data_3VQX # _model_server_result.job_id U9Rp_ZQM5aMr9Khuvb6pqA _model_server_result.datetime_utc '2025-01-11 13:00:51' _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 3vqx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 3VQX # _exptl.entry_id 3VQX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 575.509 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S)-2-azanyl-6-[(2-methylpropan-2-yl)oxycarbonylamino]hexanoate' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 106.92 _cell.angle_beta 91.41 _cell.angle_gamma 113.83 _cell.entry_id 3VQX _cell.length_a 62.798 _cell.length_b 69.422 _cell.length_c 83.326 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VQX _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,M,N 1 1 C,D,I,J,K,L,O,P 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 I N N ? 4 K N N # _chem_comp.formula 'C21 H34 N7 O10 P' _chem_comp.formula_weight 575.509 _chem_comp.id BLK _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S)-2-azanyl-6-[(2-methylpropan-2-yl)oxycarbonylamino]hexanoate' _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 N6 C6 BLK sing 109 n n N1 C6 BLK doub 110 n y N1 C2 BLK sing 111 n y C6 C5 BLK sing 112 n y C2 N3 BLK doub 113 n y C5 N7 BLK sing 114 n y C5 C4 BLK doub 115 n y N7 C8 BLK doub 116 n y N3 C4 BLK sing 117 n y C4 N9 BLK sing 118 n y C8 N9 BLK sing 119 n y N9 C1' BLK sing 120 n n C1' C2' BLK sing 121 n n C1' O4' BLK sing 122 n n C2' C3' BLK sing 123 n n C2' O2' BLK sing 124 n n O4' C4' BLK sing 125 n n O1P P BLK doub 126 n n O2P P BLK sing 127 n n O5' P BLK sing 128 n n O5' C5' BLK sing 129 n n C3' C4' BLK sing 130 n n C3' O3' BLK sing 131 n n P O3P BLK sing 132 n n C4' C5' BLK sing 133 n n O C BLK doub 134 n n O3P C BLK sing 135 n n C CA BLK sing 136 n n CA N BLK sing 137 n n CA CB BLK sing 138 n n CB CG BLK sing 139 n n CG CD BLK sing 140 n n CD CE BLK sing 141 n n CE NZ BLK sing 142 n n CT2 CT BLK sing 143 n n CT1 CT BLK sing 144 n n O2 CZ BLK sing 145 n n O2 CT BLK sing 146 n n NZ CZ BLK sing 147 n n CZ O1 BLK doub 148 n n CT CT3 BLK sing 149 n n CT1 H1 BLK sing 150 n n CT1 H2 BLK sing 151 n n CT1 H3 BLK sing 152 n n CT2 H4 BLK sing 153 n n CT2 H5 BLK sing 154 n n CT2 H6 BLK sing 155 n n CT3 H7 BLK sing 156 n n CT3 H8 BLK sing 157 n n CT3 H9 BLK sing 158 n n NZ H10 BLK sing 159 n n CE H11 BLK sing 160 n n CE H12 BLK sing 161 n n CD H13 BLK sing 162 n n CD H14 BLK sing 163 n n CG H15 BLK sing 164 n n CG H16 BLK sing 165 n n CB H17 BLK sing 166 n n CB H18 BLK sing 167 n n CA H19 BLK sing 168 n n N H20 BLK sing 169 n n N H21 BLK sing 170 n n O2P H23 BLK sing 171 n n C5' H24 BLK sing 172 n n C5' H25 BLK sing 173 n n C4' H26 BLK sing 174 n n C3' H27 BLK sing 175 n n O3' H28 BLK sing 176 n n C2' H29 BLK sing 177 n n O2' H30 BLK sing 178 n n C1' H31 BLK sing 179 n n C8 H32 BLK sing 180 n n C2 H33 BLK sing 181 n n N6 H34 BLK sing 182 n n N6 H35 BLK sing 183 n n # _atom_sites.entry_id 3VQX _atom_sites.fract_transf_matrix[1][1] 0.015924 _atom_sites.fract_transf_matrix[1][2] 0.007033 _atom_sites.fract_transf_matrix[1][3] 0.002867 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015747 _atom_sites.fract_transf_matrix[2][3] 0.005489 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.012713 _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 E 2 AMP A 1 501 501 AMP AMP . F 3 PO4 A 1 502 5954 PO4 PO4 . G 2 AMP B 1 501 502 AMP AMP . H 3 PO4 B 1 502 5953 PO4 PO4 . I 4 BLK C 1 601 601 BLK BLK . J 3 PO4 C 1 602 603 PO4 PO4 . K 4 BLK D 1 501 501 BLK BLK . L 3 PO4 D 1 502 503 PO4 PO4 . M 5 HOH A 1 601 601 HOH HOH . M 5 HOH A 2 602 602 HOH HOH . M 5 HOH A 3 603 603 HOH HOH . M 5 HOH A 4 604 604 HOH HOH . M 5 HOH A 5 605 605 HOH HOH . M 5 HOH A 6 606 606 HOH HOH . M 5 HOH A 7 607 607 HOH HOH . M 5 HOH A 8 608 608 HOH HOH . M 5 HOH A 9 609 609 HOH HOH . M 5 HOH A 10 610 610 HOH HOH . M 5 HOH A 11 611 611 HOH HOH . M 5 HOH A 12 612 612 HOH HOH . M 5 HOH A 13 613 613 HOH HOH . M 5 HOH A 14 614 614 HOH HOH . M 5 HOH A 15 615 615 HOH HOH . M 5 HOH A 16 616 616 HOH HOH . M 5 HOH A 17 617 617 HOH HOH . M 5 HOH A 18 618 618 HOH HOH . M 5 HOH A 19 619 619 HOH HOH . M 5 HOH A 20 620 620 HOH HOH . M 5 HOH A 21 621 621 HOH HOH . M 5 HOH A 22 622 622 HOH HOH . M 5 HOH A 23 623 623 HOH HOH . M 5 HOH A 24 624 624 HOH HOH . M 5 HOH A 25 625 625 HOH HOH . M 5 HOH A 26 626 626 HOH HOH . M 5 HOH A 27 627 627 HOH HOH . M 5 HOH A 28 628 628 HOH HOH . M 5 HOH A 29 629 629 HOH HOH . M 5 HOH A 30 630 630 HOH HOH . M 5 HOH A 31 631 631 HOH HOH . M 5 HOH A 32 632 632 HOH HOH . M 5 HOH A 33 633 633 HOH HOH . M 5 HOH A 34 634 634 HOH HOH . M 5 HOH A 35 635 635 HOH HOH . M 5 HOH A 36 636 636 HOH HOH . M 5 HOH A 37 637 637 HOH HOH . M 5 HOH A 38 638 638 HOH HOH . M 5 HOH A 39 639 639 HOH HOH . M 5 HOH A 40 640 640 HOH HOH . M 5 HOH A 41 641 641 HOH HOH . M 5 HOH A 42 642 642 HOH HOH . M 5 HOH A 43 643 643 HOH HOH . M 5 HOH A 44 644 644 HOH HOH . M 5 HOH A 45 645 645 HOH HOH . M 5 HOH A 46 646 646 HOH HOH . N 5 HOH B 1 601 601 HOH HOH . N 5 HOH B 2 602 602 HOH HOH . N 5 HOH B 3 603 603 HOH HOH . N 5 HOH B 4 604 604 HOH HOH . N 5 HOH B 5 605 605 HOH HOH . N 5 HOH B 6 606 606 HOH HOH . N 5 HOH B 7 607 607 HOH HOH . N 5 HOH B 8 608 608 HOH HOH . N 5 HOH B 9 609 609 HOH HOH . N 5 HOH B 10 610 610 HOH HOH . N 5 HOH B 11 611 611 HOH HOH . N 5 HOH B 12 612 612 HOH HOH . N 5 HOH B 13 613 613 HOH HOH . N 5 HOH B 14 614 614 HOH HOH . N 5 HOH B 15 615 615 HOH HOH . N 5 HOH B 16 616 616 HOH HOH . N 5 HOH B 17 617 617 HOH HOH . N 5 HOH B 18 618 618 HOH HOH . N 5 HOH B 19 619 619 HOH HOH . N 5 HOH B 20 620 620 HOH HOH . N 5 HOH B 21 621 621 HOH HOH . N 5 HOH B 22 622 622 HOH HOH . N 5 HOH B 23 623 623 HOH HOH . N 5 HOH B 24 624 624 HOH HOH . N 5 HOH B 25 625 625 HOH HOH . N 5 HOH B 26 626 626 HOH HOH . N 5 HOH B 27 627 627 HOH HOH . N 5 HOH B 28 