data_3M01 # _model_server_result.job_id iE4roy2zYzeJjMWRmjo9Aw _model_server_result.datetime_utc '2024-10-19 13:20:02' _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 3m01 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":549}' # _entry.id 3M01 # _exptl.entry_id 3M01 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 400.317 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2Z,6E)-2-fluoro-3,7,11-trimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate' _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 90 _cell.entry_id 3M01 _cell.length_a 125.5 _cell.length_b 125.5 _cell.length_c 122.7 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3M01 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 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 _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 OD2 ASP 303 A ASP 301 1_555 D MG MG . A MG 854 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc2 A OD1 ASP 303 A ASP 301 1_555 D MG MG . A MG 854 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc3 A OD1 ASP 303 A ASP 301 1_555 E MG MG . A MG 855 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc4 A OD2 ASP 307 A ASP 305 1_555 D MG MG . A MG 854 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? metalc ? metalc5 A OD1 ASP 307 A ASP 305 1_555 D MG MG . A MG 854 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.879 ? metalc ? metalc6 A OD1 ASP 307 A ASP 305 1_555 E MG MG . A MG 855 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? metalc ? metalc7 A OD1 ASP 446 A ASP 444 1_555 C MG MG . A MG 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? metalc ? metalc8 A OG1 THR 450 A THR 448 1_555 C MG MG . A MG 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? metalc ? metalc9 B O2B FPF . A FPF 549 1_555 D MG MG . A MG 854 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc10 B O3A FPF . A FPF 549 1_555 D MG MG . A MG 854 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc11 B O2B FPF . A FPF 549 1_555 E MG MG . A MG 855 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc12 H O HOH . A HOH 675 1_555 C MG MG . A MG 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc13 H O HOH . A HOH 690 1_555 C MG MG . A MG 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc14 H O HOH . A HOH 703 1_555 D MG MG . A MG 854 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc15 H O HOH . A HOH 704 1_555 E MG MG . A MG 855 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc16 H O HOH . A HOH 705 1_555 C MG MG . A MG 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc17 H O HOH . A HOH 706 1_555 E MG MG . A MG 855 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? # _chem_comp.formula 'C15 H27 F O7 P2' _chem_comp.formula_weight 400.317 _chem_comp.id FPF _chem_comp.mon_nstd_flag . _chem_comp.name '(2Z,6E)-2-fluoro-3,7,11-trimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O1 C1 FPF sing 89 n n C1 C2 FPF sing 90 n n C1 H1 FPF sing 91 n n C1 H1A FPF sing 92 n n P1 O1 FPF sing 93 n n C3 C2 FPF doub 94 z n C2 F FPF sing 95 n n C4 C3 FPF sing 96 n n C3 C5 FPF sing 97 n n C4 H4 FPF sing 98 n n C4 H4A FPF sing 99 n n C4 H4B FPF sing 100 n n C6 C5 FPF sing 101 n n C5 H5 FPF sing 102 n n C5 H5A FPF sing 103 n n C7 C6 FPF sing 104 n n C6 H6 FPF sing 105 n n C6 H6A FPF sing 106 n n C8 C7 FPF doub 107 e n C7 H7 FPF sing 108 n n C9 C8 FPF sing 109 n n C8 C10 FPF sing 110 n n C10 H10 FPF sing 111 n n C10 H10A FPF sing 112 n n C10 H10B FPF sing 113 n n C11 C9 FPF sing 114 n n C9 H9 FPF sing 115 n n C9 H9A FPF sing 116 n n C11 C12 FPF sing 117 n n C11 H11 FPF sing 118 n n C11 H11A FPF sing 119 n n C13 C12 FPF doub 120 n n C12 H12 FPF sing 121 n n C15 C13 FPF sing 122 n n C13 C14 FPF sing 123 n n C14 H14 FPF sing 124 n n C14 H14A FPF sing 125 n n C14 H14B FPF sing 126 n n C15 H15 FPF sing 127 n n C15 H15A FPF sing 128 n n C15 H15B FPF sing 129 n n O1A P1 FPF doub 130 n n O2A P1 FPF sing 131 n n P1 O3A FPF sing 132 n n O2A HO2A FPF sing 133 n n P2 O3A FPF sing 134 n n O3B P2 FPF doub 135 n n P2 O1B FPF sing 136 n n P2 O2B FPF sing 137 n n O1B HO1B FPF sing 138 n n O2B HO2B FPF sing 139 n n # _atom_sites.entry_id 3M01 _atom_sites.fract_transf_matrix[1][1] 0.007968 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007968 _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] 0.00815 _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 FPF A 1 549 0 FPF FPF . C 3 MG A 1 853 853 MG MG . D 3 MG A 1 854 854 MG MG . E 3 MG A 1 855 855 MG MG . F 4 ACT A 1 707 707 ACT ACT . G 4 ACT A 1 708 708 ACT ACT . H 5 HOH A 1 550 550 HOH HOH . H 5 HOH A 2 551 551 HOH HOH . H 5 HOH A 3 552 552 HOH HOH . H 5 HOH A 4 553 553 HOH HOH . H 5 HOH A 5 554 554 HOH HOH . H 5 HOH A 6 555 555 HOH HOH . H 5 HOH A 7 556 556 HOH HOH . H 5 HOH A 8 557 557 HOH HOH . H 5 HOH A 9 558 558 HOH HOH . H 5 HOH A 10 559 559 HOH HOH . H 5 HOH A 11 560 560 HOH HOH . H 5 HOH A 12 561 561 HOH HOH . H 5 HOH A 13 562 562 HOH HOH . H 5 HOH A 14 563 563 HOH HOH . H 5 HOH A 15 564 564 HOH HOH . H 5 HOH A 16 565 565 HOH HOH . H 5 HOH A 17 566 566 HOH HOH . H 5 HOH A 18 567 567 HOH HOH . H 5 HOH A 19 568 568 HOH HOH . H 5 HOH A 20 569 569 HOH HOH . H 5 HOH A 21 570 570 HOH HOH . H 5 HOH A 22 571 571 HOH HOH . H 5 HOH A 23 572 572 HOH HOH . H 5 HOH A 24 573 573 HOH HOH . H 5 HOH A 25 574 574 HOH HOH . H 5 HOH A 26 575 575 HOH HOH . H 5 HOH A 27 576 576 HOH HOH . H 5 HOH A 28 577 577 HOH HOH . H 5 HOH A 29 578 578 HOH HOH . H 5 HOH A 30 579 579 HOH HOH . H 5 HOH A 31 580 580 HOH HOH . H 5 HOH A 32 581 581 HOH HOH . H 5 HOH A 33 582 582 HOH HOH . H 5 HOH A 34 583 583 HOH HOH . H 5 HOH A 35 584 584 HOH HOH . H 5 HOH A 36 585 585 HOH HOH . H 5 HOH A 37 586 586 HOH HOH . H 5 HOH A 38 587 587 HOH HOH . H 5 HOH A 39 588 588 HOH HOH . H 5 HOH A 40 589 589 HOH HOH . H 5 HOH A 41 590 590 HOH HOH . H 5 HOH A 42 591 591 HOH HOH . H 5 HOH A 43 592 592 HOH HOH . H 5 HOH A 44 593 593 HOH HOH . H 5 HOH A 45 594 594 HOH HOH . H 5 HOH A 46 595 595 HOH HOH . H 5 HOH A 47 596 596 HOH HOH . H 5 HOH A 48 597 597 HOH HOH . H 5 HOH A 49 598 598 HOH HOH . H 5 HOH A 50 599 599 HOH HOH . H 5 HOH A 51 600 600 HOH HOH . H 5 HOH A 52 601 601 HOH HOH . H 5 HOH A 53 602 602 HOH HOH . H 5 HOH A 54 603 603 HOH HOH . H 5 HOH A 55 604 604 HOH HOH . H 5 HOH A 56 605 605 HOH HOH . H 5 HOH A 57 606 606 HOH HOH . H 5 HOH A 58 607 607 HOH HOH . H 5 HOH A 59 608 608 HOH HOH . H 5 HOH A 60 609 609 HOH HOH . H 5 HOH A 61 610 610 HOH HOH . H 5 HOH A 62 611 611 HOH HOH . H 5 HOH A 63 612 612 HOH HOH . H 5 HOH A 64 613 613 HOH HOH . H 5 HOH A 65 614 614 HOH HOH . H 5 HOH A 66 615 615 HOH HOH . H 5 HOH A 67 616 616 HOH HOH . H 5 HOH A 68 617 617 HOH HOH . H 5 HOH A 69 618 618 HOH HOH . H 5 HOH A 70 619 619 HOH HOH . H 5 HOH A 71 620 620 HOH HOH . H 5 HOH A 72 621 621 HOH HOH . H 5 HOH A 73 622 622 HOH HOH . H 5 HOH A 74 623 623 HOH HOH . H 5 HOH A 75 624 624 HOH HOH . H 5 HOH A 76 625 625 HOH HOH . H 5 HOH A 77 626 626 HOH HOH . H 5 HOH A 78 627 627 HOH HOH . H 5 HOH A 79 628 628 HOH HOH . H 5 HOH A 80 629 629 HOH HOH . H 5 HOH A 81 630 630 HOH HOH . H 5 HOH A 82 631 631 HOH HOH . H 5 HOH A 83 632 632 HOH HOH . H 5 HOH A 84 633 633 HOH HOH . H 5 HOH A 85 634 634 HOH HOH . H 5 HOH A 86 635 635 HOH HOH . H 5 HOH A 87 636 636 HOH HOH . H 5 HOH A 88 637 637 HOH HOH . H 5 HOH A 89 638 638 HOH HOH . H 5 HOH A 90 639 639 HOH HOH . H 5 HOH A 91 640 640 HOH HOH . H 5 HOH A 92 641 641 HOH HOH . H 5 HOH A 93 642 642 HOH HOH . H 5 HOH A 94 643 643 HOH HOH . H 5 HOH A 95 644 644 HOH HOH . H 5 HOH A 96 645 645 HOH HOH . H 5 HOH A 97 646 646 HOH HOH . H 5 HOH A 98 647 647 HOH HOH . H 5 HOH A 99 648 648 HOH HOH . H 5 HOH A 100 649 649 HOH HOH . H 5 HOH A 101 650 650 HOH HOH . H 5 HOH A 102 651 651 HOH HOH . H 5 HOH A 103 652 652 HOH HOH . H 5 HOH A 104 653 653 HOH HOH . H 5 HOH A 105 654 654 HOH HOH . H 5 HOH A 106 655 655 HOH HOH . H 5 HOH A 107 656 656 HOH HOH . H 5 HOH A 108 657 657 HOH HOH . H 5 HOH A 109 658 658 HOH HOH . H 5 HOH A 110 659 659 HOH HOH . H 5 HOH A 111 660 660 HOH HOH . H 5 HOH A 112 661 661 HOH HOH . H 5 HOH A 113 662 662 HOH HOH . H 5 HOH A 114 663 663 HOH HOH . H 5 HOH A 115 664 664 HOH HOH . H 5 HOH A 116 665 665 HOH HOH . H 5 HOH A 117 666 666 HOH HOH . H 5 HOH A 118 667 667 HOH HOH . H 5 HOH A 119 668 668 HOH HOH . H 5 HOH A 120 669 669 HOH HOH . H 5 HOH A 121 670 670 HOH HOH . H 5 HOH A 122 671 671 HOH HOH . H 5 HOH A 123 672 672 HOH HOH . H 5 HOH A 124 673 673 HOH HOH . H 5 HOH A 125 674 674 HOH HOH . H 5 HOH A 126 675 675 HOH HOH . H 5 HOH A 127 676 676 HOH HOH . H 5 HOH A 128 677 677 HOH HOH . H 5 HOH A 129 678 678 HOH HOH . H 5 HOH A 130 679 679 HOH HOH . H 5 HOH A 131 680 680 HOH HOH . H 5 HOH A 132 681 681 HOH