data_2ZIO # _model_server_result.job_id Wg1wJfqdf7x4tKeVVh5McQ _model_server_result.datetime_utc '2024-11-25 16:05:19' _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 2zio # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 2ZIO # _exptl.entry_id 2ZIO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 561.483 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-({(2S)-2-amino-6-[(propoxycarbonyl)amino]hexanoyl}oxy)(hydroxy)phosphoryl]adenosine" _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 2ZIO _cell.length_a 104.15 _cell.length_b 104.15 _cell.length_c 71.06 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZIO _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 52.075 90.196546 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C20 H32 N7 O10 P' _chem_comp.formula_weight 561.483 _chem_comp.id AYB _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(S)-({(2S)-2-amino-6-[(propoxycarbonyl)amino]hexanoyl}oxy)(hydroxy)phosphoryl]adenosine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "NE-ALLYLOXYCARBONYL-L-LYSINE-5'-ADENOSINE MONOPHOSPHATE" # 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 C4 C5 AYB doub 83 n y C4 N3 AYB sing 84 n y C4 N9 AYB sing 85 n y C5 C6 AYB sing 86 n y C5 N7 AYB sing 87 n y C6 N1 AYB doub 88 n y C6 N6 AYB sing 89 n n C8 N9 AYB sing 90 n y C8 N7 AYB doub 91 n y N1 C2 AYB sing 92 n y N3 C2 AYB doub 93 n y CAA CAJ AYB sing 94 n n CAJ CAO AYB sing 95 n n CAO OAW AYB sing 96 n n OAW CBA AYB sing 97 n n CBA OAD AYB doub 98 n n CBA NAV AYB sing 99 n n NAV CAP AYB sing 100 n n CAP CAM AYB sing 101 n n CAM CAN AYB sing 102 n n CAN CB AYB sing 103 n n CB CA AYB sing 104 n n CA N AYB sing 105 n n CA C AYB sing 106 n n C O AYB doub 107 n n C OAY AYB sing 108 n n OAY PBL AYB sing 109 n n PBL OAI AYB doub 110 n n PBL OAF AYB sing 111 n n PBL O5' AYB sing 112 n n O5' C5' AYB sing 113 n n C5' C4' AYB sing 114 n n C4' O4' AYB sing 115 n n C4' C3' AYB sing 116 n n O4' C1' AYB sing 117 n n C3' O3' AYB sing 118 n n C3' C2' AYB sing 119 n n C2' O2' AYB sing 120 n n C2' C1' AYB sing 121 n n C1' N9 AYB sing 122 n n C8 H8 AYB sing 123 n n CAA HAA AYB sing 124 n n CAA HAAA AYB sing 125 n n CAA HAAB AYB sing 126 n n CAJ HAJ AYB sing 127 n n CAJ HAJA AYB sing 128 n n CAO HAO AYB sing 129 n n CAO HAOA AYB sing 130 n n NAV HNAV AYB sing 131 n n CAP HAP AYB sing 132 n n CAP HAPA AYB sing 133 n n CAM HAM AYB sing 134 n n CAM HAMA AYB sing 135 n n CAN HAN AYB sing 136 n n CAN HANA AYB sing 137 n n CB HB AYB sing 138 n n CB HBA AYB sing 139 n n CA HA AYB sing 140 n n N HN AYB sing 141 n n N HNA AYB sing 142 n n OAF HOAF AYB sing 143 n n C5' H5' AYB sing 144 n n C5' "H5'A" AYB sing 145 n n C4' H4' AYB sing 146 n n C3' H3' AYB sing 147 n n O3' HO3' AYB sing 148 n n C2' H2' AYB sing 149 n n O2' HO2' AYB sing 150 n n C1' H1' AYB sing 151 n n C2 H2 AYB sing 152 n n N6 HN6 AYB sing 153 n n N6 HN6A AYB sing 154 n n # _atom_sites.entry_id 2ZIO _atom_sites.fract_transf_matrix[1][1] 0.009602 _atom_sites.fract_transf_matrix[1][2] 0.005543 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011087 _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] 0.014073 _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 2PN A 1 1 1 2PN 2PN . C 3 AYB A 1 601 601 AYB AYB . D 4 HOH A 1 604 604 HOH HOH . D 4 HOH A 2 605 605 HOH HOH . D 4 HOH A 3 606 606 HOH HOH . D 4 HOH A 4 607 607 HOH HOH . D 4 HOH A 5 608 608 HOH HOH . D 4 HOH A 6 609 609 HOH HOH . D 4 HOH A 7 610 610 HOH HOH . D 4 HOH A 8 611 611 HOH HOH . D 4 HOH A 9 612 612 HOH HOH . D 4 HOH A 10 613 613 HOH HOH . D 4 HOH A 11 614 614 HOH HOH . D 4 HOH A 12 615 615 HOH HOH . D 4 HOH A 13 616 616 HOH HOH . D 4 HOH A 14 617 617 HOH HOH . D 4 HOH A 15 618 618 HOH HOH . D 4 HOH A 16 619 619 HOH HOH . D 4 HOH A 17 620 620 HOH HOH . D 4 HOH A 18 621 621 HOH HOH . D 4 HOH A 19 622 622 HOH HOH . D 4 HOH A 20 623 623 HOH HOH . D 4 HOH A 21 624 624 HOH HOH . D 4 HOH A 22 625 625 HOH HOH . D 4 HOH A 23 626 626 HOH HOH . D 4 HOH A 24 627 627 HOH HOH . D 4 HOH A 25 628 628 HOH HOH . D 4 HOH A 26 629 629 HOH HOH . D 4 HOH A 27 630 630 HOH HOH . D 4 HOH A 28 631 631 HOH HOH . D 4 HOH A 29 632 632 HOH HOH . D 4 HOH A 30 633 633 HOH HOH . D 4 HOH A 31 634 634 HOH HOH . D 4 HOH A 32 635 635 HOH HOH . D 4 HOH A 33 636 636 HOH HOH . D 4 HOH A 34 637 637 HOH HOH . D 4 HOH A 35 638 638 HOH HOH . D 4 HOH A 36 639 639 HOH HOH . D 4 HOH A 37 640 640 HOH HOH . D 4 HOH A 38 641 641 HOH HOH . D 4 HOH A 39 642 642 HOH HOH . D 4 HOH A 40 643 643 HOH HOH . D 4 HOH A 41 644 644 HOH HOH . D 4 HOH A 42 645 645 HOH HOH . D 4 HOH A 43 646 646 HOH HOH . D 4 HOH A 44 647 647 HOH HOH . D 4 HOH A 45 648 648 HOH HOH . D 4 HOH A 46 649 649 HOH HOH . D 4 HOH A 47 650 650 HOH HOH . D 4 HOH A 48 651 651 HOH HOH . D 4 HOH A 49 652 652 HOH HOH . D 4 HOH A 50 653 653 HOH HOH . D 4 HOH A 51 654 654 HOH HOH . D 4 HOH A 52 655 655 HOH HOH . D 4 HOH A 53 656 656 HOH HOH . D 4 HOH A 54 657 657 HOH HOH . D 4 HOH A 55 658 658 HOH HOH . D 4 HOH A 56 659 659 HOH HOH . D 4 HOH A 57 660 660 HOH HOH . D 4 HOH A 58 661 661 HOH HOH . D 4 HOH A 59 662 662 HOH HOH . D 4 HOH A 60 663 663 HOH HOH . D 4 HOH A 61 664 664 HOH HOH . D 4 HOH A 62 665 665 HOH HOH . D 4 HOH A 63 666 666 HOH HOH . D 4 HOH A 64 667 667 HOH HOH . D 4 HOH A 65 668 668 HOH HOH . D 4 HOH A 66 669 669 HOH HOH . D 4 HOH A 67 670 670 HOH HOH . D 4 HOH A 68 671 671 HOH HOH . D 4 HOH A 69 672 672 HOH HOH . D 4 HOH A 70 673 673 HOH HOH . D 4 HOH A 71 674 674 HOH HOH . D 4 HOH A 72 675 675 HOH HOH . D 4 HOH A 73 676 676 HOH HOH . D 4 HOH A 74 677 677 HOH HOH . D 4 HOH A 75 678 678 HOH HOH . D 4 HOH A 76 679 679 HOH HOH . D 4 HOH A 77 680 680 HOH HOH . D 4 HOH A 78 681 681 HOH HOH . D 4 HOH A 79 682 682 HOH HOH . D 4 HOH A 80 683 683 HOH HOH . D 4 HOH A 81 684 684 HOH HOH . D 4 HOH A 82 685 685 HOH HOH . D 4 HOH A 83 686 686 HOH HOH . D 4 HOH A 84 687 687 HOH HOH . D 4 HOH A 85 688 688 HOH HOH . D 4 HOH A 86 689 689 HOH HOH . D 4 HOH A 87 690 690 HOH HOH . D 4 HOH A 88 691 691 HOH HOH . D 4 HOH A 89 692 692 HOH HOH . D 4 HOH A 90 693 693 HOH HOH . D 4 HOH A 91 694 694 HOH HOH . D 4 HOH A 92 695 695 HOH HOH . D 4 HOH A 93 696 696 HOH HOH . D 4 HOH A 94 697 697 HOH HOH . D 4 HOH A 95 698 698 HOH HOH . D 4 HOH A 96 699 699 HOH HOH . D 4 HOH A 97 700 700 HOH HOH . D 4 HOH A 98 701 701 HOH HOH . D 4 HOH A 99 702 702 HOH HOH . D 4 HOH A 100 703 703 HOH HOH . D 4 HOH A 101 704 704 HOH HOH . D 4 HOH A 102 705 705 HOH HOH . D 4 HOH A 103 706 706 HOH HOH . D 4 HOH A 104 707 707 HOH HOH . D 4 HOH A 105 708 708 HOH HOH . D 4 HOH A 106 709 709 HOH HOH . D 4 HOH A 107 710 710 HOH HOH . D 4 HOH A 108 711 711 HOH HOH . D 4 HOH A 109 712 712 HOH HOH . D 4 HOH A 110 713 713 HOH HOH . D 4 HOH A 111 714 714 HOH HOH . D 4 HOH A 112 715 715 HOH HOH . D 4 HOH A 113 716 716 HOH HOH . D 4 HOH A 114 717 717 HOH HOH . D 4 HOH A 115 718 718 HOH HOH . D 4 HOH A 116 719 719 HOH HOH . D 4 HOH A 117 720 720 HOH HOH . D 4 HOH A 118 721 721 HOH HOH . D 4 HOH A 119 722 722 HOH HOH . D 4 HOH A 120 723 723 HOH HOH . D 4 HOH A 121 724 724 HOH HOH . D 4 HOH A 122 725 725 HOH HOH . D 4 HOH A 123 726 726 HOH HOH . D 4 HOH A 124 727 727 HOH HOH . D 4 HOH A 125 728 728 HOH HOH . D 4 HOH A 126 729 729 HOH HOH . D 4 HOH A 127 730 730 HOH HOH . D 4 HOH A 128 731 731 HOH HOH . D 4 HOH A 129 732 732 HOH HOH . D 4 HOH A 130 733 733 HOH HOH . D 4 HOH A 131 734 734 HOH HOH . D 4 HOH A 132 735 735 HOH HOH . D 4 HOH A 133 736 736 HOH HOH . D 4 HOH A 134 737 737 HOH HOH . D 4 HOH A 135 738 738 HOH HOH . D 4 HOH A 136 739 739 HOH HOH . D 4 HOH A 137 740 740 HOH HOH . D 4 HOH A 138 741 741 HOH HOH . D 4 HOH A 139 742 742 HOH HOH . D 4 HOH A 140 743 743 HOH HOH . D 4 HOH A 141 744 744 HOH HOH . D 4 HOH A 142 745 745 HOH HOH . D 4 HOH A 143 746 746 HOH HOH . D 4 HOH A 144 747 747 HOH HOH . D 4 HOH A 145 748 748 HOH HOH . D 4 HOH A 146 749 749 HOH HOH . D 4 HOH A 147 750 750 HOH HOH . D 4 HOH A 148 751 751 HOH HOH . D 4 HOH A 149 752 752 HOH HOH . D 4 HOH A 150 753 753 HOH HOH . D 4 HOH A 151 754 754 HOH HOH . D 4 HOH A 152 755 755 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 C4 AYB . . . C 3 14.36 35.801 4.517 1 81.51 ? C4 AYB 601 A 1 HETATM 2 C C5 AYB . . . C 3 14.62 35.764 5.879 1 79.03 ? C5 AYB 601 A 1 HETATM 3 C C6 AYB . . . C 3 15.618 34.911 6.333 1 75.79 ? C6 AYB 601 A 1 HETATM 4 C C8 AYB . . . C 3 13.045 37.184 5.52 1 80.38 ? C8 AYB 601 A 1 HETATM 5 N N1 AYB . . . C 3 16.286 34.159 5.446 1 70.86 ? N1 AYB 601 A 1 HETATM 6 N N3 AYB . . . C 3 15.068 35.021 3.688 1 73.33 ? N3 AYB 601 A 1 HETATM 7 C CAA AYB . . . C 3 6.672 51.9 1.654 1 77.66 ? CAA AYB 601 A 1 HETATM 8 C CAJ AYB . . . C 3 7.652 51.099 2.23 1 72.39 ? CAJ AYB 601 A 1 HETATM 9 C CAO AYB . . . C 3 7.302 50.169 3.202 1 76.51 ? CAO AYB 601 A 1 HETATM 10 O OAW AYB . . . C 3 7.168 48.87 2.608 1 76.06 ? OAW AYB 601 A 1 HETATM 11 C CBA AYB . . . C 3 6.687 47.995 3.532 1 87.82 ? CBA AYB 601 A 1 HETATM 12 O OAD AYB . . . C 3 6.423 48.412 4.659 1 85.73 ? OAD AYB 601 A 1 HETATM 13 N NAV AYB . . . C 3 6.478 46.731 3.173 1 89.89 ? NAV AYB 601 A 1 HETATM 14 C CAP AYB . . . C 3 6.737 46.236 1.813 1 80.68 ? CAP AYB 601 A 1 HETATM 15 C CAM AYB . . . C 3 6.345 44.759 1.735 1 89.75 ? CAM AYB 601 A 1 HETATM 16 C CAN AYB . . . C 3 7.599 43.882 1.74 1 98.02 ? CAN AYB 601 A 1 HETATM 17 C CB AYB . . . C 3 7.687 42.918 2.926 1 104.99 ? CB AYB 601 A 1 HETATM 18 C CA AYB . . . C 3 8.833 43.275 3.876 1 111.85 ? CA AYB 601 A 1 HETATM 19 N N AYB . . . C 3 9.996 43.74 3.107 1 111.03 ? N AYB 601 A 1 HETATM 20 C C AYB . . . C 3 9.228 42.068 4.73 1 117.64 ? C AYB 601 A 1 HETATM 21 O O AYB . . . C 3 10.272 42.079 5.38 1 116.58 ? O AYB 601 A 1 HETATM 22 O OAY AYB . . . C 3 8.357 41.023 4.688 1 124.19 ? OAY AYB 601 A 1 HETATM 23 P PBL AYB . . . C 3 8.823 39.843 5.686 1 125.37 ? PBL AYB 601 A 1 HETATM 24 O OAI AYB . . . C 3 9.658 40.405 6.774 1 129.3 ? OAI AYB 601 A 1 HETATM 25 O OAF AYB . . . C 3 7.822 38.624 5.993 1 128.23 ? OAF AYB 601 A 1 HETATM 26 O O5' AYB . . . C 3 9.99 39.194 4.789 1 116.59 ? O5' AYB 601 A 1 HETATM 27 C C5' AYB . . . C 3 9.864 39.209 3.365 1 101.86 ? C5' AYB 601 A 1 HETATM 28 C C4' AYB . . . C 3 10.825 38.199 2.737 1 87.76 ? C4' AYB 601 A 1 HETATM 29 O O4' AYB . . . C 3 12.18 38.365 3.182 1 92.72 ? O4' AYB 601 A 1 HETATM 30 C C3' AYB . . . C 3 10.507 36.782 3.208 1 75.42 ? C3' AYB 601 A 1 HETATM 31 O O3' AYB . . . C 3 9.3 36.346 2.577 1 60.19 ? O3' AYB 601 A 1 HETATM 32 C C2' AYB . . . C 3 11.729 36.13 2.564 1 73.56 ? C2' AYB 601 A 1 HETATM 33 O O2' AYB . . . C 3 11.634 36.202 1.139 1 53.5 ? O2' AYB 601 A 1 HETATM 34 C C1' AYB . . . C 3 12.829 37.09 3.021 1 81.16 ? C1' AYB 601 A 1 HETATM 35 N N9 AYB . . . C 3 13.387 36.689 4.332 1 78.7 ? N9 AYB 601 A 1 HETATM 36 N N7 AYB . . . C 3 13.795 36.625 6.468 1 80.31 ? N7 AYB 601 A 1 HETATM 37 C C2 AYB . . . C 3 16.009 34.221 4.155 1 67.25 ? C2 AYB 601 A 1 HETATM 38 N N6 AYB . . . C 3 15.914 34.854 7.628 1 81.26 ? N6 AYB 601 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 38 #