data_1I5D # _model_server_result.job_id WNjf-3xt2nbrNDQmJ6w2Lw _model_server_result.datetime_utc '2025-08-30 23:30:56' _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 1i5d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":999}' # _entry.id 1I5D # _exptl.entry_id 1I5D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 718.27 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE" _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 1I5D _cell.length_a 85.19 _cell.length_b 85.19 _cell.length_c 73.77 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1I5D _symmetry.cell_setting tetragonal _symmetry.Int_Tables_number 95 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C16 H17 N8 O19 P3' _chem_comp.formula_weight 718.27 _chem_comp.id 128 _chem_comp.mon_nstd_flag . _chem_comp.name "SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE" _chem_comp.type 'rna linking' _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 PG O1G 128 doub 1 n n PG O2G 128 sing 2 n n PG O3G 128 sing 3 n n PG O3B 128 sing 4 n n O2G HOG2 128 sing 5 n n O3G HOG3 128 sing 6 n n PB O1B 128 doub 7 n n PB O2B 128 sing 8 n n PB O3B 128 sing 9 n n PB O3A 128 sing 10 n n O2B HOB2 128 sing 11 n n PA O1A 128 doub 12 n n PA O2A 128 sing 13 n n PA O3A 128 sing 14 n n PA O5' 128 sing 15 n n O2A HOA2 128 sing 16 n n O5' C5' 128 sing 17 n n C5' C4' 128 sing 18 n n C5' H5' 128 sing 19 n n C5' "H5''" 128 sing 20 n n C4' O4' 128 sing 21 n n C4' C3' 128 sing 22 n n C4' H4' 128 sing 23 n n O4' C1' 128 sing 24 n n C3' O3' 128 sing 25 n n C3' C2' 128 sing 26 n n C3' H3' 128 sing 27 n n O3' C1F 128 sing 28 n n C2' O2' 128 sing 29 n n C2' C1' 128 sing 30 n n C2' H2' 128 sing 31 n n O2' C1F 128 sing 32 n n C1' N9 128 sing 33 n n C1' H1' 128 sing 34 n n N9 C8 128 sing 35 n y N9 C4 128 sing 36 n y C8 N7 128 doub 37 n y C8 H8 128 sing 38 n n N7 C5 128 sing 39 n y C5 C6 128 sing 40 n y C5 C4 128 doub 41 n y C6 N6 128 sing 42 n n C6 N1 128 doub 43 n y N6 HN61 128 sing 44 n n N6 HN62 128 sing 45 n n N1 C2 128 sing 46 n y C2 N3 128 doub 47 n y C2 H2 128 sing 48 n n N3 C4 128 sing 49 n y C1F C2F 128 sing 50 n n C1F C6F 128 sing 51 n n C2F C3F 128 doub 52 n n C2F N2F 128 sing 53 n n C3F C4F 128 sing 54 n n C3F H3F 128 sing 55 n n C4F C5F 128 sing 56 n n C4F N4F 128 doub 57 n n O4F H4F 128 sing 58 n n C5F C6F 128 doub 59 n n C5F H5F 128 sing 60 n n C6F N6F 128 sing 61 n n N2F O2F 128 doub 62 n n N2F O3F 128 sing 63 n n N4F O4F 128 sing 64 n n N4F O5F 128 sing 65 n n N6F O6F 128 doub 66 n n N6F O7F 128 sing 67 n n # _atom_sites.entry_id 1I5D _atom_sites.fract_transf_matrix[1][1] 0.011738 _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] 0.011738 _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] 0.013556 _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 SO4 A 1 1 1 SO4 SO4 . C 2 SO4 A 1 2 2 SO4 SO4 . D 3 128 A 1 999 999 128 128 . E 4 HOH A 1 5 5 HOH HOH . E 4 HOH A 2 6 6 HOH HOH . E 4 HOH A 3 7 7 HOH HOH . E 4 HOH A 4 8 8 HOH HOH . E 4 HOH A 5 9 9 HOH HOH . E 4 HOH A 6 10 10 HOH HOH . E 4 HOH A 7 11 11 HOH HOH . E 4 HOH A 8 12 12 HOH HOH . E 4 HOH A 9 13 13 HOH HOH . E 4 HOH A 10 14 14 HOH HOH . E 4 HOH A 11 15 15 HOH HOH . E 4 HOH A 12 16 16 HOH HOH . E 4 HOH A 13 17 17 HOH HOH . E 4 HOH A 14 18 18 HOH HOH . E 4 HOH A 15 19 19 HOH HOH . E 4 HOH A 16 20 20 HOH HOH . E 4 HOH A 17 21 21 HOH HOH . E 4 HOH A 18 22 22 HOH HOH . E 4 HOH A 19 23 23 HOH HOH . E 4 HOH A 20 24 24 HOH HOH . E 4 HOH A 21 25 25 HOH HOH . E 4 HOH A 22 26 26 HOH HOH . E 4 HOH A 23 27 27 HOH HOH . E 4 HOH A 24 29 29 HOH HOH . E 4 HOH A 25 30 30 HOH HOH . E 4 HOH A 26 31 31 HOH HOH . E 4 HOH A 27 32 32 HOH HOH . E 4 HOH A 28 33 33 HOH HOH . E 4 HOH A 29 34 34 HOH HOH . E 4 HOH A 30 35 35 HOH HOH . E 4 HOH A 31 36 36 HOH HOH . E 4 HOH A 32 37 37 HOH HOH . E 4 HOH A 33 38 38 HOH HOH . E 4 HOH A 34 39 39 HOH HOH . E 4 HOH A 35 40 40 HOH HOH . E 4 HOH A 36 41 41 HOH HOH . E 4 HOH A 37 42 42 HOH HOH . E 4 HOH A 38 43 43 HOH HOH . E 4 HOH A 39 44 44 HOH HOH . E 4 HOH A 40 45 45 HOH HOH . E 4 HOH A 41 46 46 HOH HOH . E 4 HOH A 42 47 47 HOH HOH . E 4 HOH A 43 94 94 HOH HOH . E 4 HOH A 44 95 95 HOH HOH . E 4 HOH A 45 96 96 HOH HOH . E 4 HOH A 46 97 97 HOH HOH . E 4 HOH A 47 98 98 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 PG 128 . . . D 3 12.178 64.572 12.762 1 171.99 ? PG 128 999 A 1 HETATM 2 O O1G 128 . . . D 3 13.105 64.54 11.548 1 171.11 ? O1G 128 999 A 1 HETATM 3 O O2G 128 . . . D 3 12.74 63.706 13.882 1 168.48 ? O2G 128 999 A 1 HETATM 4 O O3G 128 . . . D 3 11.613 65.972 13.203 1 175.42 ? O3G 128 999 A 1 HETATM 5 P PB 128 . . . D 3 9.506 64.044 11.199 1 177.8 ? PB 128 999 A 1 HETATM 6 O O1B 128 . . . D 3 10.301 64.699 10.05 1 178.81 ? O1B 128 999 A 1 HETATM 7 O O2B 128 . . . D 3 8.309 64.832 11.713 1 180.38 ? O2B 128 999 A 1 HETATM 8 O O3B 128 . . . D 3 10.649 63.852 12.341 1 175.93 ? O3B 128 999 A 1 HETATM 9 P PA 128 . . . D 3 7.864 61.441 11.015 1 171.58 ? PA 128 999 A 1 HETATM 10 O O1A 128 . . . D 3 7.076 61.92 12.29 1 166.23 ? O1A 128 999 A 1 HETATM 11 O O2A 128 . . . D 3 6.954 60.885 9.95 1 169.97 ? O2A 128 999 A 1 HETATM 12 O O3A 128 . . . D 3 8.72 62.684 10.506 1 173.88 ? O3A 128 999 A 1 HETATM 13 O O5' 128 . . . D 3 9.071 60.587 11.746 1 161.81 ? O5' 128 999 A 1 HETATM 14 C C5' 128 . . . D 3 9.957 61.195 12.796 1 140.26 ? C5' 128 999 A 1 HETATM 15 C C4' 128 . . . D 3 11.301 60.3 12.755 1 127.58 ? C4' 128 999 A 1 HETATM 16 O O4' 128 . . . D 3 11.638 59.758 14.039 1 121.73 ? O4' 128 999 A 1 HETATM 17 C C3' 128 . . . D 3 11.372 59.14 11.902 1 124.37 ? C3' 128 999 A 1 HETATM 18 O O3' 128 . . . D 3 12.594 59.262 11.203 1 137.8 ? O3' 128 999 A 1 HETATM 19 C C2' 128 . . . D 3 11.585 57.905 12.803 1 115.89 ? C2' 128 999 A 1 HETATM 20 O O2' 128 . . . D 3 12.482 56.946 12.199 1 122.34 ? O2' 128 999 A 1 HETATM 21 C C1' 128 . . . D 3 12.122 58.446 14.165 1 114.55 ? C1' 128 999 A 1 HETATM 22 N N9 128 . . . D 3 11.312 57.778 15.377 1 109.56 ? N9 128 999 A 1 HETATM 23 C C8 128 . . . D 3 11.757 57.676 16.665 1 104.64 ? C8 128 999 A 1 HETATM 24 N N7 128 . . . D 3 10.842 57.07 17.433 1 95.36 ? N7 128 999 A 1 HETATM 25 C C5 128 . . . D 3 9.815 56.783 16.629 1 94.03 ? C5 128 999 A 1 HETATM 26 C C6 128 . . . D 3 8.565 56.139 16.942 1 84.94 ? C6 128 999 A 1 HETATM 27 N N6 128 . . . D 3 8.329 55.717 18.198 1 62.11 ? N6 128 999 A 1 HETATM 28 N N1 128 . . . D 3 7.623 55.943 15.935 1 79.35 ? N1 128 999 A 1 HETATM 29 C C2 128 . . . D 3 7.939 56.393 14.693 1 87.43 ? C2 128 999 A 1 HETATM 30 N N3 128 . . . D 3 9.109 57.001 14.406 1 104.47 ? N3 128 999 A 1 HETATM 31 C C4 128 . . . D 3 10.084 57.222 15.339 1 102.68 ? C4 128 999 A 1 HETATM 32 C C1F 128 . . . D 3 13.043 57.851 11.131 1 138.14 ? C1F 128 999 A 1 HETATM 33 C C2F 128 . . . D 3 12.697 57.105 9.928 1 144.9 ? C2F 128 999 A 1 HETATM 34 C C3F 128 . . . D 3 13.628 56.738 9.019 1 152.09 ? C3F 128 999 A 1 HETATM 35 C C4F 128 . . . D 3 14.957 56.991 9.104 1 155.98 ? C4F 128 999 A 1 HETATM 36 C C5F 128 . . . D 3 15.365 57.68 10.226 1 148.43 ? C5F 128 999 A 1 HETATM 37 C C6F 128 . . . D 3 14.459 58.131 11.267 1 140.77 ? C6F 128 999 A 1 HETATM 38 N N2F 128 . . . D 3 11.346 56.728 9.649 1 149.11 ? N2F 128 999 A 1 HETATM 39 N N4F 128 . . . D 3 15.889 56.644 8.231 1 161.76 ? N4F 128 999 A 1 HETATM 40 N N6F 128 . . . D 3 15.05 58.812 12.333 1 137.24 ? N6F 128 999 A 1 HETATM 41 O O2F 128 . . . D 3 10.415 56.991 10.363 1 153.45 ? O2F 128 999 A 1 HETATM 42 O O3F 128 . . . D 3 11.078 56.117 8.639 1 153.98 ? O3F 128 999 A 1 HETATM 43 O O4F 128 . . . D 3 17.06 56.908 8.367 1 161.98 ? O4F 128 999 A 1 HETATM 44 O O5F 128 . . . D 3 15.613 56.057 7.236 1 167.14 ? O5F 128 999 A 1 HETATM 45 O O6F 128 . . . D 3 16.25 58.976 12.322 1 130.38 ? O6F 128 999 A 1 HETATM 46 O O7F 128 . . . D 3 14.464 59.262 13.267 1 131.02 ? O7F 128 999 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 46 #