data_4Y4M # _model_server_result.job_id tAqgvgEaB1Mx6uB6QosoEA _model_server_result.datetime_utc '2025-07-16 19:04:58' _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 4y4m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":301}' # _entry.id 4Y4M # _exptl.entry_id 4Y4M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 2 _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] [(2R,3R)-2,3,5-tris(oxidanyl)-4-oxidanylidene-pentyl] hydrogen phosphate' _entity.pdbx_number_of_molecules 8 _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 120 _cell.entry_id 4Y4M _cell.length_a 180.76 _cell.length_b 180.76 _cell.length_c 73.328 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y4M _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 I N N ? 2 K N N ? 2 L N N ? 2 N N N ? 2 O N N ? 2 P N N ? 2 R N N ? 2 T N N # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id 48F _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] [(2R,3R)-2,3,5-tris(oxidanyl)-4-oxidanylidene-pentyl] hydrogen phosphate' _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 O3' C3' 48F sing 1 n n O2' C2' 48F sing 2 n n C3' C2' 48F sing 3 n n C3' C4' 48F sing 4 n n C2' C1' 48F sing 5 n n C4' C5' 48F sing 6 n n C4' O4' 48F sing 7 n n C1' N9 48F sing 8 n n C1' O4' 48F sing 9 n n O2A PA 48F doub 10 n n O4D C4D 48F sing 11 n n N3 C2 48F doub 12 n y N3 C4 48F sing 13 n y C2 N1 48F sing 14 n y C5' O5' 48F sing 15 n n N9 C4 48F sing 16 n y N9 C8 48F sing 17 n y C4 C5 48F doub 18 n y O5' PA 48F sing 19 n n PA O1A 48F sing 20 n n PA O3A 48F sing 21 n n N1 C6 48F doub 22 n y C4D C3D 48F sing 23 n n C4D C5D 48F sing 24 n n C8 N7 48F doub 25 n y C3D O3D 48F sing 26 n n C3D C2D 48F sing 27 n n C5 C6 48F sing 28 n y C5 N7 48F sing 29 n y C6 N6 48F sing 30 n n O5D C5D 48F sing 31 n n O5D PB 48F sing 32 n n O3A PB 48F sing 33 n n C2D O2D 48F doub 34 n n C2D C1D 48F sing 35 n n O1B PB 48F doub 36 n n PB O2B 48F sing 37 n n O1D C1D 48F sing 38 n n O1A H1 48F sing 39 n n C5D H2 48F sing 40 n n C5D H3 48F sing 41 n n C4D H4 48F sing 42 n n O4D H5 48F sing 43 n n C3D H6 48F sing 44 n n C1D H7 48F sing 45 n n C1D H8 48F sing 46 n n O1D H9 48F sing 47 n n O3D H10 48F sing 48 n n O2B H11 48F sing 49 n n C5' H12 48F sing 50 n n C5' H13 48F sing 51 n n C4' H14 48F sing 52 n n C1' H15 48F sing 53 n n C2' H16 48F sing 54 n n O2' H17 48F sing 55 n n C3' H18 48F sing 56 n n O3' H19 48F sing 57 n n C8 H20 48F sing 58 n n N6 H21 48F sing 59 n n N6 H22 48F sing 60 n n C2 H23 48F sing 61 n n # _atom_sites.entry_id 4Y4M _atom_sites.fract_transf_matrix[1][1] 0.005532 _atom_sites.fract_transf_matrix[1][2] 0.003194 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006388 _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] 0.013637 _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 I 2 48F A 1 301 1 48F Apl . J 3 NHE A 1 302 2 NHE NHE . K 2 48F B 1 301 1 48F Apl . L 2 48F C 1 301 1 48F Apl . M 3 NHE C 1 302 2 NHE NHE . N 2 48F D 1 301 1 48F Apl . O 2 48F E 1 301 1 48F Apl . P 2 48F F 1 301 1 48F Apl . Q 3 NHE F 1 302 2 NHE NHE . R 2 48F G 1 301 1 48F Apl . S 3 NHE G 1 302 2 NHE NHE . T 2 48F H 1 301 1 48F Apl . U 3 NHE H 1 302 2 NHE NHE . V 4 HOH B 1 401 5 HOH HOH . V 4 HOH B 2 402 6 HOH HOH . V 4 HOH B 3 403 16 HOH HOH . W 4 HOH C 1 401 10 HOH HOH . W 4 HOH C 2 402 21 HOH HOH . X 4 HOH D 1 401 9 HOH HOH . X 4 HOH D 2 402 17 HOH HOH . Y 4 HOH E 1 401 18 HOH HOH . Z 4 HOH F 1 401 2 HOH HOH . Z 4 HOH F 2 402 3 HOH HOH . Z 4 HOH F 3 403 12 HOH HOH . Z 4 HOH F 4 404 19 HOH HOH . Z 4 HOH F 5 405 20 HOH HOH . AA 4 HOH G 1 401 1 HOH HOH . AA 4 HOH G 2 402 4 HOH HOH . AA 4 HOH G 3 403 7 HOH HOH . AA 4 HOH G 4 404 8 HOH HOH . AA 4 HOH G 5 405 11 HOH HOH . AA 4 HOH G 6 406 13 HOH HOH . AA 4 HOH G 7 407 14 HOH HOH . AA 4 HOH G 8 408 15 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 O O1A 48F . . . O 2 24.732 -30.726 -1.736 1 63.6 ? O1A 48F 301 E 1 HETATM 2 P PA 48F . . . O 2 23.295 -30.739 -2.236 1 64.86 ? PA 48F 301 E 1 HETATM 3 O O2A 48F . . . O 2 22.849 -31.896 -3.115 1 62.55 ? O2A 48F 301 E 1 HETATM 4 O O3A 48F . . . O 2 22.339 -30.589 -0.924 1 65.3 ? O3A 48F 301 E 1 HETATM 5 P PB 48F . . . O 2 21.095 -31.497 -0.401 1 56.78 ? PB 48F 301 E 1 HETATM 6 O O1B 48F . . . O 2 19.877 -31.135 -1.216 1 62.18 ? O1B 48F 301 E 1 HETATM 7 O O5D 48F . . . O 2 21.527 -33.04 -0.702 1 70.7 ? O5D 48F 301 E 1 HETATM 8 C C5D 48F . . . O 2 22.757 -33.605 -0.205 1 76.07 ? C5D 48F 301 E 1 HETATM 9 C C4D 48F . . . O 2 23.186 -34.917 -0.901 1 82.27 ? C4D 48F 301 E 1 HETATM 10 O O4D 48F . . . O 2 23.557 -34.69 -2.275 1 72.12 ? O4D 48F 301 E 1 HETATM 11 C C3D 48F . . . O 2 24.39 -35.588 -0.204 1 83.7 ? C3D 48F 301 E 1 HETATM 12 C C2D 48F . . . O 2 24.041 -36.701 0.769 1 89.33 ? C2D 48F 301 E 1 HETATM 13 C C1D 48F . . . O 2 25.185 -37.343 1.58 1 103.35 ? C1D 48F 301 E 1 HETATM 14 O O1D 48F . . . O 2 25.078 -37.311 3.024 1 106.51 ? O1D 48F 301 E 1 HETATM 15 O O2D 48F . . . O 2 22.883 -37.1 0.866 1 82.25 ? O2D 48F 301 E 1 HETATM 16 O O3D 48F . . . O 2 25.176 -34.596 0.479 1 82.04 ? O3D 48F 301 E 1 HETATM 17 O O2B 48F . . . O 2 21.028 -31.228 1.082 1 58.69 ? O2B 48F 301 E 1 HETATM 18 O O5' 48F . . . O 2 22.954 -29.363 -3.003 1 62.86 ? O5' 48F 301 E 1 HETATM 19 C C5' 48F . . . O 2 23.479 -28.127 -2.554 1 64.72 ? C5' 48F 301 E 1 HETATM 20 C C4' 48F . . . O 2 23.406 -27.125 -3.694 1 68.14 ? C4' 48F 301 E 1 HETATM 21 O O4' 48F . . . O 2 23.59 -25.787 -3.204 1 72.14 ? O4' 48F 301 E 1 HETATM 22 C C1' 48F . . . O 2 24.466 -25.047 -4.068 1 68.16 ? C1' 48F 301 E 1 HETATM 23 C C2' 48F . . . O 2 25.392 -26.114 -4.647 1 67.62 ? C2' 48F 301 E 1 HETATM 24 O O2' 48F . . . O 2 25.968 -25.723 -5.898 1 61.86 ? O2' 48F 301 E 1 HETATM 25 C C3' 48F . . . O 2 24.477 -27.337 -4.758 1 69.21 ? C3' 48F 301 E 1 HETATM 26 O O3' 48F . . . O 2 23.815 -27.453 -6.029 1 73.73 ? O3' 48F 301 E 1 HETATM 27 N N9 48F . . . O 2 25.072 -23.959 -3.251 1 64.19 ? N9 48F 301 E 1 HETATM 28 C C8 48F . . . O 2 25.866 -24.094 -2.157 1 64.13 ? C8 48F 301 E 1 HETATM 29 N N7 48F . . . O 2 26.219 -22.88 -1.629 1 56.57 ? N7 48F 301 E 1 HETATM 30 C C5 48F . . . O 2 25.622 -21.943 -2.398 1 58.23 ? C5 48F 301 E 1 HETATM 31 C C4 48F . . . O 2 24.862 -22.661 -3.462 1 59.29 ? C4 48F 301 E 1 HETATM 32 C C6 48F . . . O 2 25.557 -20.456 -2.415 1 53.28 ? C6 48F 301 E 1 HETATM 33 N N6 48F . . . O 2 26.212 -19.733 -1.481 1 49.12 ? N6 48F 301 E 1 HETATM 34 N N1 48F . . . O 2 24.833 -19.868 -3.406 1 53.39 ? N1 48F 301 E 1 HETATM 35 C C2 48F . . . O 2 24.148 -20.58 -4.343 1 56.77 ? C2 48F 301 E 1 HETATM 36 N N3 48F . . . O 2 24.157 -21.942 -4.388 1 58.89 ? N3 48F 301 E 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 412 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #