data_7EM5 # _model_server_result.job_id uVXIKEtuC9FPTGpDf5HbHQ _model_server_result.datetime_utc '2024-11-14 23:33:58' _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 7em5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 7EM5 # _exptl.entry_id 7EM5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 444.185 _entity.id 2 _entity.src_method man _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]methyl phosphono hydrogen phosphate' _entity.pdbx_number_of_molecules 2 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N N # _chem_comp.formula 'C10 H14 N4 O12 P2' _chem_comp.formula_weight 444.185 _chem_comp.id CZC _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]methyl phosphono hydrogen phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'xanthosine diphosphate' # 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 O12 P2 CZC doub 83 n n O11 P2 CZC sing 84 n n P2 O10 CZC sing 85 n n P2 O7 CZC sing 86 n n O7 P1 CZC sing 87 n n C6 O3 CZC sing 88 n n C6 C5 CZC sing 89 n n C6 C7 CZC sing 90 n n O2 C5 CZC sing 91 n n C8 C7 CZC sing 92 n n C8 O5 CZC sing 93 n n O9 P1 CZC doub 94 n n P1 O5 CZC sing 95 n n P1 O8 CZC sing 96 n n C5 C4 CZC sing 97 n n C7 O4 CZC sing 98 n n C4 O4 CZC sing 99 n n C4 N4 CZC sing 100 n n N4 C10 CZC sing 101 n y N4 C2 CZC sing 102 n y C10 N3 CZC doub 103 n y C2 N2 CZC sing 104 n n C2 C3 CZC doub 105 n y N2 C1 CZC sing 106 n n N3 C3 CZC sing 107 n y C3 C9 CZC sing 108 n n C1 O1 CZC doub 109 n n C1 N1 CZC sing 110 n n C9 N1 CZC sing 111 n n C9 O6 CZC doub 112 n n C4 H1 CZC sing 113 n n C5 H2 CZC sing 114 n n C6 H3 CZC sing 115 n n C7 H4 CZC sing 116 n n C8 H5 CZC sing 117 n n C8 H6 CZC sing 118 n n C10 H7 CZC sing 119 n n N1 H8 CZC sing 120 n n N2 H9 CZC sing 121 n n O2 H10 CZC sing 122 n n O3 H11 CZC sing 123 n n O8 H12 CZC sing 124 n n O10 H13 CZC sing 125 n n O11 H14 CZC sing 126 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 CZC . . . E 2 34.621 1.838 -18.898 1 106.64 ? C1 CZC 501 B 1 HETATM 2 C C2 CZC . . . E 2 33.581 2.185 -21.034 1 118.16 ? C2 CZC 501 B 1 HETATM 3 C C3 CZC . . . E 2 32.591 2.874 -20.436 1 118.16 ? C3 CZC 501 B 1 HETATM 4 C C4 CZC . . . E 2 34.077 1.557 -23.508 1 134.82 ? C4 CZC 501 B 1 HETATM 5 C C5 CZC . . . E 2 33.333 0.387 -24.112 1 141.82 ? C5 CZC 501 B 1 HETATM 6 C C6 CZC . . . E 2 33.736 0.431 -25.569 1 146.97 ? C6 CZC 501 B 1 HETATM 7 C C7 CZC . . . E 2 33.502 1.915 -25.778 1 149.12 ? C7 CZC 501 B 1 HETATM 8 C C8 CZC . . . E 2 32.006 2.255 -25.829 1 156.24 ? C8 CZC 501 B 1 HETATM 9 C C9 CZC . . . E 2 32.558 3.078 -19.113 1 109.11 ? C9 CZC 501 B 1 HETATM 10 C C10 CZC . . . E 2 32.209 2.82 -22.553 1 119.96 ? C10 CZC 501 B 1 HETATM 11 N N1 CZC . . . E 2 33.574 2.559 -18.314 1 109.29 ? N1 CZC 501 B 1 HETATM 12 N N2 CZC . . . E 2 34.626 1.652 -20.277 1 114.03 ? N2 CZC 501 B 1 HETATM 13 N N3 CZC . . . E 2 31.746 3.261 -21.389 1 119.81 ? N3 CZC 501 B 1 HETATM 14 N N4 CZC . . . E 2 33.341 2.154 -22.347 1 121.11 ? N4 CZC 501 B 1 HETATM 15 O O1 CZC . . . E 2 35.529 1.378 -18.21 1 97.44 ? O1 CZC 501 B 1 HETATM 16 O O2 CZC . . . E 2 33.801 -0.812 -23.496 1 144.32 ? O2 CZC 501 B 1 HETATM 17 O O3 CZC . . . E 2 35.133 0.118 -25.749 1 149.9 ? O3 CZC 501 B 1 HETATM 18 O O4 CZC . . . E 2 34.171 2.51 -24.613 1 143.48 ? O4 CZC 501 B 1 HETATM 19 O O5 CZC . . . E 2 31.868 3.462 -26.599 1 168.55 ? O5 CZC 501 B 1 HETATM 20 O O6 CZC . . . E 2 31.643 3.709 -18.581 1 109.21 ? O6 CZC 501 B 1 HETATM 21 O O7 CZC . . . E 2 30.504 3.402 -28.884 1 191.49 ? O7 CZC 501 B 1 HETATM 22 O O8 CZC . . . E 2 29.372 2.971 -26.606 1 180.83 ? O8 CZC 501 B 1 HETATM 23 O O9 CZC . . . E 2 30.124 5.332 -27.184 1 181.36 ? O9 CZC 501 B 1 HETATM 24 O O10 CZC . . . E 2 32.293 5.244 -29.377 1 203.08 ? O10 CZC 501 B 1 HETATM 25 O O11 CZC . . . E 2 32.663 2.857 -30.257 1 202.04 ? O11 CZC 501 B 1 HETATM 26 O O12 CZC . . . E 2 30.849 4.391 -31.282 1 200.84 ? O12 CZC 501 B 1 HETATM 27 P P1 CZC . . . E 2 30.475 3.893 -27.319 1 181.09 ? P1 CZC 501 B 1 HETATM 28 P P2 CZC . . . E 2 31.633 3.889 -29.956 1 199.22 ? P2 CZC 501 B 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #