data_6AYB # _model_server_result.job_id Kq-rQdOif86H5NJ2kUwhBA _model_server_result.datetime_utc '2024-10-12 23:28:06' _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 6ayb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6AYB # _exptl.entry_id 6AYB _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 100.13 _cell.angle_gamma 90 _cell.entry_id 6AYB _cell.length_a 119.21 _cell.length_b 55.25 _cell.length_c 71.62 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6AYB _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,D,E,F,G,H,I,J _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 covale ? covale1 A C GLU 345 A GLU 370 1_555 A N CSO 346 A CSO 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale2 A C CSO 346 A CSO 371 1_555 A N GLU 347 A GLU 372 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C ARG 366 A ARG 391 1_555 A N CSO 367 A CSO 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C CSO 367 A CSO 392 1_555 A N THR 368 A THR 393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? metalc ? metalc1 A O LEU 59 A LEU 84 1_555 H CA CA . A CA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.883 ? metalc ? metalc2 A SG CYS 405 A CYS 430 1_555 B FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc3 B FE HEM . A HEM 501 1_555 I N2 KKK . A KKK 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? # _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 152 n n CHA C4D HEM doub 153 n n CHA HHA HEM sing 154 n n CHB C4A HEM sing 155 n n CHB C1B HEM doub 156 n n CHB HHB HEM sing 157 n n CHC C4B HEM sing 158 n n CHC C1C HEM doub 159 n n CHC HHC HEM sing 160 n n CHD C4C HEM doub 161 n n CHD C1D HEM sing 162 n n CHD HHD HEM sing 163 n n C1A C2A HEM doub 164 n y C1A NA HEM sing 165 n y C2A C3A HEM sing 166 n y C2A CAA HEM sing 167 n n C3A C4A HEM doub 168 n y C3A CMA HEM sing 169 n n C4A NA HEM sing 170 n y CMA HMA HEM sing 171 n n CMA HMAA HEM sing 172 n n CMA HMAB HEM sing 173 n n CAA CBA HEM sing 174 n n CAA HAA HEM sing 175 n n CAA HAAA HEM sing 176 n n CBA CGA HEM sing 177 n n CBA HBA HEM sing 178 n n CBA HBAA HEM sing 179 n n CGA O1A HEM doub 180 n n CGA O2A HEM sing 181 n n C1B C2B HEM sing 182 n n C1B NB HEM sing 183 n n C2B C3B HEM doub 184 n n C2B CMB HEM sing 185 n n C3B C4B HEM sing 186 n n C3B CAB HEM sing 187 n n C4B NB HEM doub 188 n n CMB HMB HEM sing 189 n n CMB HMBA HEM sing 190 n n CMB HMBB HEM sing 191 n n CAB CBB HEM doub 192 n n CAB HAB HEM sing 193 n n CBB HBB HEM sing 194 n n CBB HBBA HEM sing 195 n n C1C C2C HEM sing 196 n y C1C NC HEM sing 197 n y C2C C3C HEM doub 198 n y C2C CMC HEM sing 199 n n C3C C4C HEM sing 200 n y C3C CAC HEM sing 201 n n C4C NC HEM sing 202 n y CMC HMC HEM sing 203 n n CMC HMCA HEM sing 204 n n CMC HMCB HEM sing 205 n n CAC CBC HEM doub 206 n n CAC HAC HEM sing 207 n n CBC HBC HEM sing 208 n n CBC HBCA HEM sing 209 n n C1D C2D HEM sing 210 n n C1D ND HEM doub 211 n n C2D C3D HEM doub 212 n n C2D CMD HEM sing 213 n n C3D C4D HEM sing 214 n n C3D CAD HEM sing 215 n n C4D ND HEM sing 216 n n CMD HMD HEM sing 217 n n CMD HMDA HEM sing 218 n n CMD HMDB HEM sing 219 n n CAD CBD HEM sing 220 n n CAD HAD HEM sing 221 n n CAD HADA HEM sing 222 n n CBD CGD HEM sing 223 n n CBD HBD HEM sing 224 n n CBD HBDA HEM sing 225 n n CGD O1D HEM doub 226 n n CGD O2D HEM sing 227 n n O2A H2A HEM sing 228 n n O2D H2D HEM sing 229 n n FE NA HEM sing 230 n n FE NB HEM sing 231 n n FE NC HEM sing 232 n n FE ND HEM sing 233 n n # _atom_sites.entry_id 6AYB _atom_sites.fract_transf_matrix[1][1] 0.008389 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001499 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0181 _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] 0.014184 _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 1 HEM HEM . C 3 EDO A 1 502 1 EDO EDO . D 3 EDO A 1 503 2 EDO EDO . E 3 EDO A 1 504 3 EDO EDO . F 3 EDO A 1 505 4 EDO EDO . G 3 EDO A 1 506 5 EDO EDO . H 4 CA A 1 507 1 CA CA . I 5 KKK A 1 508 1 KKK KKK . J 6 HOH A 1 601 50 HOH HOH . J 6 HOH A 2 602 64 HOH HOH . J 6 HOH A 3 603 23 HOH HOH . J 6 HOH A 4 604 36 HOH HOH . J 6 HOH A 5 605 74 HOH HOH . J 6 HOH A 6 606 59 HOH HOH . J 6 HOH A 7 607 19 HOH HOH . J 6 HOH A 8 608 79 HOH HOH . J 6 HOH A 9 609 32 HOH HOH . J 6 HOH A 10 610 62 HOH HOH . J 6 HOH A 11 611 6 HOH HOH . J 6 HOH A 12 612 47 HOH HOH . J 6 HOH A 13 613 34 HOH HOH . J 6 HOH A 14 614 78 HOH HOH . J 6 HOH A 15 615 81 HOH HOH . J 6 HOH A 16 616 7 HOH HOH . J 6 HOH A 17 617 17 HOH HOH . J 6 HOH A 18 618 67 HOH HOH . J 6 HOH A 19 619 13 HOH HOH . J 6 HOH A 20 620 30 HOH HOH . J 6 HOH A 21 621 38 HOH HOH . J 6 HOH A 22 622 26 HOH HOH . J 6 HOH A 23 623 15 HOH HOH . J 6 HOH A 24 624 57 HOH HOH . J 6 HOH A 25 625 21 HOH HOH . J 6 HOH A 26 626 35 HOH HOH . J 6 HOH A 27 627 68 HOH HOH . J 6 HOH A 28 628 8 HOH HOH . J 6 HOH A 29 629 20 HOH HOH . J 6 HOH A 30 630 63 HOH HOH . J 6 HOH A 31 631 25 HOH HOH . J 6 HOH A 32 632 10 HOH HOH . J 6 HOH A 33 633 3 HOH HOH . J 6 HOH A 34 634 1 HOH HOH . J 6 HOH A 35 635 55 HOH HOH . J 6 HOH A 36 636 29 HOH HOH . J 6 HOH A 37 637 76 HOH HOH . J 6 HOH A 38 638 83 HOH HOH . J 6 HOH A 39 639 56 HOH HOH . J 6 HOH A 40 640 85 HOH HOH . J 6 HOH A 41 641 51 HOH HOH . J 6 HOH A 42 642 31 HOH HOH . J 6 HOH A 43 643 28 HOH HOH . J 6 HOH A 44 644 2 HOH HOH . J 6 HOH A 45 645 27 HOH HOH . J 6 HOH A 46 646 5 HOH HOH . J 6 HOH A 47 647 22 HOH HOH . J 6 HOH A 48 648 33 HOH HOH . J 6 HOH A 49 649 12 HOH HOH . J 6 HOH A 50 650 9 HOH HOH . J 6 HOH A 51 651 75 HOH HOH . J 6 HOH A 52 652 54 HOH HOH . J 6 HOH A 53 653 65 HOH HOH . J 6 HOH A 54 654 53 HOH HOH . J 6 HOH A 55 655 45 HOH HOH . J 6 HOH A 56 656 14 HOH HOH . J 6 HOH A 57 657 77 HOH HOH . J 6 HOH A 58 658 40 HOH HOH . J 6 HOH A 59 659 4 HOH HOH . J 6 HOH A 60 660 24 HOH HOH . J 6 HOH A 61 661 60 HOH HOH . J 6 HOH A 62 662 18 HOH HOH . J 6 HOH A 63 663 16 HOH HOH . J 6 HOH A 64 664 69 HOH HOH . J 6 HOH A 65 665 61 HOH HOH . J 6 HOH A 66 666 43 HOH HOH . J 6 HOH A 67 667 48 HOH HOH . J 6 HOH A 68 668 58 HOH HOH . J 6 HOH A 69 669 82 HOH HOH . J 6 HOH A 70 670 42 HOH HOH . J 6 HOH A 71 671 37 HOH HOH . J 6 HOH A 72 672 46 HOH HOH . J 6 HOH A 73 673 49 HOH HOH . J 6 HOH A 74 674 44 HOH HOH . J 6 HOH A 75 675 84 HOH HOH . J 6 HOH A 76 676 41 HOH HOH . J 6 HOH A 77 677 70 HOH HOH . J 6 HOH A 78 678 80 HOH HOH . J 6 HOH A 79 679 52 HOH HOH . J 6 HOH A 80 680 71 HOH HOH . J 6 HOH A 81 681 39 HOH HOH . J 6 HOH A 82 682 66 HOH HOH . J 6 HOH A 83 683 72 HOH HOH . J 6 HOH A 84 684 11 HOH HOH . J 6 HOH A 85 685 73 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 4.236 19.982 94.222 1 29.72 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . B 2 2.81 24.264 92.628 1 29.38 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . B 2 7.447 25.678 92.421 1 26.36 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . B 2 8.821 21.205 93.415 1 28.84 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . B 2 3.506 21.02 93.863 1 31.1 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . B 2 2.069 21.048 93.848 1 28.92 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . B 2 1.698 22.235 93.395 1 28.56 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . B 2 2.854 22.976 93.099 1 31.74 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . B 2 0.266 22.733 93.219 1 31.17 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . B 2 1.106 19.946 94.279 1 34.8 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . B 2 1.027 18.89 93.197 1 33.95 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . B 2 0.06 17.805 93.643 1 40.42 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . B 2 -0.369 16.946 92.831 1 33.83 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . B 2 -0.32 17.75 94.83 1 41.11 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . B 2 3.962 25.035 92.454 1 27.88 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . B 2 3.915 26.426 92.072 1 28.4 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . B 2 5.234 26.869 92.012 1 27.62 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . B 2 6.067 25.661 92.372 1 25.09 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . B 2 2.643 27.203 91.804 1 34.2 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . B 2 5.784 28.242 91.703 1 31.77 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . B 2 4.995 29.339 91.597 1 33.22 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . B 2 8.231 24.574 92.668 1 27.87 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . B 2 9.649 24.56 92.693 1 25.51 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . B 2 10.006 23.249 92.983 1 25.61 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . B 2 8.822 22.497 93.121 1 29.56 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . B 2 10.594 25.734 92.475 1 27.65 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . B 2 11.336 22.647 93.101 1 33.37 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . B 2 12.413 23.312 92.809 1 35.67 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . B 2 7.675 20.531 93.725 1 29 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . B 2 7.721 19.17 94.164 1 27.35 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . B 2 6.49 18.787 94.42 1 33.14 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . B 2 5.609 19.975 94.104 1 26.9 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . B 2 8.965 18.338 94.316 1 28.61 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . B 2 6.173 17.36 94.874 1 40.06 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . B 2 5.163 17.217 95.961 1 41.92 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . B 2 4.7 15.769 95.964 1 44.28 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . B 2 4.199 15.244 94.923 1 47.75 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . B 2 4.816 15.09 96.988 1 45.63 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . B 2 3.955 22.225 93.386 1 24.52 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . B 2 5.24 24.648 92.609 1 27.56 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . B 2 7.778 23.306 92.93 1 23.69 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . B 2 6.415 20.974 93.695 1 29.15 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . B 2 5.847 22.741 93.179 1 29.33 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #