data_7EM7 # _model_server_result.job_id GbwR4gH24JVxItTAKvAQAw _model_server_result.datetime_utc '2024-11-24 23:34:27' _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":"C","auth_seq_id":501}' # _entry.id 7EM7 # _exptl.entry_id 7EM7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 444.185 _entity.id 2 _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]methyl 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 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 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 CZC . A . C 2 45.799 57.938 -1.516 0.5 101.78 ? C1 CZC 501 A 1 HETATM 2 C C1 CZC . B . C 2 42.584 59.42 -0.128 0.5 103.95 ? C1 CZC 501 A 1 HETATM 3 C C2 CZC . A . C 2 44.788 60.022 -2.3 0.5 106.83 ? C2 CZC 501 A 1 HETATM 4 C C2 CZC . B . C 2 43.664 60.397 -2.07 0.5 108.77 ? C2 CZC 501 A 1 HETATM 5 C C3 CZC . A . C 2 43.812 59.869 -1.397 0.5 106.16 ? C3 CZC 501 A 1 HETATM 6 C C3 CZC . B . C 2 44.72 59.611 -1.849 0.5 106.18 ? C3 CZC 501 A 1 HETATM 7 C C4 CZC . A . C 2 45.246 61.897 -4.109 0.5 112.4 ? C4 CZC 501 A 1 HETATM 8 C C4 CZC . B . C 2 43.163 62.195 -3.904 0.5 115.55 ? C4 CZC 501 A 1 HETATM 9 C C5 CZC . A . C 2 44.746 61.518 -5.499 0.5 113.65 ? C5 CZC 501 A 1 HETATM 10 C C5 CZC . B . C 2 43.763 63.583 -3.76 0.5 115.2 ? C5 CZC 501 A 1 HETATM 11 C C6 CZC . A . C 2 45.336 62.655 -6.27 0.5 116.74 ? C6 CZC 501 A 1 HETATM 12 C C6 CZC . B . C 2 43.039 64.236 -4.897 0.5 119.77 ? C6 CZC 501 A 1 HETATM 13 C C7 CZC . A . C 2 44.8 63.815 -5.419 0.5 117.55 ? C7 CZC 501 A 1 HETATM 14 C C7 CZC . B . C 2 43.475 63.239 -5.996 0.5 118.79 ? C7 CZC 501 A 1 HETATM 15 C C8 CZC . A . C 2 43.3 64.062 -5.718 0.5 119.95 ? C8 CZC 501 A 1 HETATM 16 C C8 CZC . B . C 2 44.986 63.367 -6.32 0.5 117.78 ? C8 CZC 501 A 1 HETATM 17 C C9 CZC . A . C 2 43.772 58.828 -0.562 0.5 102.38 ? C9 CZC 501 A 1 HETATM 18 C C9 CZC . B . C 2 44.76 58.749 -0.832 0.5 102.34 ? C9 CZC 501 A 1 HETATM 19 C C10 CZC . A . C 2 43.431 61.691 -2.486 0.5 112.06 ? C10 CZC 501 A 1 HETATM 20 C C10 CZC . B . C 2 45.137 60.807 -3.595 0.5 111.17 ? C10 CZC 501 A 1 HETATM 21 N N1 CZC . A . C 2 44.758 57.839 -0.592 0.5 100.64 ? N1 CZC 501 A 1 HETATM 22 N N1 CZC . B . C 2 43.699 58.625 0.057 0.5 99.83 ? N1 CZC 501 A 1 HETATM 23 N N2 CZC . A . C 2 45.813 59.052 -2.381 0.5 105.99 ? N2 CZC 501 A 1 HETATM 24 N N2 CZC . B . C 2 42.562 60.318 -1.208 0.5 108.5 ? N2 CZC 501 A 1 HETATM 25 N N3 CZC . A . C 2 42.983 60.899 -1.521 0.5 108.73 ? N3 CZC 501 A 1 HETATM 26 N N3 CZC . B . C 2 45.623 59.867 -2.794 0.5 107.4 ? N3 CZC 501 A 1 HETATM 27 N N4 CZC . A . C 2 44.548 61.161 -2.977 0.5 110.67 ? N4 CZC 501 A 1 HETATM 28 N N4 CZC . B . C 2 43.927 61.143 -3.153 0.5 112.76 ? N4 CZC 501 A 1 HETATM 29 O O1 CZC . A . C 2 46.671 57.064 -1.567 0.5 98.27 ? O1 CZC 501 A 1 HETATM 30 O O1 CZC . B . C 2 41.641 59.323 0.657 0.5 104.8 ? O1 CZC 501 A 1 HETATM 31 O O2 CZC . A . C 2 45.321 60.271 -5.925 0.5 111.41 ? O2 CZC 501 A 1 HETATM 32 O O2 CZC . B . C 2 43.392 64.165 -2.51 0.5 114.36 ? O2 CZC 501 A 1 HETATM 33 O O3 CZC . A . C 2 46.759 62.581 -6.177 0.5 119.74 ? O3 CZC 501 A 1 HETATM 34 O O3 CZC . B . C 2 41.612 64.166 -4.658 0.5 119.6 ? O3 CZC 501 A 1 HETATM 35 O O4 CZC . A . C 2 45.006 63.351 -4.037 0.5 113.07 ? O4 CZC 501 A 1 HETATM 36 O O4 CZC . B . C 2 43.216 61.949 -5.364 0.5 118.4 ? O4 CZC 501 A 1 HETATM 37 O O5 CZC . A . C 2 42.886 65.393 -5.318 0.5 122.67 ? O5 CZC 501 A 1 HETATM 38 O O5 CZC . B . C 2 45.407 62.389 -7.302 0.5 118.14 ? O5 CZC 501 A 1 HETATM 39 O O6 CZC . A . C 2 42.863 58.72 0.259 0.5 101.72 ? O6 CZC 501 A 1 HETATM 40 O O6 CZC . B . C 2 45.742 58.032 -0.663 0.5 100.61 ? O6 CZC 501 A 1 HETATM 41 O O7 CZC . A . C 2 41.318 65.406 -7.424 0.5 122.2 ? O7 CZC 501 A 1 HETATM 42 O O7 CZC . B . C 2 46.675 63.717 -9.2 0.5 124.56 ? O7 CZC 501 A 1 HETATM 43 O O8 CZC . A . C 2 40.313 65.641 -5.059 0.5 127.37 ? O8 CZC 501 A 1 HETATM 44 O O8 CZC . B . C 2 47.912 63.116 -7.056 0.5 122.31 ? O8 CZC 501 A 1 HETATM 45 O O9 CZC . A . C 2 41.662 67.572 -6.08 0.5 125.81 ? O9 CZC 501 A 1 HETATM 46 O O9 CZC . B . C 2 47.375 61.239 -8.673 0.5 122.72 ? O9 CZC 501 A 1 HETATM 47 O O10 CZC . A . C 2 40.795 67.473 -8.865 0.5 124.2 ? O10 CZC 501 A 1 HETATM 48 O O10 CZC . B . C 2 46.38 64.226 -11.742 0.5 121.81 ? O10 CZC 501 A 1 HETATM 49 O O11 CZC . A . C 2 43.268 66.786 -8.499 0.5 118.68 ? O11 CZC 501 A 1 HETATM 50 O O11 CZC . B . C 2 45.186 62.24 -10.773 0.5 118.01 ? O11 CZC 501 A 1 HETATM 51 O O12 CZC . A . C 2 41.728 65.373 -10.014 0.5 119.9 ? O12 CZC 501 A 1 HETATM 52 O O12 CZC . B . C 2 44.42 64.626 -10.097 0.5 116.37 ? O12 CZC 501 A 1 HETATM 53 P P1 CZC . A . C 2 41.568 66.096 -5.971 0.5 123.84 ? P1 CZC 501 A 1 HETATM 54 P P1 CZC . B . C 2 46.844 62.51 -8.104 0.5 123.78 ? P1 CZC 501 A 1 HETATM 55 P P2 CZC . A . C 2 41.779 66.189 -8.769 0.5 125.43 ? P2 CZC 501 A 1 HETATM 56 P P2 CZC . B . C 2 45.588 63.759 -10.405 0.5 117.63 ? P2 CZC 501 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 66 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 982 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 56 #