C4D ND HEM sing 251 n n CMD HMD HEM sing 252 n n CMD HMDA HEM sing 253 n n CMD HMDB HEM sing 254 n n CAD CBD HEM sing 255 n n CAD HAD HEM sing 256 n n CAD HADA HEM sing 257 n n CBD CGD HEM sing 258 n n CBD HBD HEM sing 259 n n CBD HBDA HEM sing 260 n n CGD O1D HEM doub 261 n n CGD O2D HEM sing 262 n n O2A H2A HEM sing 263 n n O2D H2D HEM sing 264 n n FE NA HEM sing 265 n n FE NB HEM sing 266 n n FE NC HEM sing 267 n n FE ND HEM sing 268 n n # _atom_sites.entry_id 5L92 _atom_sites.fract_transf_matrix[1][1] 0.01653 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007505 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007369 _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] 0.017838 _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 1 501 501 HEM HEM . D 3 C0R A 1 502 503 C0R C0R . E 4 MLA A 1 503 504 MLA MLA . F 2 HEM B 1 501 501 HEM HEM . G 5 HOH A 1 601 624 HOH HOH . G 5 HOH A 2 602 655 HOH HOH . G 5 HOH A 3 603 645 HOH HOH . G 5 HOH A 4 604 631 HOH HOH . G 5 HOH A 5 605 627 HOH HOH . G 5 HOH A 6 606 605 HOH HOH . G 5 HOH A 7 607 654 HOH HOH . G 5 HOH A 8 608 647 HOH HOH . G 5 HOH A 9 609 604 HOH HOH . G 5 HOH A 10 610 618 HOH HOH . G 5 HOH A 11 611 616 HOH HOH . G 5 HOH A 12 612 660 HOH HOH . G 5 HOH A 13 613 626 HOH HOH . G 5 HOH A 14 614 612 HOH HOH . G 5 HOH A 15 615 658 HOH HOH . G 5 HOH A 16 616 650 HOH HOH . G 5 HOH A 17 617 643 HOH HOH . G 5 HOH A 18 618 644 HOH HOH . G 5 HOH A 19 619 628 HOH HOH . G 5 HOH A 20 620 639 HOH HOH . G 5 HOH A 21 621 661 HOH HOH . G 5 HOH A 22 622 600 HOH HOH . G 5 HOH A 23 623 625 HOH HOH . G 5 HOH A 24 624 662 HOH HOH . G 5 HOH A 25 625 651 HOH HOH . G 5 HOH A 26 626 632 HOH HOH . G 5 HOH A 27 627 634 HOH HOH . G 5 HOH A 28 628 606 HOH HOH . G 5 HOH A 29 629 610 HOH HOH . G 5 HOH A 30 630 613 HOH HOH . G 5 HOH A 31 631 617 HOH HOH . G 5 HOH A 32 632 621 HOH HOH . G 5 HOH A 33 633 629 HOH HOH . G 5 HOH A 34 634 607 HOH HOH . G 5 HOH A 35 635 622 HOH HOH . G 5 HOH A 36 636 615 HOH HOH . G 5 HOH A 37 637 601 HOH HOH . G 5 HOH A 38 638 608 HOH HOH . G 5 HOH A 39 639 640 HOH HOH . G 5 HOH A 40 640 653 HOH HOH . G 5 HOH A 41 641 649 HOH HOH . G 5 HOH A 42 642 635 HOH HOH . G 5 HOH A 43 643 620 HOH HOH . G 5 HOH A 44 644 646 HOH HOH . G 5 HOH A 45 645 602 HOH HOH . G 5 HOH A 46 646 609 HOH HOH . G 5 HOH A 47 647 659 HOH HOH . G 5 HOH A 48 648 637 HOH HOH . G 5 HOH A 49 649 664 HOH HOH . G 5 HOH A 50 650 623 HOH HOH . G 5 HOH A 51 651 603 HOH HOH . G 5 HOH A 52 652 638 HOH HOH . G 5 HOH A 53 653 630 HOH HOH . G 5 HOH A 54 654 611 HOH HOH . G 5 HOH A 55 655 663 HOH HOH . G 5 HOH A 56 656 641 HOH HOH . G 5 HOH A 57 657 652 HOH HOH . G 5 HOH A 58 658 619 HOH HOH . G 5 HOH A 59 659 648 HOH HOH . G 5 HOH A 60 660 614 HOH HOH . G 5 HOH A 61 661 656 HOH HOH . G 5 HOH A 62 662 633 HOH HOH . G 5 HOH A 63 663 642 HOH HOH . G 5 HOH A 64 664 657 HOH HOH . G 5 HOH A 65 665 636 HOH HOH . G 5 HOH A 66 666 665 HOH HOH . H 5 HOH B 1 601 649 HOH HOH . H 5 HOH B 2 602 638 HOH HOH . H 5 HOH B 3 603 640 HOH HOH . H 5 HOH B 4 604 628 HOH HOH . H 5 HOH B 5 605 625 HOH HOH . H 5 HOH B 6 606 612 HOH HOH . H 5 HOH B 7 607 652 HOH HOH . H 5 HOH B 8 608 626 HOH HOH . H 5 HOH B 9 609 642 HOH HOH . H 5 HOH B 10 610 627 HOH HOH . H 5 HOH B 11 611 608 HOH HOH . H 5 HOH B 12 612 645 HOH HOH . H 5 HOH B 13 613 620 HOH HOH . H 5 HOH B 14 614 641 HOH HOH . H 5 HOH B 15 615 623 HOH HOH . H 5 HOH B 16 616 602 HOH HOH . H 5 HOH B 17 617 603 HOH HOH . H 5 HOH B 18 618 648 HOH HOH . H 5 HOH B 19 619 606 HOH HOH . H 5 HOH B 20 620 643 HOH HOH . H 5 HOH B 21 621 647 HOH HOH . H 5 HOH B 22 622 615 HOH HOH . H 5 HOH B 23 623 611 HOH HOH . H 5 HOH B 24 624 631 HOH HOH . H 5 HOH B 25 625 610 HOH HOH . H 5 HOH B 26 626 616 HOH HOH . H 5 HOH B 27 627 651 HOH HOH . H 5 HOH B 28 628 646 HOH HOH . H 5 HOH B 29 629 634 HOH HOH . H 5 HOH B 30 630 635 HOH HOH . H 5 HOH B 31 631 639 HOH HOH . H 5 HOH B 32 632 637 HOH HOH . H 5 HOH B 33 633 653 HOH HOH . H 5 HOH B 34 634 607 HOH HOH . H 5 HOH B 35 635 605 HOH HOH . H 5 HOH B 36 636 629 HOH HOH . H 5 HOH B 37 637 604 HOH HOH . H 5 HOH B 38 638 654 HOH HOH . H 5 HOH B 39 639 614 HOH HOH . H 5 HOH B 40 640 644 HOH HOH . H 5 HOH B 41 641 600 HOH HOH . H 5 HOH B 42 642 621 HOH HOH . H 5 HOH B 43 643 617 HOH HOH . H 5 HOH B 44 644 613 HOH HOH . H 5 HOH B 45 645 601 HOH HOH . H 5 HOH B 46 646 619 HOH HOH . H 5 HOH B 47 647 630 HOH HOH . H 5 HOH B 48 648 636 HOH HOH . H 5 HOH B 49 649 609 HOH HOH . H 5 HOH B 50 650 618 HOH HOH . H 5 HOH B 51 651 650 HOH HOH . H 5 HOH B 52 652 624 HOH HOH . H 5 HOH B 53 653 632 HOH HOH . H 5 HOH B 54 654 656 HOH HOH . H 5 HOH B 55 655 633 HOH HOH . H 5 HOH B 56 656 655 HOH HOH . H 5 HOH B 57 657 622 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 -33.662 -7.312 16.597 1 26.11 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . C 2 -30.667 -10.316 14.162 1 24.31 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . C 2 -28.506 -6.584 12.039 1 25.51 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . C 2 -31.145 -3.641 14.835 1 26.34 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . C 2 -33.057 -8.447 16.071 1 25.59 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . C 2 -33.48 -9.808 16.319 1 25.52 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . C 2 -32.648 -10.629 15.661 1 25.46 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . C 2 -31.685 -9.822 14.948 1 25 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . C 2 -32.718 -12.169 15.639 1 25.6 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . C 2 -34.674 -10.243 17.213 1 25.6 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . C 2 -34.426 -9.963 18.696 1 26.25 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . C 2 -35.413 -10.676 19.582 1 27.06 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . C 2 -36.467 -11.122 19.111 1 25.97 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . C 2 -35.154 -10.834 20.787 1 28.18 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . C 2 -29.839 -9.6 13.331 1 24.65 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . C 2 -28.937 -10.122 12.313 1 25.53 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . C 2 -28.335 -9.063 11.746 1 25.72 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . C 2 -28.832 -7.864 12.392 1 25.22 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . C 2 -28.773 -11.613 11.961 1 24.7 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . C 2 -27.321 -8.994 10.585 1 25.76 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . C 2 -27.202 -9.96 9.66 1 27.93 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . C 2 -29.04 -5.453 12.612 1 25.88 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . C 2 -28.616 -4.102 12.361 1 26.4 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . C 2 -29.351 -3.303 13.113 1 27.2 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . C 2 -30.239 -4.102 13.912 1 25.62 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . C 2 -27.539 -3.628 11.351 1 26.76 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . C 2 -29.155 -1.782 13.119 1 27.57 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . C 2 -30.168 -0.977 12.814 1 32.84 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . C 2 -32.051 -4.361 15.559 1 26.38 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . C 2 -32.997 -3.795 16.499 1 27.87 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . C 2 -33.719 -4.808 17 1 28.09 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . C 2 -33.219 -6.035 16.388 1 27.22 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . C 2 -33.073 -2.276 16.809 1 27.92 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . C 2 -34.866 -4.757 18.04 1 28.95 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . C 2 -36.24 -4.684 17.345 1 29.65 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . C 2 -37.415 -4.782 18.298 1 31.41 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . C 2 -38.535 -4.354 17.936 1 32.45 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . C 2 -37.282 -5.311 19.431 1 31.7 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . C 2 -31.958 -8.466 15.223 1 26.91 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . C 2 -29.726 -8.227 13.355 1 25.96 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . C 2 -30.03 -5.416 13.578 1 27.49 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . C 2 -32.199 -5.723 15.55 1 27.57 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . C 2 -31.022 -6.922 14.344 1 22.92 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 10 _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 #