HOH . H 5 HOH A 133 682 682 HOH HOH . H 5 HOH A 134 683 683 HOH HOH . H 5 HOH A 135 684 684 HOH HOH . H 5 HOH A 136 685 685 HOH HOH . H 5 HOH A 137 686 686 HOH HOH . H 5 HOH A 138 687 687 HOH HOH . H 5 HOH A 139 688 688 HOH HOH . H 5 HOH A 140 689 689 HOH HOH . H 5 HOH A 141 690 690 HOH HOH . H 5 HOH A 142 691 691 HOH HOH . H 5 HOH A 143 692 692 HOH HOH . H 5 HOH A 144 693 693 HOH HOH . H 5 HOH A 145 694 694 HOH HOH . H 5 HOH A 146 695 695 HOH HOH . H 5 HOH A 147 696 696 HOH HOH . H 5 HOH A 148 697 697 HOH HOH . H 5 HOH A 149 698 698 HOH HOH . H 5 HOH A 150 699 699 HOH HOH . H 5 HOH A 151 700 700 HOH HOH . H 5 HOH A 152 701 701 HOH HOH . H 5 HOH A 153 702 702 HOH HOH . H 5 HOH A 154 703 703 HOH HOH . H 5 HOH A 155 704 704 HOH HOH . H 5 HOH A 156 705 705 HOH HOH . H 5 HOH A 157 706 706 HOH HOH . H 5 HOH A 158 709 549 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 C1 FPF . . . B 2 110.41 42.475 49.75 1 85.54 ? C1 FPF 549 A 1 HETATM 2 O O1 FPF . . . B 2 109.189 42.87 50.375 1 82.28 ? O1 FPF 549 A 1 HETATM 3 C C2 FPF . . . B 2 110.384 42.781 48.249 1 86.17 ? C2 FPF 549 A 1 HETATM 4 F F FPF . . . B 2 111.213 43.75 47.924 1 87.75 ? F FPF 549 A 1 HETATM 5 C C3 FPF . . . B 2 109.618 42.153 47.328 1 85.79 ? C3 FPF 549 A 1 HETATM 6 C C4 FPF . . . B 2 108.656 41.029 47.675 1 86.17 ? C4 FPF 549 A 1 HETATM 7 C C5 FPF . . . B 2 109.615 42.475 45.836 1 84.82 ? C5 FPF 549 A 1 HETATM 8 C C6 FPF . . . B 2 110.863 42.149 44.981 1 85.1 ? C6 FPF 549 A 1 HETATM 9 C C7 FPF . . . B 2 111.284 40.699 45.11 1 85.69 ? C7 FPF 549 A 1 HETATM 10 C C8 FPF . . . B 2 112.346 40.189 45.782 1 86.73 ? C8 FPF 549 A 1 HETATM 11 C C10 FPF . . . B 2 113.356 41.022 46.56 1 86.79 ? C10 FPF 549 A 1 HETATM 12 C C9 FPF . . . B 2 112.634 38.698 45.836 1 86.93 ? C9 FPF 549 A 1 HETATM 13 C C11 FPF . . . B 2 112.292 37.949 47.148 1 88.94 ? C11 FPF 549 A 1 HETATM 14 C C12 FPF . . . B 2 110.793 37.817 47.381 1 89.52 ? C12 FPF 549 A 1 HETATM 15 C C13 FPF . . . B 2 110.162 37.151 48.381 1 89.5 ? C13 FPF 549 A 1 HETATM 16 C C14 FPF . . . B 2 108.646 37.122 48.465 1 88.95 ? C14 FPF 549 A 1 HETATM 17 C C15 FPF . . . B 2 110.855 36.391 49.487 1 88.06 ? C15 FPF 549 A 1 HETATM 18 P P1 FPF . . . B 2 108.36 41.877 51.319 1 80.75 ? P1 FPF 549 A 1 HETATM 19 O O1A FPF . . . B 2 108.501 42.273 52.993 1 83.6 ? O1A FPF 549 A 1 HETATM 20 O O2A FPF . . . B 2 108.83 40.374 51.084 1 83.49 ? O2A FPF 549 A 1 HETATM 21 O O3A FPF . . . B 2 106.879 41.954 50.756 1 80.96 ? O3A FPF 549 A 1 HETATM 22 P P2 FPF . . . B 2 105.809 40.78 50.747 1 79.79 ? P2 FPF 549 A 1 HETATM 23 O O1B FPF . . . B 2 105.529 40.419 52.27 1 79.68 ? O1B FPF 549 A 1 HETATM 24 O O2B FPF . . . B 2 104.464 41.458 50.226 1 80.66 ? O2B FPF 549 A 1 HETATM 25 O O3B FPF . . . B 2 106.257 39.379 49.834 1 81.8 ? O3B FPF 549 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 363 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #