data_5KS7 # _model_server_result.job_id BneD2Faqu0ce0wpJDnEoWw _model_server_result.datetime_utc '2024-12-03 18:49:59' _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 5ks7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 5KS7 # _exptl.entry_id 5KS7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 658.412 _entity.id 2 _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 94.94 _cell.angle_gamma 90 _cell.entry_id 5KS7 _cell.length_a 52.342 _cell.length_b 43.861 _cell.length_c 68.841 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KS7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 2 _struct_asym.id C _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 5KS7 _atom_sites.fract_transf_matrix[1][1] 0.019105 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00165 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022799 _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] 0.01458 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id 2BA _pdbx_nonpoly_scheme.pdb_strand_id B _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 500 _pdbx_nonpoly_scheme.auth_seq_num 500 _pdbx_nonpoly_scheme.pdb_mon_id 2BA _pdbx_nonpoly_scheme.auth_mon_id 2BA _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . C 2 -22.457 4.626 -21.225 1 20.4 ? P 2BA 500 B 1 HETATM 2 O O1P 2BA . . . C 2 -22.932 6.026 -21.629 1 18.86 ? O1P 2BA 500 B 1 HETATM 3 O O2P 2BA . . . C 2 -22.052 3.594 -22.263 1 21.56 ? O2P 2BA 500 B 1 HETATM 4 O O5' 2BA . . . C 2 -21.24 4.696 -20.142 1 19.36 ? O5' 2BA 500 B 1 HETATM 5 C C5' 2BA . . . C 2 -20.537 3.504 -19.782 1 17.91 ? C5' 2BA 500 B 1 HETATM 6 C C4' 2BA . . . C 2 -20.225 3.357 -18.293 1 17.47 ? C4' 2BA 500 B 1 HETATM 7 O O4' 2BA . . . C 2 -18.823 3.328 -18.184 1 17.09 ? O4' 2BA 500 B 1 HETATM 8 C C3' 2BA . . . C 2 -20.622 4.434 -17.262 1 17.52 ? C3' 2BA 500 B 1 HETATM 9 O O3' 2BA . . . C 2 -21.517 3.828 -16.347 1 17.79 ? O3' 2BA 500 B 1 HETATM 10 C C2' 2BA . . . C 2 -19.354 4.838 -16.499 1 16.84 ? C2' 2BA 500 B 1 HETATM 11 O O2' 2BA . . . C 2 -19.56 4.956 -15.085 1 16.12 ? O2' 2BA 500 B 1 HETATM 12 C C1' 2BA . . . C 2 -18.514 3.625 -16.815 1 16.8 ? C1' 2BA 500 B 1 HETATM 13 N N9 2BA . . . C 2 -17.033 3.655 -16.7 1 16.27 ? N9 2BA 500 B 1 HETATM 14 C C8 2BA . . . C 2 -16.143 4.445 -17.349 1 15.64 ? C8 2BA 500 B 1 HETATM 15 N N7 2BA . . . C 2 -14.875 4.117 -17.019 1 14.89 ? N7 2BA 500 B 1 HETATM 16 C C5 2BA . . . C 2 -14.947 3.085 -16.162 1 15.49 ? C5 2BA 500 B 1 HETATM 17 C C6 2BA . . . C 2 -13.981 2.246 -15.418 1 15.35 ? C6 2BA 500 B 1 HETATM 18 N N6 2BA . . . C 2 -12.647 2.45 -15.537 1 15.22 ? N6 2BA 500 B 1 HETATM 19 N N1 2BA . . . C 2 -14.478 1.278 -14.62 1 15.69 ? N1 2BA 500 B 1 HETATM 20 C C2 2BA . . . C 2 -15.808 1.05 -14.49 1 16.14 ? C2 2BA 500 B 1 HETATM 21 N N3 2BA . . . C 2 -16.756 1.77 -15.134 1 16.12 ? N3 2BA 500 B 1 HETATM 22 C C4 2BA . . . C 2 -16.373 2.776 -15.965 1 16.05 ? C4 2BA 500 B 1 HETATM 23 P P1 2BA . . . C 2 -22.506 4.711 -15.458 1 19.14 ? P1 2BA 500 B 1 HETATM 24 O O1P1 2BA . . . C 2 -21.73 5.964 -15.013 1 17.98 ? O1P1 2BA 500 B 1 HETATM 25 O O2P1 2BA . . . C 2 -23.128 3.808 -14.409 1 18.19 ? O2P1 2BA 500 B 1 HETATM 26 O "O5'1" 2BA . . . C 2 -23.66 4.971 -16.578 1 18.4 ? "O5'1" 2BA 500 B 1 HETATM 27 C "C5'1" 2BA . . . C 2 -24.582 3.9 -16.871 1 18.1 ? "C5'1" 2BA 500 B 1 HETATM 28 C "C4'1" 2BA . . . C 2 -24.654 3.486 -18.346 1 17.89 ? "C4'1" 2BA 500 B 1 HETATM 29 O "O4'1" 2BA . . . C 2 -25.995 3.086 -18.684 1 18.01 ? "O4'1" 2BA 500 B 1 HETATM 30 C "C3'1" 2BA . . . C 2 -24.367 4.551 -19.393 1 18.22 ? "C3'1" 2BA 500 B 1 HETATM 31 O "O3'1" 2BA . . . C 2 -23.599 3.88 -20.378 1 18.61 ? "O3'1" 2BA 500 B 1 HETATM 32 C "C2'1" 2BA . . . C 2 -25.713 4.965 -19.987 1 17.61 ? "C2'1" 2BA 500 B 1 HETATM 33 O "O2'1" 2BA . . . C 2 -25.64 5.385 -21.343 1 17.66 ? "O2'1" 2BA 500 B 1 HETATM 34 C "C1'1" 2BA . . . C 2 -26.462 3.668 -19.94 1 17.27 ? "C1'1" 2BA 500 B 1 HETATM 35 N N91 2BA . . . C 2 -27.944 3.747 -19.986 1 16.2 ? N91 2BA 500 B 1 HETATM 36 C C81 2BA . . . C 2 -28.718 4.589 -19.276 1 16.59 ? C81 2BA 500 B 1 HETATM 37 N N71 2BA . . . C 2 -30.044 4.336 -19.483 1 16.24 ? N71 2BA 500 B 1 HETATM 38 C C51 2BA . . . C 2 -30.125 3.311 -20.342 1 15.62 ? C51 2BA 500 B 1 HETATM 39 C C61 2BA . . . C 2 -31.241 2.57 -20.983 1 15.39 ? C61 2BA 500 B 1 HETATM 40 N N61 2BA . . . C 2 -32.551 2.899 -20.735 1 15.03 ? N61 2BA 500 B 1 HETATM 41 N N11 2BA . . . C 2 -30.883 1.56 -21.812 1 15.04 ? N11 2BA 500 B 1 HETATM 42 C C21 2BA . . . C 2 -29.583 1.253 -22.064 1 14.86 ? C21 2BA 500 B 1 HETATM 43 N N31 2BA . . . C 2 -28.541 1.902 -21.516 1 14.79 ? N31 2BA 500 B 1 HETATM 44 C C41 2BA . . . C 2 -28.742 2.916 -20.659 1 15.46 ? C41 2BA 500 B 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 44 #