data_6IYF # _model_server_result.job_id ShAeaNGnWEXC91eZfvTTkw _model_server_result.datetime_utc '2024-11-28 05:57:27' _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 6iyf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":401}' # _entry.id 6IYF # _exptl.entry_id 6IYF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 658.412 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide" _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 6IYF _cell.length_a 49.785 _cell.length_b 65.896 _cell.length_c 100.571 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6IYF _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,H,I,J,K,L,M _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 3 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C20 H24 N10 O12 P2' _chem_comp.formula_weight 658.412 _chem_comp.id 2BA _chem_comp.mon_nstd_flag . _chem_comp.name "(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "bis-(3',5')-cyclic-dimeric-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 P O1P 2BA doub 1 n n P O2P 2BA sing 2 n n P O5' 2BA sing 3 n n P "O3'1" 2BA sing 4 n n O5' C5' 2BA sing 5 n n C5' C4' 2BA sing 6 n n C4' O4' 2BA sing 7 n n C4' C3' 2BA sing 8 n n O4' C1' 2BA sing 9 n n C3' O3' 2BA sing 10 n n C3' C2' 2BA sing 11 n n O3' P1 2BA sing 12 n n C2' O2' 2BA sing 13 n n C2' C1' 2BA sing 14 n n C1' N9 2BA sing 15 n n N9 C8 2BA sing 16 n y N9 C4 2BA sing 17 n y C8 N7 2BA doub 18 n y N7 C5 2BA sing 19 n y C5 C6 2BA doub 20 n y C5 C4 2BA sing 21 n y C6 N6 2BA sing 22 n n C6 N1 2BA sing 23 n y N1 C2 2BA doub 24 n y C2 N3 2BA sing 25 n y N3 C4 2BA doub 26 n y P1 O1P1 2BA doub 27 n n P1 O2P1 2BA sing 28 n n P1 "O5'1" 2BA sing 29 n n "O5'1" "C5'1" 2BA sing 30 n n "C5'1" "C4'1" 2BA sing 31 n n "C4'1" "O4'1" 2BA sing 32 n n "C4'1" "C3'1" 2BA sing 33 n n "O4'1" "C1'1" 2BA sing 34 n n "C3'1" "O3'1" 2BA sing 35 n n "C3'1" "C2'1" 2BA sing 36 n n "C2'1" "O2'1" 2BA sing 37 n n "C2'1" "C1'1" 2BA sing 38 n n "C1'1" N91 2BA sing 39 n n N91 C81 2BA sing 40 n y N91 C41 2BA sing 41 n y C81 N71 2BA doub 42 n y N71 C51 2BA sing 43 n y C51 C61 2BA doub 44 n y C51 C41 2BA sing 45 n y C61 N61 2BA sing 46 n n C61 N11 2BA sing 47 n y N11 C21 2BA doub 48 n y C21 N31 2BA sing 49 n y N31 C41 2BA doub 50 n y C5' H5' 2BA sing 51 n n C5' "H5'A" 2BA sing 52 n n C4' H4' 2BA sing 53 n n C3' H3' 2BA sing 54 n n C2' H2' 2BA sing 55 n n O2' HO2' 2BA sing 56 n n C1' H1' 2BA sing 57 n n C8 H8 2BA sing 58 n n N6 HN6 2BA sing 59 n n N6 HN6A 2BA sing 60 n n C2 H2 2BA sing 61 n n "C5'1" HC5' 2BA sing 62 n n "C5'1" HC5A 2BA sing 63 n n "C4'1" HC4' 2BA sing 64 n n "C3'1" HC3' 2BA sing 65 n n "C2'1" HC2' 2BA sing 66 n n "O2'1" HO2A 2BA sing 67 n n "C1'1" HC1' 2BA sing 68 n n C81 HC8 2BA sing 69 n n N61 H1N6 2BA sing 70 n n N61 H1NA 2BA sing 71 n n C21 HC2 2BA sing 72 n n O2P H2P 2BA sing 73 n n O2P1 H2OP 2BA sing 74 n n # _atom_sites.entry_id 6IYF _atom_sites.fract_transf_matrix[1][1] 0.020086 _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] 0.015175 _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] 0.009943 _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 C 2 SO4 A 1 401 1 SO4 SO4 . D 2 SO4 A 1 402 3 SO4 SO4 . E 2 SO4 A 1 403 5 SO4 SO4 . F 2 SO4 A 1 404 6 SO4 SO4 . G 2 SO4 A 1 405 8 SO4 SO4 . H 3 2BA B 1 401 358 2BA 2BA . I 2 SO4 B 1 402 2 SO4 SO4 . J 2 SO4 B 1 403 4 SO4 SO4 . K 2 SO4 B 1 404 7 SO4 SO4 . L 4 HOH A 1 501 149 HOH HOH . L 4 HOH A 2 502 29 HOH HOH . L 4 HOH A 3 503 127 HOH HOH . L 4 HOH A 4 504 41 HOH HOH . L 4 HOH A 5 505 31 HOH HOH . L 4 HOH A 6 506 33 HOH HOH . L 4 HOH A 7 507 47 HOH HOH . L 4 HOH A 8 508 136 HOH HOH . L 4 HOH A 9 509 44 HOH HOH . L 4 HOH A 10 510 69 HOH HOH . L 4 HOH A 11 511 16 HOH HOH . L 4 HOH A 12 512 132 HOH HOH . L 4 HOH A 13 513 155 HOH HOH . L 4 HOH A 14 514 30 HOH HOH . L 4 HOH A 15 515 71 HOH HOH . L 4 HOH A 16 516 119 HOH HOH . L 4 HOH A 17 517 129 HOH HOH . L 4 HOH A 18 518 117 HOH HOH . L 4 HOH A 19 519 24 HOH HOH . L 4 HOH A 20 520 88 HOH HOH . L 4 HOH A 21 521 4 HOH HOH . L 4 HOH A 22 522 125 HOH HOH . L 4 HOH A 23 523 28 HOH HOH . L 4 HOH A 24 524 9 HOH HOH . L 4 HOH A 25 525 36 HOH HOH . L 4 HOH A 26 526 45 HOH HOH . L 4 HOH A 27 527 79 HOH HOH . L 4 HOH A 28 528 39 HOH HOH . L 4 HOH A 29 529 85 HOH HOH . L 4 HOH A 30 530 147 HOH HOH . L 4 HOH A 31 531 144 HOH HOH . L 4 HOH A 32 532 40 HOH HOH . L 4 HOH A 33 533 48 HOH HOH . L 4 HOH A 34 534 5 HOH HOH . L 4 HOH A 35 535 3 HOH HOH . L 4 HOH A 36 536 1 HOH HOH . L 4 HOH A 37 537 50 HOH HOH . L 4 HOH A 38 538 114 HOH HOH . L 4 HOH A 39 539 98 HOH HOH . L 4 HOH A 40 540 128 HOH HOH . L 4 HOH A 41 541 87 HOH HOH . L 4 HOH A 42 542 23 HOH HOH . L 4 HOH A 43 543 122 HOH HOH . L 4 HOH A 44 544 89 HOH HOH . L 4 HOH A 45 545 20 HOH HOH . L 4 HOH A 46 546 80 HOH HOH . L 4 HOH A 47 547 94 HOH HOH . L 4 HOH A 48 548 96 HOH HOH . L 4 HOH A 49 549 43 HOH HOH . L 4 HOH A 50 550 81 HOH HOH . L 4 HOH A 51 551 72 HOH HOH . L 4 HOH A 52 552 65 HOH HOH . L 4 HOH A 53 553 140 HOH HOH . L 4 HOH A 54 554 76 HOH HOH . L 4 HOH A 55 555 116 HOH HOH . L 4 HOH A 56 556 34 HOH HOH . L 4 HOH A 57 557 58 HOH HOH . L 4 HOH A 58 558 78 HOH HOH . L 4 HOH A 59 559 145 HOH HOH . L 4 HOH A 60 560 57 HOH HOH . L 4 HOH A 61 561 86 HOH HOH . L 4 HOH A 62 562 75 HOH HOH . L 4 HOH A 63 563 133 HOH HOH . L 4 HOH A 64 564 54 HOH HOH . L 4 HOH A 65 565 131 HOH HOH . L 4 HOH A 66 566 146 HOH HOH . L 4 HOH A 67 567 90 HOH HOH . M 4 HOH B 1 501 154 HOH HOH . M 4 HOH B 2 502 142 HOH HOH . M 4 HOH B 3 503 107 HOH HOH . M 4 HOH B 4 504 153 HOH HOH . M 4 HOH B 5 505 51 HOH HOH . M 4 HOH B 6 506 6 HOH HOH . M 4 HOH B 7 507 74 HOH HOH . M 4 HOH B 8 508 113 HOH HOH . M 4 HOH B 9 509 135 HOH HOH . M 4 HOH B 10 510 12 HOH HOH . M 4 HOH B 11 511 35 HOH HOH . M 4 HOH B 12 512 7 HOH HOH . M 4 HOH B 13 513 26 HOH HOH . M 4 HOH B 14 514 2 HOH HOH . M 4 HOH B 15 515 112 HOH HOH . M 4 HOH B 16 516 111 HOH HOH . M 4 HOH B 17 517 143 HOH HOH . M 4 HOH B 18 518 151 HOH HOH . M 4 HOH B 19 519 66 HOH HOH . M 4 HOH B 20 520 148 HOH HOH . M 4 HOH B 21 521 8 HOH HOH . M 4 HOH B 22 522 42 HOH HOH . M 4 HOH B 23 523 92 HOH HOH . M 4 HOH B 24 524 18 HOH HOH . M 4 HOH B 25 525 83 HOH HOH . M 4 HOH B 26 526 38 HOH HOH . M 4 HOH B 27 527 67 HOH HOH . M 4 HOH B 28 528 138 HOH HOH . M 4 HOH B 29 529 68 HOH HOH . M 4 HOH B 30 530 11 HOH HOH . M 4 HOH B 31 531 97 HOH HOH . M 4 HOH B 32 532 110 HOH HOH . M 4 HOH B 33 533 14 HOH HOH . M 4 HOH B 34 534 32 HOH HOH . M 4 HOH B 35 535 141 HOH HOH . M 4 HOH B 36 536 22 HOH HOH . M 4 HOH B 37 537 82 HOH HOH . M 4 HOH B 38 538 63 HOH HOH . M 4 HOH B 39 539 27 HOH HOH . M 4 HOH B 40 540 61 HOH HOH . M 4 HOH B 41 541 37 HOH HOH . M 4 HOH B 42 542 19 HOH HOH . M 4 HOH B 43 543 100 HOH HOH . M 4 HOH B 44 544 46 HOH HOH . M 4 HOH B 45 545 10 HOH HOH . M 4 HOH B 46 546 15 HOH HOH . M 4 HOH B 47 547 137 HOH HOH . M 4 HOH B 48 548 108 HOH HOH . M 4 HOH B 49 549 13 HOH HOH . M 4 HOH B 50 550 17 HOH HOH . M 4 HOH B 51 551 56 HOH HOH . M 4 HOH B 52 552 49 HOH HOH . M 4 HOH B 53 553 21 HOH HOH . M 4 HOH B 54 554 84 HOH HOH . M 4 HOH B 55 555 60 HOH HOH . M 4 HOH B 56 556 73 HOH HOH . M 4 HOH B 57 557 106 HOH HOH . M 4 HOH B 58 558 126 HOH HOH . M 4 HOH B 59 559 59 HOH HOH . M 4 HOH B 60 560 130 HOH HOH . M 4 HOH B 61 561 91 HOH HOH . M 4 HOH B 62 562 53 HOH HOH . M 4 HOH B 63 563 55 HOH HOH . M 4 HOH B 64 564 77 HOH HOH . M 4 HOH B 65 565 109 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 P P 2BA . . . H 3 -6.397 3.111 -29.345 1 22.67 ? P 2BA 401 B 1 HETATM 2 O O1P 2BA . . . H 3 -7.52 3.934 -29.413 1 19.13 ? O1P 2BA 401 B 1 HETATM 3 O O2P 2BA . . . H 3 -5.232 3.523 -28.749 1 18.69 ? O2P 2BA 401 B 1 HETATM 4 O O5' 2BA . . . H 3 -6.003 2.661 -30.719 1 16.89 ? O5' 2BA 401 B 1 HETATM 5 C C5' 2BA . . . H 3 -6.952 2.196 -31.59 1 14.86 ? C5' 2BA 401 B 1 HETATM 6 C C4' 2BA . . . H 3 -6.377 1.563 -32.858 1 14.82 ? C4' 2BA 401 B 1 HETATM 7 O O4' 2BA . . . H 3 -5.522 2.431 -33.48 1 15.33 ? O4' 2BA 401 B 1 HETATM 8 C C3' 2BA . . . H 3 -5.517 0.346 -32.583 1 16.5 ? C3' 2BA 401 B 1 HETATM 9 O O3' 2BA . . . H 3 -6.184 -0.872 -32.365 1 17.49 ? O3' 2BA 401 B 1 HETATM 10 C C2' 2BA . . . H 3 -4.627 0.323 -33.79 1 16.25 ? C2' 2BA 401 B 1 HETATM 11 O O2' 2BA . . . H 3 -5.334 -0.207 -34.839 1 16.78 ? O2' 2BA 401 B 1 HETATM 12 C C1' 2BA . . . H 3 -4.368 1.783 -34.016 1 16.98 ? C1' 2BA 401 B 1 HETATM 13 N N9 2BA . . . H 3 -3.164 2.163 -33.327 1 17.87 ? N9 2BA 401 B 1 HETATM 14 C C8 2BA . . . H 3 -3.09 2.901 -32.241 1 21.37 ? C8 2BA 401 B 1 HETATM 15 N N7 2BA . . . H 3 -1.873 3.093 -31.765 1 16.19 ? N7 2BA 401 B 1 HETATM 16 C C5 2BA . . . H 3 -1.103 2.497 -32.626 1 18.38 ? C5 2BA 401 B 1 HETATM 17 C C6 2BA . . . H 3 0.326 2.275 -32.757 1 25.94 ? C6 2BA 401 B 1 HETATM 18 N N6 2BA . . . H 3 1.095 2.829 -31.838 1 22.26 ? N6 2BA 401 B 1 HETATM 19 N N1 2BA . . . H 3 0.76 1.556 -33.792 1 23.98 ? N1 2BA 401 B 1 HETATM 20 C C2 2BA . . . H 3 -0.079 1.025 -34.663 1 21.15 ? C2 2BA 401 B 1 HETATM 21 N N3 2BA . . . H 3 -1.373 1.136 -34.624 1 18.06 ? N3 2BA 401 B 1 HETATM 22 C C4 2BA . . . H 3 -1.95 1.848 -33.649 1 20.2 ? C4 2BA 401 B 1 HETATM 23 P P1 2BA . . . H 3 -5.544 -2.014 -31.562 1 17.5 ? P1 2BA 401 B 1 HETATM 24 O O1P1 2BA . . . H 3 -6.448 -3.113 -31.635 1 15.83 ? O1P1 2BA 401 B 1 HETATM 25 O O2P1 2BA . . . H 3 -4.266 -2.253 -31.951 1 19.25 ? O2P1 2BA 401 B 1 HETATM 26 O "O5'1" 2BA . . . H 3 -5.566 -1.594 -30.099 1 15.8 ? "O5'1" 2BA 401 B 1 HETATM 27 C "C5'1" 2BA . . . H 3 -6.75 -1.349 -29.416 1 17.75 ? "C5'1" 2BA 401 B 1 HETATM 28 C "C4'1" 2BA . . . H 3 -6.497 -0.612 -28.099 1 20.07 ? "C4'1" 2BA 401 B 1 HETATM 29 O "O4'1" 2BA . . . H 3 -5.609 -1.293 -27.272 1 15.68 ? "O4'1" 2BA 401 B 1 HETATM 30 C "C3'1" 2BA . . . H 3 -5.935 0.811 -28.3 1 13.36 ? "C3'1" 2BA 401 B 1 HETATM 31 O "O3'1" 2BA . . . H 3 -6.859 1.81 -28.656 1 18.82 ? "O3'1" 2BA 401 B 1 HETATM 32 C "C2'1" 2BA . . . H 3 -5.355 1.034 -26.947 1 21.98 ? "C2'1" 2BA 401 B 1 HETATM 33 O "O2'1" 2BA . . . H 3 -6.384 1.439 -26.093 1 25.39 ? "O2'1" 2BA 401 B 1 HETATM 34 C "C1'1" 2BA . . . H 3 -4.833 -0.336 -26.575 1 19.8 ? "C1'1" 2BA 401 B 1 HETATM 35 N N91 2BA . . . H 3 -3.444 -0.383 -26.999 1 20.22 ? N91 2BA 401 B 1 HETATM 36 C C81 2BA . . . H 3 -3.018 -0.869 -28.105 1 19.37 ? C81 2BA 401 B 1 HETATM 37 N N71 2BA . . . H 3 -1.712 -0.722 -28.272 1 23.26 ? N71 2BA 401 B 1 HETATM 38 C C51 2BA . . . H 3 -1.264 -0.112 -27.179 1 19.1 ? C51 2BA 401 B 1 HETATM 39 C C61 2BA . . . H 3 0.044 0.318 -26.665 1 20.52 ? C61 2BA 401 B 1 HETATM 40 N N61 2BA . . . H 3 1.17 0.142 -27.345 1 18.33 ? N61 2BA 401 B 1 HETATM 41 N N11 2BA . . . H 3 0.041 0.907 -25.503 1 20.42 ? N11 2BA 401 B 1 HETATM 42 C C21 2BA . . . H 3 -1.042 1.074 -24.818 1 21.73 ? C21 2BA 401 B 1 HETATM 43 N N31 2BA . . . H 3 -2.229 0.715 -25.22 1 24.43 ? N31 2BA 401 B 1 HETATM 44 C C41 2BA . . . H 3 -2.407 0.111 -26.367 1 21.5 ? C41 2BA 401 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 44 #