628 628 HOH HOH . N 5 HOH B 29 629 629 HOH HOH . N 5 HOH B 30 630 630 HOH HOH . N 5 HOH B 31 631 631 HOH HOH . N 5 HOH B 32 632 632 HOH HOH . N 5 HOH B 33 633 633 HOH HOH . N 5 HOH B 34 634 634 HOH HOH . N 5 HOH B 35 635 635 HOH HOH . N 5 HOH B 36 636 636 HOH HOH . N 5 HOH B 37 637 637 HOH HOH . N 5 HOH B 38 638 638 HOH HOH . N 5 HOH B 39 639 639 HOH HOH . N 5 HOH B 40 640 640 HOH HOH . N 5 HOH B 41 641 641 HOH HOH . N 5 HOH B 42 642 642 HOH HOH . N 5 HOH B 43 643 643 HOH HOH . N 5 HOH B 44 644 644 HOH HOH . N 5 HOH B 45 645 645 HOH HOH . N 5 HOH B 46 646 646 HOH HOH . N 5 HOH B 47 647 647 HOH HOH . N 5 HOH B 48 648 648 HOH HOH . N 5 HOH B 49 649 649 HOH HOH . O 5 HOH C 1 701 701 HOH HOH . O 5 HOH C 2 702 702 HOH HOH . O 5 HOH C 3 703 703 HOH HOH . O 5 HOH C 4 704 704 HOH HOH . O 5 HOH C 5 705 705 HOH HOH . O 5 HOH C 6 706 706 HOH HOH . O 5 HOH C 7 707 707 HOH HOH . O 5 HOH C 8 708 708 HOH HOH . O 5 HOH C 9 709 709 HOH HOH . O 5 HOH C 10 710 710 HOH HOH . O 5 HOH C 11 711 711 HOH HOH . O 5 HOH C 12 712 712 HOH HOH . O 5 HOH C 13 713 713 HOH HOH . O 5 HOH C 14 714 714 HOH HOH . O 5 HOH C 15 715 715 HOH HOH . O 5 HOH C 16 716 716 HOH HOH . O 5 HOH C 17 717 717 HOH HOH . O 5 HOH C 18 718 718 HOH HOH . O 5 HOH C 19 719 719 HOH HOH . O 5 HOH C 20 720 720 HOH HOH . O 5 HOH C 21 721 721 HOH HOH . O 5 HOH C 22 722 722 HOH HOH . O 5 HOH C 23 723 723 HOH HOH . O 5 HOH C 24 724 724 HOH HOH . O 5 HOH C 25 725 725 HOH HOH . O 5 HOH C 26 726 726 HOH HOH . O 5 HOH C 27 727 727 HOH HOH . O 5 HOH C 28 728 728 HOH HOH . O 5 HOH C 29 729 729 HOH HOH . O 5 HOH C 30 730 730 HOH HOH . O 5 HOH C 31 731 731 HOH HOH . O 5 HOH C 32 732 732 HOH HOH . O 5 HOH C 33 733 733 HOH HOH . O 5 HOH C 34 734 734 HOH HOH . O 5 HOH C 35 735 735 HOH HOH . O 5 HOH C 36 736 736 HOH HOH . O 5 HOH C 37 737 737 HOH HOH . O 5 HOH C 38 738 738 HOH HOH . O 5 HOH C 39 739 739 HOH HOH . P 5 HOH D 1 601 601 HOH HOH . P 5 HOH D 2 602 602 HOH HOH . P 5 HOH D 3 603 603 HOH HOH . P 5 HOH D 4 604 604 HOH HOH . P 5 HOH D 5 605 605 HOH HOH . P 5 HOH D 6 606 606 HOH HOH . P 5 HOH D 7 607 607 HOH HOH . P 5 HOH D 8 608 608 HOH HOH . P 5 HOH D 9 609 609 HOH HOH . P 5 HOH D 10 610 610 HOH HOH . P 5 HOH D 11 611 611 HOH HOH . P 5 HOH D 12 612 612 HOH HOH . P 5 HOH D 13 613 613 HOH HOH . P 5 HOH D 14 614 614 HOH HOH . P 5 HOH D 15 615 615 HOH HOH . P 5 HOH D 16 616 616 HOH HOH . P 5 HOH D 17 617 617 HOH HOH . P 5 HOH D 18 618 618 HOH HOH . P 5 HOH D 19 619 619 HOH HOH . P 5 HOH D 20 620 620 HOH HOH . P 5 HOH D 21 621 621 HOH HOH . P 5 HOH D 22 622 622 HOH HOH . P 5 HOH D 23 623 623 HOH HOH . P 5 HOH D 24 624 624 HOH HOH . P 5 HOH D 25 625 625 HOH HOH . P 5 HOH D 26 626 626 HOH HOH . P 5 HOH D 27 627 627 HOH HOH . P 5 HOH D 28 628 628 HOH HOH . P 5 HOH D 29 629 629 HOH HOH . P 5 HOH D 30 630 630 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 CT1 BLK . . . K 4 46.918 18.79 22.347 1 57.17 ? CT1 BLK 501 D 1 HETATM 2 C CT BLK . . . K 4 46.915 18.22 23.768 1 58.28 ? CT BLK 501 D 1 HETATM 3 C CT2 BLK . . . K 4 45.756 17.238 23.945 1 57.53 ? CT2 BLK 501 D 1 HETATM 4 C CT3 BLK . . . K 4 46.806 19.357 24.785 1 59.4 ? CT3 BLK 501 D 1 HETATM 5 O O2 BLK . . . K 4 48.149 17.534 23.994 1 58.95 ? O2 BLK 501 D 1 HETATM 6 C CZ BLK . . . K 4 48.195 17.036 25.258 1 60.23 ? CZ BLK 501 D 1 HETATM 7 O O1 BLK . . . K 4 47.225 17.2 26.002 1 63.27 ? O1 BLK 501 D 1 HETATM 8 N NZ BLK . . . K 4 49.298 16.405 25.643 1 60.42 ? NZ BLK 501 D 1 HETATM 9 C CE BLK . . . K 4 50.455 16.246 24.749 1 60.94 ? CE BLK 501 D 1 HETATM 10 C CD BLK . . . K 4 51.288 15.107 25.336 1 62.15 ? CD BLK 501 D 1 HETATM 11 C CG BLK . . . K 4 52.479 14.72 24.458 1 64.44 ? CG BLK 501 D 1 HETATM 12 C CB BLK . . . K 4 52.911 13.331 24.93 1 66.29 ? CB BLK 501 D 1 HETATM 13 C CA BLK . . . K 4 54.043 12.732 24.094 1 67.68 ? CA BLK 501 D 1 HETATM 14 N N BLK . . . K 4 53.656 12.687 22.675 1 67.64 ? N BLK 501 D 1 HETATM 15 C C BLK . . . K 4 54.219 11.309 24.624 1 68.2 ? C BLK 501 D 1 HETATM 16 O O BLK . . . K 4 55.014 10.526 24.109 1 68.17 ? O BLK 501 D 1 HETATM 17 O O3P BLK . . . K 4 53.453 11.074 25.727 1 68.32 ? O3P BLK 501 D 1 HETATM 18 P P BLK . . . K 4 53.496 9.531 26.178 1 67.66 ? P BLK 501 D 1 HETATM 19 O O1P BLK . . . K 4 54.572 8.801 25.225 1 68.64 ? O1P BLK 501 D 1 HETATM 20 O O2P BLK . . . K 4 52.143 8.93 26.082 1 67.9 ? O2P BLK 501 D 1 HETATM 21 O O5' BLK . . . K 4 54.111 9.432 27.666 1 65.57 ? O5' BLK 501 D 1 HETATM 22 C C5' BLK . . . K 4 53.981 10.5 28.611 1 61.31 ? C5' BLK 501 D 1 HETATM 23 C C4' BLK . . . K 4 54.376 10.009 30.008 1 58.29 ? C4' BLK 501 D 1 HETATM 24 O O4' BLK . . . K 4 53.322 9.284 30.668 1 57.46 ? O4' BLK 501 D 1 HETATM 25 C C3' BLK . . . K 4 55.577 9.063 30.005 1 56.87 ? C3' BLK 501 D 1 HETATM 26 O O3' BLK . . . K 4 56.78 9.836 29.938 1 54.39 ? O3' BLK 501 D 1 HETATM 27 C C2' BLK . . . K 4 55.416 8.503 31.417 1 56.85 ? C2' BLK 501 D 1 HETATM 28 O O2' BLK . . . K 4 55.678 9.528 32.382 1 55.51 ? O2' BLK 501 D 1 HETATM 29 C C1' BLK . . . K 4 53.917 8.195 31.4 1 55.82 ? C1' BLK 501 D 1 HETATM 30 N N9 BLK . . . K 4 53.669 6.95 30.64 1 55.26 ? N9 BLK 501 D 1 HETATM 31 C C8 BLK . . . K 4 53.376 6.848 29.344 1 54.19 ? C8 BLK 501 D 1 HETATM 32 N N7 BLK . . . K 4 53.188 5.567 29.03 1 53.82 ? N7 BLK 501 D 1 HETATM 33 C C5 BLK . . . K 4 53.363 4.843 30.134 1 54.82 ? C5 BLK 501 D 1 HETATM 34 C C4 BLK . . . K 4 53.673 5.725 31.158 1 54.86 ? C4 BLK 501 D 1 HETATM 35 N N3 BLK . . . K 4 53.895 5.25 32.393 1 52.72 ? N3 BLK 501 D 1 HETATM 36 C C2 BLK . . . K 4 53.813 3.955 32.638 1 52.38 ? C2 BLK 501 D 1 HETATM 37 N N1 BLK . . . K 4 53.52 3.082 31.686 1 52.78 ? N1 BLK 501 D 1 HETATM 38 C C6 BLK . . . K 4 53.294 3.486 30.429 1 54.69 ? C6 BLK 501 D 1 HETATM 39 N N6 BLK . . . K 4 53.018 2.598 29.476 1 53.73 ? N6 BLK 501 D 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 39 #