data_6HDY # _model_server_result.job_id XY-RtYPyjk68ZhluKCWB_g _model_server_result.datetime_utc '2024-11-14 18:52:56' _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 6hdy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 6HDY # _exptl.entry_id 6HDY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 433.31 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (3~{S})-3-oxidanylbutanoate' _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 6HDY _cell.length_a 84.19 _cell.length_b 84.19 _cell.length_c 219.81 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6HDY _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 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,E,F,G _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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 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 'C14 H20 N5 O9 P' _chem_comp.formula_weight 433.31 _chem_comp.id 8LQ _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (3~{S})-3-oxidanylbutanoate' _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 OAD PBC 8LQ doub 15 n n OAH PBC 8LQ sing 16 n n PBC OAQ 8LQ sing 17 n n PBC O5' 8LQ sing 18 n n OAQ CAS 8LQ sing 19 n n O5' C5' 8LQ sing 20 n n CAA CAZ 8LQ sing 21 n n C5' C4' 8LQ sing 22 n n CAS OAC 8LQ doub 23 n n CAS CAL 8LQ sing 24 n n C4' C3' 8LQ sing 25 n n C4' O4' 8LQ sing 26 n n O3' C3' 8LQ sing 27 n n CAZ CAL 8LQ sing 28 n n CAZ OAE 8LQ sing 29 n n C3' C2' 8LQ sing 30 n n O4' C1' 8LQ sing 31 n n O2' C2' 8LQ sing 32 n n C2' C1' 8LQ sing 33 n n C1' N9 8LQ sing 34 n n C8 N9 8LQ sing 35 n y C8 N7 8LQ doub 36 n y N9 C4 8LQ sing 37 n y N7 C5 8LQ sing 38 n y C4 C5 8LQ doub 39 n y C4 N3 8LQ sing 40 n y C5 C6 8LQ sing 41 n y N3 C2 8LQ doub 42 n y C6 N6 8LQ sing 43 n n C6 N1 8LQ doub 44 n y C2 N1 8LQ sing 45 n y C8 H1 8LQ sing 46 n n N6 H2 8LQ sing 47 n n N6 H3 8LQ sing 48 n n C2 H4 8LQ sing 49 n n CAA H5 8LQ sing 50 n n CAA H6 8LQ sing 51 n n CAA H7 8LQ sing 52 n n CAZ H8 8LQ sing 53 n n OAE H9 8LQ sing 54 n n CAL H10 8LQ sing 55 n n CAL H11 8LQ sing 56 n n OAH H12 8LQ sing 57 n n C5' H13 8LQ sing 58 n n C5' H14 8LQ sing 59 n n C4' H15 8LQ sing 60 n n C3' H16 8LQ sing 61 n n O3' H17 8LQ sing 62 n n C2' H18 8LQ sing 63 n n O2' H19 8LQ sing 64 n n C1' H20 8LQ sing 65 n n # _atom_sites.entry_id 6HDY _atom_sites.fract_transf_matrix[1][1] 0.011878 _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] 0.011878 _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] 0.004549 _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 3HL A 1 501 501 3HL 3HL . C 3 8LQ A 1 502 502 8LQ 8LQ . D 4 SO4 A 1 503 503 SO4 SO4 . E 4 SO4 A 1 504 504 SO4 SO4 . F 4 SO4 A 1 505 505 SO4 SO4 . G 5 HOH A 1 601 601 HOH HOH . G 5 HOH A 2 602 602 HOH HOH . G 5 HOH A 3 603 603 HOH HOH . G 5 HOH A 4 604 604 HOH HOH . G 5 HOH A 5 605 605 HOH HOH . G 5 HOH A 6 606 606 HOH HOH . G 5 HOH A 7 607 607 HOH HOH . G 5 HOH A 8 608 608 HOH HOH . G 5 HOH A 9 609 609 HOH HOH . G 5 HOH A 10 610 610 HOH HOH . G 5 HOH A 11 611 611 HOH HOH . G 5 HOH A 12 612 612 HOH HOH . G 5 HOH A 13 613 613 HOH HOH . G 5 HOH A 14 614 614 HOH HOH . G 5 HOH A 15 615 615 HOH HOH . G 5 HOH A 16 616 616 HOH HOH . G 5 HOH A 17 617 617 HOH HOH . G 5 HOH A 18 618 618 HOH HOH . G 5 HOH A 19 619 619 HOH HOH . G 5 HOH A 20 620 620 HOH HOH . G 5 HOH A 21 621 621 HOH HOH . G 5 HOH A 22 622 622 HOH HOH . G 5 HOH A 23 623 623 HOH HOH . G 5 HOH A 24 624 624 HOH HOH . G 5 HOH A 25 625 625 HOH HOH . G 5 HOH A 26 626 626 HOH HOH . G 5 HOH A 27 627 627 HOH HOH . G 5 HOH A 28 628 628 HOH HOH . G 5 HOH A 29 629 629 HOH HOH . G 5 HOH A 30 630 630 HOH HOH . G 5 HOH A 31 631 631 HOH HOH . G 5 HOH A 32 632 632 HOH HOH . G 5 HOH A 33 633 633 HOH HOH . G 5 HOH A 34 634 634 HOH HOH . G 5 HOH A 35 635 635 HOH HOH . G 5 HOH A 36 636 636 HOH HOH . G 5 HOH A 37 637 637 HOH HOH . G 5 HOH A 38 638 638 HOH HOH . G 5 HOH A 39 639 639 HOH HOH . G 5 HOH A 40 640 640 HOH HOH . G 5 HOH A 41 641 641 HOH HOH . G 5 HOH A 42 642 642 HOH HOH . G 5 HOH A 43 643 643 HOH HOH . G 5 HOH A 44 644 644 HOH HOH . G 5 HOH A 45 645 645 HOH HOH . G 5 HOH A 46 646 646 HOH HOH . G 5 HOH A 47 647 647 HOH HOH . G 5 HOH A 48 648 648 HOH HOH . G 5 HOH A 49 649 649 HOH HOH . G 5 HOH A 50 650 650 HOH HOH . G 5 HOH A 51 651 651 HOH HOH . G 5 HOH A 52 652 652 HOH HOH . G 5 HOH A 53 653 653 HOH HOH . G 5 HOH A 54 654 654 HOH HOH . G 5 HOH A 55 655 655 HOH HOH . G 5 HOH A 56 656 656 HOH HOH . G 5 HOH A 57 657 657 HOH HOH . G 5 HOH A 58 658 658 HOH HOH . G 5 HOH A 59 659 659 HOH HOH . G 5 HOH A 60 660 660 HOH HOH . G 5 HOH A 61 661 661 HOH HOH . G 5 HOH A 62 662 662 HOH HOH . G 5 HOH A 63 663 663 HOH HOH . G 5 HOH A 64 664 664 HOH HOH . G 5 HOH A 65 665 665 HOH HOH . G 5 HOH A 66 666 666 HOH HOH . G 5 HOH A 67 667 667 HOH HOH . G 5 HOH A 68 668 668 HOH HOH . G 5 HOH A 69 669 669 HOH HOH . G 5 HOH A 70 670 670 HOH HOH . G 5 HOH A 71 671 671 HOH HOH . G 5 HOH A 72 672 672 HOH HOH . G 5 HOH A 73 673 673 HOH HOH . G 5 HOH A 74 674 674 HOH HOH . G 5 HOH A 75 675 675 HOH HOH . G 5 HOH A 76 676 676 HOH HOH . G 5 HOH A 77 677 677 HOH HOH . G 5 HOH A 78 678 678 HOH HOH . G 5 HOH A 79 679 679 HOH HOH . G 5 HOH A 80 680 680 HOH HOH . G 5 HOH A 81 681 681 HOH HOH . G 5 HOH A 82 682 682 HOH HOH . G 5 HOH A 83 683 683 HOH HOH . G 5 HOH A 84 684 684 HOH HOH . G 5 HOH A 85 685 685 HOH HOH . G 5 HOH A 86 686 686 HOH HOH . G 5 HOH A 87 687 687 HOH HOH . G 5 HOH A 88 688 688 HOH HOH . G 5 HOH A 89 689 689 HOH HOH . G 5 HOH A 90 690 690 HOH HOH . G 5 HOH A 91 691 691 HOH HOH . G 5 HOH A 92 692 692 HOH HOH . G 5 HOH A 93 693 693 HOH HOH . G 5 HOH A 94 694 694 HOH HOH . G 5 HOH A 95 695 695 HOH HOH . G 5 HOH A 96 696 696 HOH HOH . G 5 HOH A 97 697 697 HOH HOH . G 5 HOH A 98 698 698 HOH HOH . G 5 HOH A 99 699 699 HOH HOH . G 5 HOH A 100 700 700 HOH HOH . G 5 HOH A 101 701 701 HOH HOH . G 5 HOH A 102 702 702 HOH HOH . G 5 HOH A 103 703 703 HOH HOH . G 5 HOH A 104 704 704 HOH HOH . G 5 HOH A 105 705 705 HOH HOH . G 5 HOH A 106 706 706 HOH HOH . G 5 HOH A 107 707 707 HOH HOH . G 5 HOH A 108 708 708 HOH HOH . G 5 HOH A 109 709 709 HOH HOH . G 5 HOH A 110 710 710 HOH HOH . G 5 HOH A 111 711 711 HOH HOH . G 5 HOH A 112 712 712 HOH HOH . G 5 HOH A 113 713 713 HOH HOH . G 5 HOH A 114 714 714 HOH HOH . G 5 HOH A 115 715 715 HOH HOH . G 5 HOH A 116 716 716 HOH HOH . G 5 HOH A 117 717 717 HOH HOH . G 5 HOH A 118 718 718 HOH HOH . G 5 HOH A 119 719 719 HOH HOH . G 5 HOH A 120 720 720 HOH HOH . G 5 HOH A 121 721 721 HOH HOH . G 5 HOH A 122 722 722 HOH HOH . G 5 HOH A 123 723 723 HOH HOH . G 5 HOH A 124 724 724 HOH HOH . G 5 HOH A 125 725 725 HOH HOH . G 5 HOH A 126 726 726 HOH HOH . G 5 HOH A 127 727 727 HOH HOH . G 5 HOH A 128 728 728 HOH HOH . G 5 HOH A 129 729 729 HOH HOH . G 5 HOH A 130 730 730 HOH HOH . G 5 HOH A 131 731 731 HOH HOH . G 5 HOH A 132 732 732 HOH HOH . G 5 HOH A 133 733 733 HOH HOH . G 5 HOH A 134 734 734 HOH HOH . G 5 HOH A 135 735 735 HOH HOH . G 5 HOH A 136 736 736 HOH HOH . G 5 HOH A 137 737 737 HOH HOH . G 5 HOH A 138 738 738 HOH HOH . G 5 HOH A 139 739 739 HOH HOH . G 5 HOH A 140 740 740 HOH HOH . G 5 HOH A 141 741 741 HOH HOH . G 5 HOH A 142 742 742 HOH HOH . G 5 HOH A 143 743 743 HOH HOH . G 5 HOH A 144 744 744 HOH HOH . G 5 HOH A 145 745 745 HOH HOH . G 5 HOH A 146 746 746 HOH HOH . G 5 HOH A 147 747 747 HOH HOH . G 5 HOH A 148 748 748 HOH HOH . G 5 HOH A 149 749 749 HOH HOH . G 5 HOH A 150 750 750 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 N N9 8LQ . B . C 3 -14.932 -39.978 9.289 1 38.02 ? N9 8LQ 502 A 1 HETATM 2 C C8 8LQ . B . C 3 -16.247 -39.963 9.018 1 39.25 ? C8 8LQ 502 A 1 HETATM 3 N N7 8LQ . B . C 3 -16.919 -40.049 10.161 1 39.26 ? N7 8LQ 502 A 1 HETATM 4 C C5 8LQ . B . C 3 -16.02 -40.143 11.155 1 39.51 ? C5 8LQ 502 A 1 HETATM 5 C C6 8LQ . B . C 3 -16.127 -40.199 12.501 1 36.41 ? C6 8LQ 502 A 1 HETATM 6 N N6 8LQ . B . C 3 -17.338 -40.231 13.035 1 30.16 ? N6 8LQ 502 A 1 HETATM 7 N N1 8LQ . B . C 3 -15.043 -40.261 13.298 1 38.77 ? N1 8LQ 502 A 1 HETATM 8 C C2 8LQ . B . C 3 -13.759 -40.228 12.749 1 35.87 ? C2 8LQ 502 A 1 HETATM 9 N N3 8LQ . B . C 3 -13.671 -40.096 11.371 1 36 ? N3 8LQ 502 A 1 HETATM 10 C C4 8LQ . B . C 3 -14.789 -40.09 10.607 1 38.6 ? C4 8LQ 502 A 1 HETATM 11 C CAA 8LQ . B . C 3 -21.002 -39.386 4.849 0.5 17.86 ? CAA 8LQ 502 A 1 HETATM 12 C CAZ 8LQ . B . C 3 -20.543 -39.402 6.331 0.5 21.54 ? CAZ 8LQ 502 A 1 HETATM 13 O OAE 8LQ . B . C 3 -20.534 -38.073 6.844 0.5 17.92 ? OAE 8LQ 502 A 1 HETATM 14 C CAL 8LQ . B . C 3 -19.135 -40.004 6.506 0.5 28.86 ? CAL 8LQ 502 A 1 HETATM 15 C CAS 8LQ . B . C 3 -18.114 -39.265 5.631 0.5 38.33 ? CAS 8LQ 502 A 1 HETATM 16 O OAC 8LQ . B . C 3 -17.674 -38.176 5.988 0.5 40.65 ? OAC 8LQ 502 A 1 HETATM 17 O OAQ 8LQ . B . C 3 -17.822 -39.872 4.424 1 43.29 ? OAQ 8LQ 502 A 1 HETATM 18 P PBC 8LQ . B . C 3 -16.588 -39.434 3.505 1 41.42 ? PBC 8LQ 502 A 1 HETATM 19 O OAH 8LQ . B . C 3 -16.929 -37.948 3.061 1 41.96 ? OAH 8LQ 502 A 1 HETATM 20 O OAD 8LQ . B . C 3 -16.361 -40.335 2.361 1 50.88 ? OAD 8LQ 502 A 1 HETATM 21 O O5' 8LQ . B . C 3 -15.344 -39.475 4.478 1 37.9 ? O5' 8LQ 502 A 1 HETATM 22 C C5' 8LQ . B . C 3 -15.126 -40.693 5.187 1 34.53 ? C5' 8LQ 502 A 1 HETATM 23 C C4' 8LQ . B . C 3 -13.928 -40.543 6.089 1 32.16 ? C4' 8LQ 502 A 1 HETATM 24 O O4' 8LQ . B . C 3 -14.167 -39.462 7.03 1 31.98 ? O4' 8LQ 502 A 1 HETATM 25 C C3' 8LQ . B . C 3 -13.843 -41.763 6.903 1 32.79 ? C3' 8LQ 502 A 1 HETATM 26 O O3' 8LQ . B . C 3 -13.102 -42.794 6.191 1 32.3 ? O3' 8LQ 502 A 1 HETATM 27 C C2' 8LQ . B . C 3 -13.095 -41.24 8.131 1 34.3 ? C2' 8LQ 502 A 1 HETATM 28 O O2' 8LQ . B . C 3 -11.657 -41.024 7.841 1 35.31 ? O2' 8LQ 502 A 1 HETATM 29 C C1' 8LQ . B . C 3 -13.775 -39.906 8.337 1 31.59 ? C1' 8LQ 502 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #