data_7EM7 # _model_server_result.job_id 9t59mQ1w52KrWO5G2FNyhA _model_server_result.datetime_utc '2024-11-14 23:22:11' _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 7em7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 7EM7 # _exptl.entry_id 7EM7 _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 7EM7 _cell.length_a 109.213 _cell.length_b 185.857 _cell.length_c 106.961 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EM7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall 'C 2c 2' _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 _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 7EM7 _atom_sites.fract_transf_matrix[1][1] 0.009156 _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] 0.00538 _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] 0.009349 _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 CZF . D 3 CZF A 1 502 502 CZF CZF . # 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 51.95 49.445 -22.448 1 108.23 ? C1 CZF 502 A 1 HETATM 2 C C2 CZF . . . D 3 56.562 49.13 -21.475 1 110.11 ? C2 CZF 502 A 1 HETATM 3 C C3 CZF . . . D 3 51.952 50.047 -23.838 1 109.73 ? C3 CZF 502 A 1 HETATM 4 C C4 CZF . . . D 3 50.809 51.02 -23.549 1 111.19 ? C4 CZF 502 A 1 HETATM 5 C C5 CZF . . . D 3 54.288 48.39 -21.84 1 107.21 ? C5 CZF 502 A 1 HETATM 6 C C6 CZF . . . D 3 49.775 50.096 -22.836 1 107.31 ? C6 CZF 502 A 1 HETATM 7 C C7 CZF . . . D 3 54.692 47.116 -21.596 1 110.23 ? C7 CZF 502 A 1 HETATM 8 C C8 CZF . . . D 3 48.493 49.831 -23.643 1 103.43 ? C8 CZF 502 A 1 HETATM 9 C C9 CZF . . . D 3 55.97 46.799 -21.294 1 107.6 ? C9 CZF 502 A 1 HETATM 10 C C10 CZF . . . D 3 52.578 47.103 -22.03 1 109.43 ? C10 CZF 502 A 1 HETATM 11 N N1 CZF . . . D 3 56.945 47.797 -21.223 1 109.65 ? N1 CZF 502 A 1 HETATM 12 N N2 CZF . . . D 3 55.214 49.439 -21.783 1 106.61 ? N2 CZF 502 A 1 HETATM 13 N N3 CZF . . . D 3 53.618 46.328 -21.717 1 109.62 ? N3 CZF 502 A 1 HETATM 14 N N4 CZF . . . D 3 52.976 48.377 -22.121 1 106.87 ? N4 CZF 502 A 1 HETATM 15 O O1 CZF . . . D 3 57.406 50.027 -21.414 1 113.48 ? O1 CZF 502 A 1 HETATM 16 O O2 CZF . . . D 3 53.157 50.746 -24.173 1 105.85 ? O2 CZF 502 A 1 HETATM 17 O O3 CZF . . . D 3 51.274 51.98 -22.583 1 107.67 ? O3 CZF 502 A 1 HETATM 18 O O4 CZF . . . D 3 50.572 48.901 -22.565 1 108.17 ? O4 CZF 502 A 1 HETATM 19 O O5 CZF . . . D 3 48.06 48.487 -23.499 1 97.4 ? O5 CZF 502 A 1 HETATM 20 O O6 CZF . . . D 3 56.309 45.634 -21.081 1 105.67 ? O6 CZF 502 A 1 HETATM 21 O O7 CZF . . . D 3 47.437 46.364 -24.971 1 121.56 ? O7 CZF 502 A 1 HETATM 22 O O8 CZF . . . D 3 49.145 48.077 -25.965 1 112.22 ? O8 CZF 502 A 1 HETATM 23 O O9 CZF . . . D 3 49.769 46.647 -23.916 1 114.1 ? O9 CZF 502 A 1 HETATM 24 O O10 CZF . . . D 3 46.941 45.985 -27.527 1 123.96 ? O10 CZF 502 A 1 HETATM 25 O O11 CZF . . . D 3 46.681 43.971 -25.813 1 114.79 ? O11 CZF 502 A 1 HETATM 26 O O12 CZF . . . D 3 49.014 44.775 -26.331 1 104.86 ? O12 CZF 502 A 1 HETATM 27 O O13 CZF . . . D 3 44.415 45.421 -26.906 1 123.58 ? O13 CZF 502 A 1 HETATM 28 O O14 CZF . . . D 3 45.236 47.953 -26.982 1 109.95 ? O14 CZF 502 A 1 HETATM 29 O O15 CZF . . . D 3 44.878 46.513 -29.118 1 122.53 ? O15 CZF 502 A 1 HETATM 30 P P1 CZF . . . D 3 48.659 47.382 -24.544 1 122.21 ? P1 CZF 502 A 1 HETATM 31 P P2 CZF . . . D 3 47.613 45.251 -26.172 1 118.7 ? P2 CZF 502 A 1 HETATM 32 P P3 CZF . . . D 3 45.354 46.488 -27.708 1 125.33 ? P3 CZF 502 A 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 32 #