data_7EM2 # _model_server_result.job_id HrcQ9KaODRdXIu9TbB369A _model_server_result.datetime_utc '2024-11-24 23:46:37' _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 7em2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 7EM2 # _exptl.entry_id 7EM2 _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 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 7EM2 _cell.length_a 109.848 _cell.length_b 185.138 _cell.length_c 105.81 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EM2 _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,G _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 7EM2 _atom_sites.fract_transf_matrix[1][1] 0.009103 _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] 0.005401 _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] 0.009451 _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 . G 4 HOH B 1 601 601 HOH HOH . G 4 HOH B 2 602 602 HOH HOH . G 4 HOH B 3 603 603 HOH HOH . G 4 HOH B 4 604 604 HOH HOH . G 4 HOH B 5 605 605 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 . A . E 2 31.978 3.5 -19.297 0.5 128.74 ? C1 CZC 501 B 1 HETATM 2 C C1 CZC . B . E 2 34.892 1.515 -19.149 0.5 126.37 ? C1 CZC 501 B 1 HETATM 3 C C2 CZC . A . E 2 32.871 2.39 -21.263 0.5 130.2 ? C2 CZC 501 B 1 HETATM 4 C C2 CZC . B . E 2 33.694 1.943 -21.194 0.5 130.12 ? C2 CZC 501 B 1 HETATM 5 C C3 CZC . A . E 2 33.831 1.845 -20.51 0.5 129.41 ? C3 CZC 501 B 1 HETATM 6 C C3 CZC . B . E 2 32.715 2.533 -20.495 0.5 129.59 ? C3 CZC 501 B 1 HETATM 7 C C4 CZC . A . E 2 32.328 2.231 -23.769 0.5 133.83 ? C4 CZC 501 B 1 HETATM 8 C C4 CZC . B . E 2 34.115 1.472 -23.678 0.5 133.38 ? C4 CZC 501 B 1 HETATM 9 C C5 CZC . A . E 2 33.072 3.208 -24.65 0.5 137.09 ? C5 CZC 501 B 1 HETATM 10 C C5 CZC . B . E 2 33.408 0.29 -24.32 0.5 136.66 ? C5 CZC 501 B 1 HETATM 11 C C6 CZC . A . E 2 32.287 2.962 -25.903 0.5 139.07 ? C6 CZC 501 B 1 HETATM 12 C C6 CZC . B . E 2 34.001 0.345 -25.691 0.5 139.4 ? C6 CZC 501 B 1 HETATM 13 C C7 CZC . A . E 2 32.535 1.47 -25.957 0.5 138.87 ? C7 CZC 501 B 1 HETATM 14 C C7 CZC . B . E 2 33.691 1.804 -25.955 0.5 138.75 ? C7 CZC 501 B 1 HETATM 15 C C8 CZC . A . E 2 34.02 1.238 -26.237 0.5 139.79 ? C8 CZC 501 B 1 HETATM 16 C C8 CZC . B . E 2 32.176 2.003 -26.069 0.5 138.86 ? C8 CZC 501 B 1 HETATM 17 C C9 CZC . A . E 2 33.916 2.077 -19.2 0.5 127.84 ? C9 CZC 501 B 1 HETATM 18 C C9 CZC . B . E 2 32.768 2.64 -19.161 0.5 128.56 ? C9 CZC 501 B 1 HETATM 19 C C10 CZC . A . E 2 34.127 1.171 -22.537 0.5 130.86 ? C10 CZC 501 B 1 HETATM 20 C C10 CZC . B . E 2 32.193 2.598 -22.585 0.5 130.91 ? C10 CZC 501 B 1 HETATM 21 N N1 CZC . A . E 2 32.995 2.909 -18.555 0.5 127.74 ? N1 CZC 501 B 1 HETATM 22 N N1 CZC . B . E 2 33.859 2.132 -18.455 0.5 126.95 ? N1 CZC 501 B 1 HETATM 23 N N2 CZC . A . E 2 31.91 3.238 -20.678 0.5 129.26 ? N2 CZC 501 B 1 HETATM 24 N N2 CZC . B . E 2 34.813 1.419 -20.538 0.5 128.87 ? N2 CZC 501 B 1 HETATM 25 N N3 CZC . A . E 2 34.599 1.099 -21.301 0.5 130.31 ? N3 CZC 501 B 1 HETATM 26 N N3 CZC . B . E 2 31.79 2.935 -21.364 0.5 129.84 ? N3 CZC 501 B 1 HETATM 27 N N4 CZC . A . E 2 33.062 1.961 -22.515 0.5 130.93 ? N4 CZC 501 B 1 HETATM 28 N N4 CZC . B . E 2 33.37 1.986 -22.488 0.5 130.87 ? N4 CZC 501 B 1 HETATM 29 O O1 CZC . A . E 2 31.165 4.235 -18.735 0.5 127.64 ? O1 CZC 501 B 1 HETATM 30 O O1 CZC . B . E 2 35.86 1.063 -18.543 0.5 123.22 ? O1 CZC 501 B 1 HETATM 31 O O2 CZC . A . E 2 32.933 4.554 -24.171 0.5 136.07 ? O2 CZC 501 B 1 HETATM 32 O O2 CZC . B . E 2 33.759 -0.931 -23.658 0.5 136.96 ? O2 CZC 501 B 1 HETATM 33 O O3 CZC . A . E 2 30.896 3.216 -25.671 0.5 137.74 ? O3 CZC 501 B 1 HETATM 34 O O3 CZC . B . E 2 35.415 0.153 -25.615 0.5 143.39 ? O3 CZC 501 B 1 HETATM 35 O O4 CZC . A . E 2 32.235 1.033 -24.602 0.5 136.83 ? O4 CZC 501 B 1 HETATM 36 O O4 CZC . B . E 2 34.182 2.464 -24.75 0.5 136.46 ? O4 CZC 501 B 1 HETATM 37 O O5 CZC . A . E 2 34.309 -0.16 -26.259 0.5 140.81 ? O5 CZC 501 B 1 HETATM 38 O O5 CZC . B . E 2 31.909 3.298 -26.62 0.5 139.37 ? O5 CZC 501 B 1 HETATM 39 O O6 CZC . A . E 2 34.815 1.558 -18.541 0.5 125.23 ? O6 CZC 501 B 1 HETATM 40 O O6 CZC . B . E 2 31.863 3.184 -18.529 0.5 127.52 ? O6 CZC 501 B 1 HETATM 41 O O7 CZC . A . E 2 36.279 0.591 -27.79 0.5 153.44 ? O7 CZC 501 B 1 HETATM 42 O O7 CZC . B . E 2 30.632 3.224 -28.891 0.5 148.81 ? O7 CZC 501 B 1 HETATM 43 O O8 CZC . A . E 2 36.733 -0.983 -25.805 0.5 145.56 ? O8 CZC 501 B 1 HETATM 44 O O8 CZC . B . E 2 29.466 2.505 -26.727 0.5 135.45 ? O8 CZC 501 B 1 HETATM 45 O O9 CZC . A . E 2 35.447 -1.842 -27.856 0.5 148.49 ? O9 CZC 501 B 1 HETATM 46 O O9 CZC . B . E 2 29.981 4.98 -27.105 0.5 142.68 ? O9 CZC 501 B 1 HETATM 47 O O10 CZC . A . E 2 34.312 0.243 -29.447 0.5 162.55 ? O10 CZC 501 B 1 HETATM 48 O O10 CZC . B . E 2 32.061 5.37 -29.005 0.5 160.38 ? O10 CZC 501 B 1 HETATM 49 O O11 CZC . A . E 2 35.676 2.395 -29.563 0.5 161.33 ? O11 CZC 501 B 1 HETATM 50 O O11 CZC . B . E 2 32.808 3.29 -30.302 0.5 160.4 ? O11 CZC 501 B 1 HETATM 51 O O12 CZC . A . E 2 36.728 0.175 -30.312 0.5 161.64 ? O12 CZC 501 B 1 HETATM 52 O O12 CZC . B . E 2 30.735 4.638 -31.053 0.5 159.6 ? O12 CZC 501 B 1 HETATM 53 P P1 CZC . A . E 2 35.659 -0.669 -26.975 0.5 146.57 ? P1 CZC 501 B 1 HETATM 54 P P1 CZC . B . E 2 30.489 3.602 -27.32 0.5 137.28 ? P1 CZC 501 B 1 HETATM 55 P P2 CZC . A . E 2 35.758 0.943 -29.278 0.5 159.83 ? P2 CZC 501 B 1 HETATM 56 P P2 CZC . B . E 2 31.627 4.059 -29.836 0.5 157.5 ? P2 CZC 501 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 353 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 56 #