data_7EM5 # _model_server_result.job_id uG0uyommJlYlkcJ9fisgnA _model_server_result.datetime_utc '2024-11-24 23:27:28' _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 7em5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 7EM5 # _exptl.entry_id 7EM5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 524.165 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate' _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 7EM5 _cell.length_a 109.561 _cell.length_b 186.153 _cell.length_c 105.655 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EM5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 _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 'C10 H15 N4 O15 P3' _chem_comp.formula_weight 524.165 _chem_comp.id CZF _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'xanthosine triphosphate' # 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 O15 P3 CZF doub 127 n n P3 O10 CZF sing 128 n n P3 O14 CZF sing 129 n n P3 O13 CZF sing 130 n n O10 P2 CZF sing 131 n n O12 P2 CZF doub 132 n n P2 O11 CZF sing 133 n n P2 O7 CZF sing 134 n n O8 P1 CZF doub 135 n n O7 P1 CZF sing 136 n n P1 O9 CZF sing 137 n n P1 O5 CZF sing 138 n n O5 C8 CZF sing 139 n n C8 C6 CZF sing 140 n n C4 C3 CZF sing 141 n n C4 C6 CZF sing 142 n n C4 O3 CZF sing 143 n n C3 O2 CZF sing 144 n n C3 C1 CZF sing 145 n n O4 C6 CZF sing 146 n n O4 C1 CZF sing 147 n n C1 N4 CZF sing 148 n n N4 C10 CZF sing 149 n y N4 C5 CZF sing 150 n y C10 N3 CZF doub 151 n y C5 N2 CZF sing 152 n n C5 C7 CZF doub 153 n y N3 C7 CZF sing 154 n y N2 C2 CZF sing 155 n n C7 C9 CZF sing 156 n n C2 O1 CZF doub 157 n n C2 N1 CZF sing 158 n n C9 N1 CZF sing 159 n n C9 O6 CZF doub 160 n n C1 H1 CZF sing 161 n n C3 H2 CZF sing 162 n n C4 H3 CZF sing 163 n n C6 H4 CZF sing 164 n n C8 H5 CZF sing 165 n n C8 H6 CZF sing 166 n n C10 H7 CZF sing 167 n n N1 H8 CZF sing 168 n n N2 H9 CZF sing 169 n n O2 H10 CZF sing 170 n n O3 H11 CZF sing 171 n n O9 H12 CZF sing 172 n n O11 H13 CZF sing 173 n n O13 H14 CZF sing 174 n n O14 H15 CZF sing 175 n n # _atom_sites.entry_id 7EM5 _atom_sites.fract_transf_matrix[1][1] 0.009127 _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] 0.005372 _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] 0.009465 _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 CZC A 1 501 501 CZC CZC . D 3 CZF A 1 502 502 CZF CZF . E 2 CZC B 1 501 501 CZC CZC . F 4 HOH A 1 601 601 HOH HOH . F 4 HOH A 2 602 602 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 C1 CZF . . . D 3 52.861 49.581 -22.431 1 102.04 ? C1 CZF 502 A 1 HETATM 2 C C2 CZF . . . D 3 57.294 48.605 -21.513 1 95.27 ? C2 CZF 502 A 1 HETATM 3 C C3 CZF . . . D 3 52.657 49.62 -23.939 1 111.29 ? C3 CZF 502 A 1 HETATM 4 C C4 CZF . . . D 3 51.743 50.809 -24.012 1 122.26 ? C4 CZF 502 A 1 HETATM 5 C C5 CZF . . . D 3 54.92 48.188 -21.807 1 96.56 ? C5 CZF 502 A 1 HETATM 6 C C6 CZF . . . D 3 50.756 50.409 -22.886 1 114.17 ? C6 CZF 502 A 1 HETATM 7 C C7 CZF . . . D 3 55.114 46.893 -21.516 1 96.38 ? C7 CZF 502 A 1 HETATM 8 C C8 CZF . . . D 3 49.453 49.887 -23.53 1 109.61 ? C8 CZF 502 A 1 HETATM 9 C C9 CZF . . . D 3 56.329 46.41 -21.232 1 96.8 ? C9 CZF 502 A 1 HETATM 10 C C10 CZF . . . D 3 53.015 47.192 -21.913 1 95.54 ? C10 CZF 502 A 1 HETATM 11 N N1 CZF . . . D 3 57.455 47.246 -21.22 1 95.78 ? N1 CZF 502 A 1 HETATM 12 N N2 CZF . . . D 3 56.01 49.076 -21.812 1 100.32 ? N2 CZF 502 A 1 HETATM 13 N N3 CZF . . . D 3 53.928 46.286 -21.583 1 93.86 ? N3 CZF 502 A 1 HETATM 14 N N4 CZF . . . D 3 53.616 48.371 -22.043 1 96.61 ? N4 CZF 502 A 1 HETATM 15 O O1 CZF . . . D 3 58.249 49.385 -21.505 1 94.54 ? O1 CZF 502 A 1 HETATM 16 O O2 CZF . . . D 3 53.869 49.848 -24.672 1 109.34 ? O2 CZF 502 A 1 HETATM 17 O O3 CZF . . . D 3 52.462 51.998 -23.654 1 138.89 ? O3 CZF 502 A 1 HETATM 18 O O4 CZF . . . D 3 51.484 49.417 -22.093 1 107.92 ? O4 CZF 502 A 1 HETATM 19 O O5 CZF . . . D 3 48.82 48.835 -22.822 1 98.42 ? O5 CZF 502 A 1 HETATM 20 O O6 CZF . . . D 3 56.469 45.216 -20.976 1 99.98 ? O6 CZF 502 A 1 HETATM 21 O O7 CZF . . . D 3 47.968 47.199 -24.765 1 125.13 ? O7 CZF 502 A 1 HETATM 22 O O8 CZF . . . D 3 50.329 47.161 -24.026 1 103.29 ? O8 CZF 502 A 1 HETATM 23 O O9 CZF . . . D 3 48.601 46.383 -22.309 1 102.88 ? O9 CZF 502 A 1 HETATM 24 O O10 CZF . . . D 3 47.03 45.345 -26.554 1 141.75 ? O10 CZF 502 A 1 HETATM 25 O O11 CZF . . . D 3 49.451 45.069 -25.576 1 124.72 ? O11 CZF 502 A 1 HETATM 26 O O12 CZF . . . D 3 49.009 47.006 -27.169 1 142 ? O12 CZF 502 A 1 HETATM 27 O O13 CZF . . . D 3 44.66 44.687 -27.649 1 141.82 ? O13 CZF 502 A 1 HETATM 28 O O14 CZF . . . D 3 45.19 47.182 -27.205 1 141.89 ? O14 CZF 502 A 1 HETATM 29 O O15 CZF . . . D 3 46.397 45.959 -29.059 1 147.9 ? O15 CZF 502 A 1 HETATM 30 P P1 CZF . . . D 3 48.879 47.362 -23.385 1 100.37 ? P1 CZF 502 A 1 HETATM 31 P P2 CZF . . . D 3 48.4 46.212 -26.077 1 137.17 ? P2 CZF 502 A 1 HETATM 32 P P3 CZF . . . D 3 45.868 45.804 -27.685 1 143.37 ? P3 CZF 502 A 1 # _model_server_stats.io_time_ms 76 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #