data_3FYH # _model_server_result.job_id sETDWNretBIKT3Lsp5ytDg _model_server_result.datetime_utc '2024-10-18 16:27:08' _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 3fyh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 3FYH # _exptl.entry_id 3FYH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-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 120 _cell.entry_id 3FYH _cell.length_a 83.16 _cell.length_b 83.16 _cell.length_c 106.85 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3FYH _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details 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,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA _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 O THR 6 A THR 6 1_555 E NA NA . A NA 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc2 A O LEU 8 A LEU 8 1_555 E NA NA . A NA 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc3 A O VAL 11 A VAL 11 1_555 E NA NA . A NA 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc4 A O GLN 98 A GLN 98 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc5 A OG1 THR 112 A THR 112 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc6 A OD1 ASP 246 A ASP 246 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc7 B O1B ADP . A ADP 401 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc8 C MG MG . A MG 501 1_555 DA O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc9 C MG MG . A MG 501 1_555 DA O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc10 C MG MG . A MG 501 1_555 DA O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc11 C MG MG . A MG 501 1_555 DA O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc12 D MG MG . A MG 502 1_555 DA O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc13 D MG MG . A MG 502 1_555 DA O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc14 D MG MG . A MG 502 1_555 DA O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc15 D MG MG . A MG 502 1_555 DA O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 3FYH _atom_sites.fract_transf_matrix[1][1] 0.012025 _atom_sites.fract_transf_matrix[1][2] 0.006943 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013885 _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] 0.009359 _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 ADP A 1 401 401 ADP ADP . C 3 MG A 1 501 501 MG MG2 . D 3 MG A 1 502 502 MG MG2 . E 4 NA A 1 509 509 NA NA1 . F 5 W A 1 511 511 W W . G 5 W A 1 512 512 W W . H 5 W A 1 513 513 W W . I 5 W A 1 514 514 W W . J 5 W A 1 515 515 W W . K 5 W A 1 516 516 W W . L 5 W A 1 517 517 W W . M 5 W A 1 518 518 W W . N 5 W A 1 519 519 W W . O 5 W A 1 520 520 W W . P 5 W A 1 521 521 W W . Q 5 W A 1 522 522 W W . R 5 W A 1 523 523 W W . S 5 W A 1 524 524 W W . T 5 W A 1 525 525 W W . U 5 W A 1 526 526 W W . V 5 W A 1 527 527 W W . W 5 W A 1 528 528 W W . X 5 W A 1 529 529 W W . Y 5 W A 1 530 530 W W . Z 5 W A 1 531 531 W W . AA 5 W A 1 532 532 W W . BA 5 W A 1 533 533 W W . CA 5 W A 1 534 534 W W . DA 6 HOH A 1 601 601 HOH TIP . DA 6 HOH A 2 602 602 HOH TIP . DA 6 HOH A 3 603 603 HOH TIP . DA 6 HOH A 4 604 604 HOH TIP . DA 6 HOH A 5 605 605 HOH TIP . DA 6 HOH A 6 606 606 HOH TIP . DA 6 HOH A 7 607 607 HOH TIP . DA 6 HOH A 8 608 608 HOH TIP . DA 6 HOH A 9 610 610 HOH TIP . DA 6 HOH A 10 611 611 HOH TIP . DA 6 HOH A 11 612 612 HOH TIP . DA 6 HOH A 12 613 613 HOH TIP . DA 6 HOH A 13 614 614 HOH TIP . DA 6 HOH A 14 615 615 HOH TIP . DA 6 HOH A 15 616 616 HOH TIP . DA 6 HOH A 16 617 617 HOH TIP . DA 6 HOH A 17 618 618 HOH TIP . DA 6 HOH A 18 619 619 HOH TIP . DA 6 HOH A 19 620 620 HOH TIP . DA 6 HOH A 20 621 621 HOH TIP . DA 6 HOH A 21 622 622 HOH TIP . DA 6 HOH A 22 623 623 HOH TIP . DA 6 HOH A 23 624 624 HOH TIP . DA 6 HOH A 24 625 625 HOH TIP . DA 6 HOH A 25 626 626 HOH TIP . DA 6 HOH A 26 627 627 HOH TIP . DA 6 HOH A 27 628 628 HOH TIP . DA 6 HOH A 28 629 629 HOH TIP . DA 6 HOH A 29 630 630 HOH TIP . DA 6 HOH A 30 631 631 HOH TIP . DA 6 HOH A 31 632 632 HOH TIP . DA 6 HOH A 32 633 633 HOH TIP . DA 6 HOH A 33 634 634 HOH TIP . DA 6 HOH A 34 635 635 HOH TIP . DA 6 HOH A 35 636 636 HOH TIP . DA 6 HOH A 36 637 637 HOH TIP . DA 6 HOH A 37 638 638 HOH TIP . DA 6 HOH A 38 639 639 HOH TIP . DA 6 HOH A 39 640 640 HOH TIP . DA 6 HOH A 40 641 641 HOH TIP . DA 6 HOH A 41 642 642 HOH TIP . DA 6 HOH A 42 643 643 HOH TIP . DA 6 HOH A 43 644 644 HOH TIP . DA 6 HOH A 44 645 645 HOH TIP . DA 6 HOH A 45 646 646 HOH TIP . DA 6 HOH A 46 647 647 HOH TIP . DA 6 HOH A 47 648 648 HOH TIP . DA 6 HOH A 48 649 649 HOH TIP . DA 6 HOH A 49 650 650 HOH TIP . DA 6 HOH A 50 651 651 HOH TIP . DA 6 HOH A 51 652 652 HOH TIP . DA 6 HOH A 52 653 653 HOH TIP . DA 6 HOH A 53 654 654 HOH TIP . DA 6 HOH A 54 655 655 HOH TIP . DA 6 HOH A 55 656 656 HOH TIP . DA 6 HOH A 56 657 657 HOH TIP . DA 6 HOH A 57 658 658 HOH TIP . DA 6 HOH A 58 659 659 HOH TIP . DA 6 HOH A 59 660 660 HOH TIP . DA 6 HOH A 60 661 661 HOH TIP . DA 6 HOH A 61 662 662 HOH TIP . DA 6 HOH A 62 663 663 HOH TIP . DA 6 HOH A 63 664 664 HOH TIP . DA 6 HOH A 64 665 665 HOH TIP . DA 6 HOH A 65 666 666 HOH TIP . DA 6 HOH A 66 667 667 HOH TIP . DA 6 HOH A 67 668 668 HOH TIP . DA 6 HOH A 68 669 669 HOH TIP . DA 6 HOH A 69 670 670 HOH TIP . DA 6 HOH A 70 671 671 HOH TIP . DA 6 HOH A 71 672 672 HOH TIP . DA 6 HOH A 72 673 673 HOH TIP . DA 6 HOH A 73 674 674 HOH TIP . DA 6 HOH A 74 675 675 HOH TIP . DA 6 HOH A 75 676 676 HOH TIP . DA 6 HOH A 76 677 677 HOH TIP . DA 6 HOH A 77 678 678 HOH TIP . DA 6 HOH A 78 679 679 HOH TIP . DA 6 HOH A 79 680 680 HOH TIP . DA 6 HOH A 80 681 681 HOH TIP . DA 6 HOH A 81 682 682 HOH TIP . DA 6 HOH A 82 683 683 HOH TIP . DA 6 HOH A 83 684 684 HOH TIP . DA 6 HOH A 84 685 685 HOH TIP . DA 6 HOH A 85 686 686 HOH TIP . DA 6 HOH A 86 687 687 HOH TIP . DA 6 HOH A 87 688 688 HOH TIP . DA 6 HOH A 88 689 689 HOH TIP . DA 6 HOH A 89 690 690 HOH TIP . DA 6 HOH A 90 691 691 HOH TIP . DA 6 HOH A 91 692 692 HOH TIP . DA 6 HOH A 92 693 693 HOH TIP . DA 6 HOH A 93 694 694 HOH TIP . DA 6 HOH A 94 695 695 HOH TIP . DA 6 HOH A 95 696 696 HOH TIP . DA 6 HOH A 96 697 697 HOH TIP . DA 6 HOH A 97 698 698 HOH TIP . DA 6 HOH A 98 699 699 HOH TIP . DA 6 HOH A 99 700 700 HOH TIP . DA 6 HOH A 100 701 701 HOH TIP . DA 6 HOH A 101 702 702 HOH TIP . DA 6 HOH A 102 703 703 HOH TIP . DA 6 HOH A 103 704 704 HOH TIP . DA 6 HOH A 104 705 705 HOH TIP . DA 6 HOH A 105 706 706 HOH TIP . DA 6 HOH A 106 707 707 HOH TIP . DA 6 HOH A 107 708 708 HOH TIP . DA 6 HOH A 108 709 709 HOH TIP . DA 6 HOH A 109 710 710 HOH TIP . DA 6 HOH A 110 711 711 HOH TIP . DA 6 HOH A 111 712 712 HOH TIP . DA 6 HOH A 112 713 713 HOH TIP . DA 6 HOH A 113 714 714 HOH TIP . DA 6 HOH A 114 715 715 HOH TIP . DA 6 HOH A 115 716 716 HOH TIP . DA 6 HOH A 116 717 717 HOH TIP . DA 6 HOH A 117 718 718 HOH TIP . DA 6 HOH A 118 719 719 HOH TIP . DA 6 HOH A 119 720 720 HOH TIP . DA 6 HOH A 120 721 721 HOH TIP . DA 6 HOH A 121 722 722 HOH TIP . DA 6 HOH A 122 723 723 HOH TIP . DA 6 HOH A 123 724 724 HOH TIP . # 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 P PB ADP . . . B 2 28.255 56.475 -10.705 1 23.56 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 27.387 56.064 -9.614 1 20.18 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 29.671 56.165 -10.443 1 22.61 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 28.077 58.006 -10.979 1 22.22 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 26.689 54.679 -12.221 1 25.21 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 26.814 53.525 -11.261 1 24.87 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 25.415 55.334 -12.046 1 24.09 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 27.884 55.725 -12.044 1 23.75 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 26.937 54.108 -13.737 1 24.62 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 26.24 54.692 -14.939 1 32.09 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 26.571 53.972 -16.032 1 30.63 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 26.081 52.579 -15.817 1 29.44 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 25.67 54.439 -17.214 1 32.23 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 25.885 55.668 -17.711 1 38.35 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 25.441 53.214 -18.061 1 33.38 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 26.595 53.144 -19.041 1 41.02 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 25.641 52.07 -17.107 1 30.93 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 24.404 51.522 -17.042 1 29.22 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 23.334 51.809 -16.144 1 28.91 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 22.301 51.071 -16.44 1 26.58 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 22.63 50.288 -17.515 1 28.58 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 21.95 49.337 -18.262 1 30.88 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 20.662 49.011 -17.969 1 30.12 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 22.615 48.716 -19.327 1 30.08 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 23.961 49.043 -19.663 1 30.06 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 24.669 49.975 -18.959 1 28.1 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 23.945 50.569 -17.888 1 29.71 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #