data_2BDM # _model_server_result.job_id m7WYfT_40d9_i5ziN9u_Lg _model_server_result.datetime_utc '2024-10-18 04:23:33' _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 2bdm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 2BDM # _exptl.entry_id 2BDM _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 90 _cell.angle_gamma 120 _cell.entry_id 2BDM _cell.length_a 203.21 _cell.length_b 203.21 _cell.length_c 103.45 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2BDM _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA,PQS dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1 A,B,C,D,E,F,G,H,I,J 2 1,2 A,B,C,D,E,F,G,H,I,J 3 1,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 203.21 0 51.725 3 'crystal symmetry operation' 12_555 x,x-y,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 17.241667 # _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 417 A CYS 436 1_555 B FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc2 B FE HEM . A HEM 500 1_555 C NAD TMI . A TMI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? # _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 207 n n CHA C4D HEM doub 208 n n CHA HHA HEM sing 209 n n CHB C4A HEM sing 210 n n CHB C1B HEM doub 211 n n CHB HHB HEM sing 212 n n CHC C4B HEM sing 213 n n CHC C1C HEM doub 214 n n CHC HHC HEM sing 215 n n CHD C4C HEM doub 216 n n CHD C1D HEM sing 217 n n CHD HHD HEM sing 218 n n C1A C2A HEM doub 219 n y C1A NA HEM sing 220 n y C2A C3A HEM sing 221 n y C2A CAA HEM sing 222 n n C3A C4A HEM doub 223 n y C3A CMA HEM sing 224 n n C4A NA HEM sing 225 n y CMA HMA HEM sing 226 n n CMA HMAA HEM sing 227 n n CMA HMAB HEM sing 228 n n CAA CBA HEM sing 229 n n CAA HAA HEM sing 230 n n CAA HAAA HEM sing 231 n n CBA CGA HEM sing 232 n n CBA HBA HEM sing 233 n n CBA HBAA HEM sing 234 n n CGA O1A HEM doub 235 n n CGA O2A HEM sing 236 n n C1B C2B HEM sing 237 n n C1B NB HEM sing 238 n n C2B C3B HEM doub 239 n n C2B CMB HEM sing 240 n n C3B C4B HEM sing 241 n n C3B CAB HEM sing 242 n n C4B NB HEM doub 243 n n CMB HMB HEM sing 244 n n CMB HMBA HEM sing 245 n n CMB HMBB HEM sing 246 n n CAB CBB HEM doub 247 n n CAB HAB HEM sing 248 n n CBB HBB HEM sing 249 n n CBB HBBA HEM sing 250 n n C1C C2C HEM sing 251 n y C1C NC HEM sing 252 n y C2C C3C HEM doub 253 n y C2C CMC HEM sing 254 n n C3C C4C HEM sing 255 n y C3C CAC HEM sing 256 n n C4C NC HEM sing 257 n y CMC HMC HEM sing 258 n n CMC HMCA HEM sing 259 n n CMC HMCB HEM sing 260 n n CAC CBC HEM doub 261 n n CAC HAC HEM sing 262 n n CBC HBC HEM sing 263 n n CBC HBCA HEM sing 264 n n C1D C2D HEM sing 265 n n C1D ND HEM doub 266 n n C2D C3D HEM doub 267 n n C2D CMD HEM sing 268 n n C3D C4D HEM sing 269 n n C3D CAD HEM sing 270 n n C4D ND HEM sing 271 n n CMD HMD HEM sing 272 n n CMD HMDA HEM sing 273 n n CMD HMDB HEM sing 274 n n CAD CBD HEM sing 275 n n CAD HAD HEM sing 276 n n CAD HADA HEM sing 277 n n CBD CGD HEM sing 278 n n CBD HBD HEM sing 279 n n CBD HBDA HEM sing 280 n n CGD O1D HEM doub 281 n n CGD O2D HEM sing 282 n n O2A H2A HEM sing 283 n n O2D H2D HEM sing 284 n n FE NA HEM sing 285 n n FE NB HEM sing 286 n n FE NC HEM sing 287 n n FE ND HEM sing 288 n n # _atom_sites.entry_id 2BDM _atom_sites.fract_transf_matrix[1][1] 0.004921 _atom_sites.fract_transf_matrix[1][2] 0.002841 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005682 _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] 0.009667 _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 1 500 500 HEM HEM . C 3 TMI A 1 501 501 TMI TMI . D 3 TMI A 1 502 502 TMI TMI . E 3 TMI A 1 503 503 TMI TMI . F 4 CM5 A 1 504 504 CM5 CM5 . G 4 CM5 A 1 505 505 CM5 CM5 . H 4 CM5 A 1 506 506 CM5 CM5 . I 4 CM5 A 1 507 507 CM5 CM5 . J 5 HOH A 1 601 601 HOH HOH . J 5 HOH A 2 602 602 HOH HOH . J 5 HOH A 3 603 603 HOH HOH . J 5 HOH A 4 604 604 HOH HOH . J 5 HOH A 5 605 605 HOH HOH . J 5 HOH A 6 606 606 HOH HOH . J 5 HOH A 7 607 607 HOH HOH . J 5 HOH A 8 608 608 HOH HOH . J 5 HOH A 9 609 609 HOH HOH . J 5 HOH A 10 610 610 HOH HOH . J 5 HOH A 11 611 611 HOH HOH . J 5 HOH A 12 612 612 HOH HOH . J 5 HOH A 13 613 613 HOH HOH . J 5 HOH A 14 614 614 HOH HOH . J 5 HOH A 15 615 615 HOH HOH . J 5 HOH A 16 616 616 HOH HOH . J 5 HOH A 17 617 617 HOH HOH . J 5 HOH A 18 618 618 HOH HOH . J 5 HOH A 19 619 619 HOH HOH . J 5 HOH A 20 620 620 HOH HOH . J 5 HOH A 21 621 621 HOH HOH . J 5 HOH A 22 622 622 HOH HOH . J 5 HOH A 23 623 623 HOH HOH . J 5 HOH A 24 624 624 HOH HOH . J 5 HOH A 25 625 625 HOH HOH . J 5 HOH A 26 626 626 HOH HOH . J 5 HOH A 27 627 627 HOH HOH . J 5 HOH A 28 628 628 HOH HOH . J 5 HOH A 29 629 629 HOH HOH . J 5 HOH A 30 630 630 HOH HOH . J 5 HOH A 31 631 631 HOH HOH . J 5 HOH A 32 632 632 HOH HOH . J 5 HOH A 33 633 633 HOH HOH . J 5 HOH A 34 634 634 HOH HOH . J 5 HOH A 35 635 635 HOH HOH . J 5 HOH A 36 636 636 HOH HOH . J 5 HOH A 37 637 637 HOH HOH . J 5 HOH A 38 638 638 HOH HOH . J 5 HOH A 39 639 639 HOH HOH . J 5 HOH A 40 640 640 HOH HOH . J 5 HOH A 41 641 641 HOH HOH . J 5 HOH A 42 642 642 HOH HOH . J 5 HOH A 43 643 643 HOH HOH . J 5 HOH A 44 644 644 HOH HOH . J 5 HOH A 45 645 645 HOH HOH . J 5 HOH A 46 646 646 HOH HOH . J 5 HOH A 47 647 647 HOH HOH . J 5 HOH A 48 648 648 HOH HOH . J 5 HOH A 49 649 649 HOH HOH . J 5 HOH A 50 650 650 HOH HOH . J 5 HOH A 51 651 651 HOH HOH . J 5 HOH A 52 652 652 HOH HOH . J 5 HOH A 53 653 653 HOH HOH . J 5 HOH A 54 654 654 HOH HOH . J 5 HOH A 55 655 655 HOH HOH . J 5 HOH A 56 656 656 HOH HOH . J 5 HOH A 57 657 657 HOH HOH . J 5 HOH A 58 658 658 HOH HOH . J 5 HOH A 59 659 659 HOH HOH . J 5 HOH A 60 660 660 HOH HOH . J 5 HOH A 61 661 661 HOH HOH . J 5 HOH A 62 662 662 HOH HOH . J 5 HOH A 63 663 663 HOH HOH . J 5 HOH A 64 664 664 HOH HOH . J 5 HOH A 65 665 665 HOH HOH . J 5 HOH A 66 666 666 HOH HOH . J 5 HOH A 67 667 667 HOH HOH . J 5 HOH A 68 668 668 HOH HOH . J 5 HOH A 69 669 669 HOH HOH . J 5 HOH A 70 670 670 HOH HOH . J 5 HOH A 71 671 671 HOH HOH . J 5 HOH A 72 672 672 HOH HOH . J 5 HOH A 73 673 673 HOH HOH . J 5 HOH A 74 674 674 HOH HOH . J 5 HOH A 75 675 675 HOH HOH . J 5 HOH A 76 676 676 HOH HOH . J 5 HOH A 77 677 677 HOH HOH . J 5 HOH A 78 678 678 HOH HOH . J 5 HOH A 79 679 679 HOH HOH . J 5 HOH A 80 680 680 HOH HOH . J 5 HOH A 81 681 681 HOH HOH . J 5 HOH A 82 682 682 HOH HOH . J 5 HOH A 83 683 683 HOH HOH . J 5 HOH A 84 684 684 HOH HOH . J 5 HOH A 85 685 685 HOH HOH . J 5 HOH A 86 686 686 HOH HOH . J 5 HOH A 87 687 687 HOH HOH . J 5 HOH A 88 688 688 HOH HOH . J 5 HOH A 89 689 689 HOH HOH . J 5 HOH A 90 690 690 HOH HOH . J 5 HOH A 91 691 691 HOH HOH . J 5 HOH A 92 692 692 HOH HOH . J 5 HOH A 93 693 693 HOH HOH . J 5 HOH A 94 694 694 HOH HOH . J 5 HOH A 95 695 695 HOH HOH . J 5 HOH A 96 696 696 HOH HOH . J 5 HOH A 97 697 697 HOH HOH . J 5 HOH A 98 698 698 HOH HOH . J 5 HOH A 99 699 699 HOH HOH . J 5 HOH A 100 700 700 HOH HOH . J 5 HOH A 101 701 701 HOH HOH . J 5 HOH A 102 702 702 HOH HOH . J 5 HOH A 103 703 703 HOH HOH . J 5 HOH A 104 704 704 HOH HOH . J 5 HOH A 105 705 705 HOH HOH . J 5 HOH A 106 706 706 HOH HOH . J 5 HOH A 107 707 707 HOH HOH . J 5 HOH A 108 708 708 HOH HOH . J 5 HOH A 109 709 709 HOH HOH . J 5 HOH A 110 710 710 HOH HOH . J 5 HOH A 111 711 711 HOH HOH . J 5 HOH A 112 712 712 HOH HOH . J 5 HOH A 113 713 713 HOH HOH . J 5 HOH A 114 714 714 HOH HOH . J 5 HOH A 115 715 715 HOH HOH . J 5 HOH A 116 716 716 HOH HOH . J 5 HOH A 117 717 717 HOH HOH . J 5 HOH A 118 718 718 HOH HOH . J 5 HOH A 119 719 719 HOH HOH . J 5 HOH A 120 720 720 HOH HOH . J 5 HOH A 121 721 721 HOH HOH . J 5 HOH A 122 722 722 HOH HOH . J 5 HOH A 123 723 723 HOH HOH . J 5 HOH A 124 724 724 HOH HOH . J 5 HOH A 125 725 725 HOH HOH . J 5 HOH A 126 726 726 HOH HOH . J 5 HOH A 127 727 727 HOH HOH . J 5 HOH A 128 728 728 HOH HOH . J 5 HOH A 129 729 729 HOH HOH . J 5 HOH A 130 730 730 HOH HOH . J 5 HOH A 131 731 731 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 86.608 36.396 11.332 1 40.11 ? CHA HEM 500 A 1 HETATM 2 C CHB HEM . . . B 2 83.899 32.576 10.694 1 38.65 ? CHB HEM 500 A 1 HETATM 3 C CHC HEM . . . B 2 86.611 31.306 7.058 1 38.68 ? CHC HEM 500 A 1 HETATM 4 C CHD HEM . . . B 2 89.422 35.029 7.83 1 41.17 ? CHD HEM 500 A 1 HETATM 5 C C1A HEM . . . B 2 85.622 35.45 11.57 1 40.54 ? C1A HEM 500 A 1 HETATM 6 C C2A HEM . . . B 2 84.618 35.53 12.532 1 40.32 ? C2A HEM 500 A 1 HETATM 7 C C3A HEM . . . B 2 83.781 34.466 12.284 1 38.46 ? C3A HEM 500 A 1 HETATM 8 C C4A HEM . . . B 2 84.323 33.793 11.179 1 40.36 ? C4A HEM 500 A 1 HETATM 9 C CMA HEM . . . B 2 82.475 34.075 13.074 1 36.11 ? CMA HEM 500 A 1 HETATM 10 C CAA HEM . . . B 2 84.491 36.598 13.631 1 39.73 ? CAA HEM 500 A 1 HETATM 11 C CBA HEM . . . B 2 83.708 37.819 13.264 1 38.99 ? CBA HEM 500 A 1 HETATM 12 C CGA HEM . . . B 2 83.579 38.79 14.416 1 40.65 ? CGA HEM 500 A 1 HETATM 13 O O1A HEM . . . B 2 84.574 39.348 14.889 1 40.72 ? O1A HEM 500 A 1 HETATM 14 O O2A HEM . . . B 2 82.473 38.996 14.905 1 39.2 ? O2A HEM 500 A 1 HETATM 15 C C1B HEM . . . B 2 84.316 31.836 9.605 1 39.17 ? C1B HEM 500 A 1 HETATM 16 C C2B HEM . . . B 2 83.742 30.618 9.131 1 38.85 ? C2B HEM 500 A 1 HETATM 17 C C3B HEM . . . B 2 84.61 30.202 8.085 1 38.44 ? C3B HEM 500 A 1 HETATM 18 C C4B HEM . . . B 2 85.625 31.209 8.032 1 38.64 ? C4B HEM 500 A 1 HETATM 19 C CMB HEM . . . B 2 82.475 29.976 9.677 1 36.97 ? CMB HEM 500 A 1 HETATM 20 C CAB HEM . . . B 2 84.552 29.051 7.234 1 39.38 ? CAB HEM 500 A 1 HETATM 21 C CBB HEM . . . B 2 83.455 28.099 6.919 1 39.8 ? CBB HEM 500 A 1 HETATM 22 C C1C HEM . . . B 2 87.633 32.224 6.858 1 39.73 ? C1C HEM 500 A 1 HETATM 23 C C2C HEM . . . B 2 88.644 32.074 5.936 1 40.36 ? C2C HEM 500 A 1 HETATM 24 C C3C HEM . . . B 2 89.583 33.086 6.218 1 42.08 ? C3C HEM 500 A 1 HETATM 25 C C4C HEM . . . B 2 89.032 33.788 7.326 1 41.27 ? C4C HEM 500 A 1 HETATM 26 C CMC HEM . . . B 2 88.716 30.992 4.812 1 39.13 ? CMC HEM 500 A 1 HETATM 27 C CAC HEM . . . B 2 90.784 33.425 5.638 1 40.49 ? CAC HEM 500 A 1 HETATM 28 C CBC HEM . . . B 2 91.117 33.603 4.276 1 43.55 ? CBC HEM 500 A 1 HETATM 29 C C1D HEM . . . B 2 88.88 35.782 8.82 1 42.55 ? C1D HEM 500 A 1 HETATM 30 C C2D HEM . . . B 2 89.402 37.003 9.29 1 43.17 ? C2D HEM 500 A 1 HETATM 31 C C3D HEM . . . B 2 88.56 37.43 10.287 1 44.71 ? C3D HEM 500 A 1 HETATM 32 C C4D HEM . . . B 2 87.58 36.434 10.363 1 41.63 ? C4D HEM 500 A 1 HETATM 33 C CMD HEM . . . B 2 90.672 37.732 8.791 1 41.34 ? CMD HEM 500 A 1 HETATM 34 C CAD HEM . . . B 2 88.586 38.711 11.189 1 44.12 ? CAD HEM 500 A 1 HETATM 35 C CBD HEM . . . B 2 87.752 39.876 10.521 1 50.19 ? CBD HEM 500 A 1 HETATM 36 C CGD HEM . . . B 2 87.609 41.239 11.278 1 56.01 ? CGD HEM 500 A 1 HETATM 37 O O1D HEM . . . B 2 87.492 42.293 10.679 1 52.29 ? O1D HEM 500 A 1 HETATM 38 O O2D HEM . . . B 2 87.602 41.245 12.521 1 55.82 ? O2D HEM 500 A 1 HETATM 39 N NA HEM . . . B 2 85.414 34.378 10.755 1 39.64 ? NA HEM 500 A 1 HETATM 40 N NB HEM . . . B 2 85.422 32.148 8.935 1 39.18 ? NB HEM 500 A 1 HETATM 41 N NC HEM . . . B 2 87.86 33.234 7.678 1 38.36 ? NC HEM 500 A 1 HETATM 42 N ND HEM . . . B 2 87.799 35.477 9.478 1 41.05 ? ND HEM 500 A 1 HETATM 43 FE FE HEM . . . B 2 86.606 33.826 9.183 1 37.82 ? FE HEM 500 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #