data_6HDX # _model_server_result.job_id ZddFMXSmiZNIyHVqOVWyMQ _model_server_result.datetime_utc '2024-11-23 04:22:46' _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 6hdx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6HDX # _exptl.entry_id 6HDX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 433.31 _entity.id 2 _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] (2~{R})-2-methyl-3-oxidanyl-propanoate' _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 6HDX _cell.length_a 83.86 _cell.length_b 83.86 _cell.length_c 219.7 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6HDX _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 _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 2 _struct_asym.id B _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 8LH _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] (2~{R})-2-methyl-3-oxidanyl-propanoate' _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 O5 P1 8LH doub 1 n n O4 P1 8LH sing 2 n n P1 O3 8LH sing 3 n n P1 O6 8LH sing 4 n n O3 C8 8LH sing 5 n n C7 C6 8LH sing 6 n n O6 C9 8LH sing 7 n n C8 C6 8LH sing 8 n n C8 O2 8LH doub 9 n n C9 C10 8LH sing 10 n n C6 C5 8LH sing 11 n n C10 C11 8LH sing 12 n n C10 O7 8LH sing 13 n n O8 C11 8LH sing 14 n n C11 C12 8LH sing 15 n n C5 O1 8LH sing 16 n n O7 C13 8LH sing 17 n n O9 C12 8LH sing 18 n n C12 C13 8LH sing 19 n n C13 N3 8LH sing 20 n n C4 N3 8LH sing 21 n y C4 N4 8LH doub 22 n y N3 C1 8LH sing 23 n y N4 C2 8LH sing 24 n y C1 C2 8LH doub 25 n y C1 N2 8LH sing 26 n y C2 C3 8LH sing 27 n y N2 C14 8LH doub 28 n y C3 N5 8LH sing 29 n n C3 N1 8LH doub 30 n y C14 N1 8LH sing 31 n y C4 H1 8LH sing 32 n n O1 H2 8LH sing 33 n n C5 H3 8LH sing 34 n n C5 H4 8LH sing 35 n n C6 H5 8LH sing 36 n n C7 H6 8LH sing 37 n n C7 H7 8LH sing 38 n n C7 H8 8LH sing 39 n n O4 H9 8LH sing 40 n n C9 H10 8LH sing 41 n n C9 H11 8LH sing 42 n n C10 H12 8LH sing 43 n n C11 H13 8LH sing 44 n n O8 H14 8LH sing 45 n n C12 H15 8LH sing 46 n n O9 H16 8LH sing 47 n n C13 H17 8LH sing 48 n n C14 H18 8LH sing 49 n n N5 H19 8LH sing 50 n n N5 H20 8LH sing 51 n n # _atom_sites.entry_id 6HDX _atom_sites.fract_transf_matrix[1][1] 0.011925 _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] 0.011925 _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] 0.004552 _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 8LH A 1 501 501 8LH 8LH . C 3 HIU A 1 502 502 HIU HIU . D 4 HOH A 1 601 601 HOH HOH . D 4 HOH A 2 602 602 HOH HOH . D 4 HOH A 3 603 603 HOH HOH . D 4 HOH A 4 604 604 HOH HOH . D 4 HOH A 5 605 605 HOH HOH . D 4 HOH A 6 606 606 HOH HOH . D 4 HOH A 7 607 607 HOH HOH . D 4 HOH A 8 608 608 HOH HOH . D 4 HOH A 9 609 609 HOH HOH . D 4 HOH A 10 610 610 HOH HOH . D 4 HOH A 11 611 611 HOH HOH . D 4 HOH A 12 612 612 HOH HOH . D 4 HOH A 13 613 613 HOH HOH . D 4 HOH A 14 614 614 HOH HOH . D 4 HOH A 15 615 615 HOH HOH . D 4 HOH A 16 616 616 HOH HOH . D 4 HOH A 17 617 617 HOH HOH . D 4 HOH A 18 618 618 HOH HOH . D 4 HOH A 19 619 619 HOH HOH . D 4 HOH A 20 620 620 HOH HOH . D 4 HOH A 21 621 621 HOH HOH . D 4 HOH A 22 622 622 HOH HOH . D 4 HOH A 23 623 623 HOH HOH . D 4 HOH A 24 624 624 HOH HOH . D 4 HOH A 25 625 625 HOH HOH . D 4 HOH A 26 626 626 HOH HOH . D 4 HOH A 27 627 627 HOH HOH . D 4 HOH A 28 628 628 HOH HOH . D 4 HOH A 29 629 629 HOH HOH . D 4 HOH A 30 630 630 HOH HOH . D 4 HOH A 31 631 631 HOH HOH . D 4 HOH A 32 632 632 HOH HOH . D 4 HOH A 33 633 633 HOH HOH . D 4 HOH A 34 634 634 HOH HOH . D 4 HOH A 35 635 635 HOH HOH . D 4 HOH A 36 636 636 HOH HOH . D 4 HOH A 37 637 637 HOH HOH . D 4 HOH A 38 638 638 HOH HOH . D 4 HOH A 39 639 639 HOH HOH . D 4 HOH A 40 640 640 HOH HOH . D 4 HOH A 41 641 641 HOH HOH . D 4 HOH A 42 642 642 HOH HOH . D 4 HOH A 43 643 643 HOH HOH . D 4 HOH A 44 644 644 HOH HOH . D 4 HOH A 45 645 645 HOH HOH . D 4 HOH A 46 646 646 HOH HOH . D 4 HOH A 47 647 647 HOH HOH . D 4 HOH A 48 648 648 HOH HOH . D 4 HOH A 49 649 649 HOH HOH . D 4 HOH A 50 650 650 HOH HOH . D 4 HOH A 51 651 651 HOH HOH . D 4 HOH A 52 652 652 HOH HOH . D 4 HOH A 53 653 653 HOH HOH . D 4 HOH A 54 654 654 HOH HOH . D 4 HOH A 55 655 655 HOH HOH . D 4 HOH A 56 656 656 HOH HOH . D 4 HOH A 57 657 657 HOH HOH . D 4 HOH A 58 658 658 HOH HOH . D 4 HOH A 59 659 659 HOH HOH . D 4 HOH A 60 660 660 HOH HOH . D 4 HOH A 61 661 661 HOH HOH . D 4 HOH A 62 662 662 HOH HOH . D 4 HOH A 63 663 663 HOH HOH . D 4 HOH A 64 664 664 HOH HOH . D 4 HOH A 65 665 665 HOH HOH . D 4 HOH A 66 666 666 HOH HOH . D 4 HOH A 67 667 667 HOH HOH . D 4 HOH A 68 668 668 HOH HOH . D 4 HOH A 69 669 669 HOH HOH . D 4 HOH A 70 670 670 HOH HOH . D 4 HOH A 71 671 671 HOH HOH . D 4 HOH A 72 672 672 HOH HOH . D 4 HOH A 73 673 673 HOH HOH . D 4 HOH A 74 674 674 HOH HOH . D 4 HOH A 75 675 675 HOH HOH . D 4 HOH A 76 676 676 HOH HOH . D 4 HOH A 77 677 677 HOH HOH . D 4 HOH A 78 678 678 HOH HOH . D 4 HOH A 79 679 679 HOH HOH . D 4 HOH A 80 680 680 HOH HOH . D 4 HOH A 81 681 681 HOH HOH . D 4 HOH A 82 682 682 HOH HOH . D 4 HOH A 83 683 683 HOH HOH . D 4 HOH A 84 684 684 HOH HOH . D 4 HOH A 85 685 685 HOH HOH . D 4 HOH A 86 686 686 HOH HOH . D 4 HOH A 87 687 687 HOH HOH . D 4 HOH A 88 688 688 HOH HOH . D 4 HOH A 89 689 689 HOH HOH . D 4 HOH A 90 690 690 HOH HOH . D 4 HOH A 91 691 691 HOH HOH . D 4 HOH A 92 692 692 HOH HOH . D 4 HOH A 93 693 693 HOH HOH . D 4 HOH A 94 694 694 HOH HOH . D 4 HOH A 95 695 695 HOH HOH . D 4 HOH A 96 696 696 HOH HOH . D 4 HOH A 97 697 697 HOH HOH . D 4 HOH A 98 698 698 HOH HOH . D 4 HOH A 99 699 699 HOH HOH . D 4 HOH A 100 700 700 HOH HOH . D 4 HOH A 101 701 701 HOH HOH . D 4 HOH A 102 702 702 HOH HOH . D 4 HOH A 103 703 703 HOH HOH . D 4 HOH A 104 704 704 HOH HOH . D 4 HOH A 105 705 705 HOH HOH . D 4 HOH A 106 706 706 HOH HOH . D 4 HOH A 107 707 707 HOH HOH . D 4 HOH A 108 708 708 HOH HOH . D 4 HOH A 109 709 709 HOH HOH . D 4 HOH A 110 710 710 HOH HOH . D 4 HOH A 111 711 711 HOH HOH . D 4 HOH A 112 712 712 HOH HOH . D 4 HOH A 113 713 713 HOH HOH . D 4 HOH A 114 714 714 HOH HOH . D 4 HOH A 115 715 715 HOH HOH . D 4 HOH A 116 716 716 HOH HOH . D 4 HOH A 117 717 717 HOH HOH . D 4 HOH A 118 718 718 HOH HOH . D 4 HOH A 119 719 719 HOH HOH . D 4 HOH A 120 720 720 HOH HOH . D 4 HOH A 121 721 721 HOH HOH . D 4 HOH A 122 722 722 HOH HOH . D 4 HOH A 123 723 723 HOH HOH . D 4 HOH A 124 724 724 HOH HOH . D 4 HOH A 125 725 725 HOH HOH . D 4 HOH A 126 726 726 HOH HOH . D 4 HOH A 127 727 727 HOH HOH . D 4 HOH A 128 728 728 HOH HOH . D 4 HOH A 129 729 729 HOH HOH . D 4 HOH A 130 730 730 HOH HOH . D 4 HOH A 131 731 731 HOH HOH . D 4 HOH A 132 732 732 HOH HOH . D 4 HOH A 133 733 733 HOH HOH . D 4 HOH A 134 734 734 HOH HOH . D 4 HOH A 135 735 735 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 8LH . A . B 2 -14.664 -39.965 10.562 1 35.11 ? C1 8LH 501 A 1 HETATM 2 C C2 8LH . A . B 2 -15.887 -40.015 11.116 1 34.6 ? C2 8LH 501 A 1 HETATM 3 C C3 8LH . A . B 2 -15.992 -40.118 12.467 1 32.6 ? C3 8LH 501 A 1 HETATM 4 C C4 8LH . A . B 2 -16.113 -39.808 8.965 1 33.43 ? C4 8LH 501 A 1 HETATM 5 N N1 8LH . A . B 2 -14.912 -40.241 13.251 1 34.36 ? N1 8LH 501 A 1 HETATM 6 N N2 8LH . A . B 2 -13.546 -40.004 11.322 1 32.39 ? N2 8LH 501 A 1 HETATM 7 O O1 8LH . A . B 2 -20.142 -38.146 7.093 0.5 18.33 ? O1 8LH 501 A 1 HETATM 8 C C5 8LH . A . B 2 -20.085 -39.544 6.92 0.5 21.33 ? C5 8LH 501 A 1 HETATM 9 C C6 8LH . A . B 2 -19.697 -39.807 5.456 0.5 30.09 ? C6 8LH 501 A 1 HETATM 10 C C7 8LH . A . B 2 -20.754 -39.263 4.477 0.5 24.8 ? C7 8LH 501 A 1 HETATM 11 C C8 8LH . A . B 2 -18.298 -39.23 5.127 0.5 38.64 ? C8 8LH 501 A 1 HETATM 12 O O2 8LH . A . B 2 -17.782 -38.338 5.805 0.5 39.26 ? O2 8LH 501 A 1 HETATM 13 O O3 8LH . A . B 2 -17.702 -39.812 4.047 1 43.26 ? O3 8LH 501 A 1 HETATM 14 P P1 8LH . A . B 2 -16.382 -39.238 3.389 1 43.2 ? P1 8LH 501 A 1 HETATM 15 O O4 8LH . A . B 2 -16.759 -37.737 3.137 1 44.09 ? O4 8LH 501 A 1 HETATM 16 O O5 8LH . A . B 2 -15.946 -39.979 2.202 1 48.4 ? O5 8LH 501 A 1 HETATM 17 O O6 8LH . A . B 2 -15.239 -39.35 4.501 1 42.22 ? O6 8LH 501 A 1 HETATM 18 C C9 8LH . A . B 2 -15.014 -40.604 5.143 1 35.99 ? C9 8LH 501 A 1 HETATM 19 C C10 8LH . A . B 2 -13.817 -40.442 6.042 1 31.47 ? C10 8LH 501 A 1 HETATM 20 O O7 8LH . A . B 2 -14.081 -39.349 6.962 1 30.34 ? O7 8LH 501 A 1 HETATM 21 C C11 8LH . A . B 2 -13.694 -41.649 6.886 1 29.46 ? C11 8LH 501 A 1 HETATM 22 O O8 8LH . A . B 2 -12.959 -42.677 6.194 1 29.05 ? O8 8LH 501 A 1 HETATM 23 C C12 8LH . A . B 2 -12.916 -41.073 8.095 1 29.46 ? C12 8LH 501 A 1 HETATM 24 O O9 8LH . A . B 2 -11.479 -40.83 7.784 1 31.02 ? O9 8LH 501 A 1 HETATM 25 C C13 8LH . A . B 2 -13.626 -39.746 8.284 1 29.66 ? C13 8LH 501 A 1 HETATM 26 N N3 8LH . A . B 2 -14.805 -39.835 9.24 1 34.99 ? N3 8LH 501 A 1 HETATM 27 N N4 8LH . A . B 2 -16.775 -39.904 10.117 1 33.01 ? N4 8LH 501 A 1 HETATM 28 C C14 8LH . A . B 2 -13.634 -40.17 12.695 1 32.39 ? C14 8LH 501 A 1 HETATM 29 N N5 8LH . A . B 2 -17.196 -40.111 13.027 1 25.72 ? N5 8LH 501 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #