data_7EM2 # _model_server_result.job_id UYP-hA5iT2BpMNvT31bscA _model_server_result.datetime_utc '2024-11-28 16:12:25' _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":"C","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 . C 2 45.946 57.704 -1.439 0.5 86.89 ? C1 CZC 501 A 1 HETATM 2 C C1 CZC . B . C 2 43.147 59.227 -0.307 0.5 88.18 ? C1 CZC 501 A 1 HETATM 3 C C2 CZC . A . C 2 45.102 59.7 -2.509 0.5 91.11 ? C2 CZC 501 A 1 HETATM 4 C C2 CZC . B . C 2 44.347 60.031 -2.249 0.5 91.03 ? C2 CZC 501 A 1 HETATM 5 C C3 CZC . A . C 2 44.096 59.729 -1.629 0.5 90 ? C3 CZC 501 A 1 HETATM 6 C C3 CZC . B . C 2 45.24 59.051 -2.076 0.5 90.23 ? C3 CZC 501 A 1 HETATM 7 C C4 CZC . A . C 2 45.764 61.228 -4.495 0.5 102.96 ? C4 CZC 501 A 1 HETATM 8 C C4 CZC . B . C 2 44.161 61.922 -4.03 0.5 103.22 ? C4 CZC 501 A 1 HETATM 9 C C5 CZC . A . C 2 45.151 60.884 -5.841 0.5 111.65 ? C5 CZC 501 A 1 HETATM 10 C C5 CZC . B . C 2 44.949 63.194 -3.807 0.5 112.47 ? C5 CZC 501 A 1 HETATM 11 C C6 CZC . A . C 2 45.916 61.859 -6.672 0.5 115.13 ? C6 CZC 501 A 1 HETATM 12 C C6 CZC . B . C 2 44.398 63.982 -4.963 0.5 116.85 ? C6 CZC 501 A 1 HETATM 13 C C7 CZC . A . C 2 45.553 63.095 -5.864 0.5 115.03 ? C7 CZC 501 A 1 HETATM 14 C C7 CZC . B . C 2 44.742 62.969 -6.028 0.5 115.46 ? C7 CZC 501 A 1 HETATM 15 C C8 CZC . A . C 2 44.051 63.362 -6.003 0.5 117.54 ? C8 CZC 501 A 1 HETATM 16 C C8 CZC . B . C 2 46.261 62.861 -6.177 0.5 115.5 ? C8 CZC 501 A 1 HETATM 17 C C9 CZC . A . C 2 43.97 58.804 -0.671 0.5 88.32 ? C9 CZC 501 A 1 HETATM 18 C C9 CZC . B . C 2 45.144 58.169 -1.078 0.5 87.72 ? C9 CZC 501 A 1 HETATM 19 C C10 CZC . A . C 2 43.873 61.407 -2.959 0.5 93.27 ? C10 CZC 501 A 1 HETATM 20 C C10 CZC . B . C 2 45.832 60.192 -3.8 0.5 93.38 ? C10 CZC 501 A 1 HETATM 21 N N1 CZC . A . C 2 44.888 57.768 -0.549 0.5 87.06 ? N1 CZC 501 A 1 HETATM 22 N N1 CZC . B . C 2 44.095 58.232 -0.165 0.5 87.13 ? N1 CZC 501 A 1 HETATM 23 N N2 CZC . A . C 2 46.062 58.68 -2.438 0.5 89.25 ? N2 CZC 501 A 1 HETATM 24 N N2 CZC . B . C 2 43.266 60.144 -1.367 0.5 89.54 ? N2 CZC 501 A 1 HETATM 25 N N3 CZC . A . C 2 43.342 60.782 -1.917 0.5 91.45 ? N3 CZC 501 A 1 HETATM 26 N N3 CZC . B . C 2 46.152 59.158 -3.034 0.5 91.23 ? N3 CZC 501 A 1 HETATM 27 N N4 CZC . A . C 2 44.96 60.743 -3.332 0.5 93.81 ? N4 CZC 501 A 1 HETATM 28 N N4 CZC . B . C 2 44.722 60.737 -3.321 0.5 93.85 ? N4 CZC 501 A 1 HETATM 29 O O1 CZC . A . C 2 46.759 56.79 -1.333 0.5 82.42 ? O1 CZC 501 A 1 HETATM 30 O O1 CZC . B . C 2 42.221 59.28 0.5 0.5 89.53 ? O1 CZC 501 A 1 HETATM 31 O O2 CZC . A . C 2 45.441 59.535 -6.239 0.5 109.59 ? O2 CZC 501 A 1 HETATM 32 O O2 CZC . B . C 2 44.623 63.794 -2.543 0.5 113.47 ? O2 CZC 501 A 1 HETATM 33 O O3 CZC . A . C 2 47.318 61.572 -6.583 0.5 118.37 ? O3 CZC 501 A 1 HETATM 34 O O3 CZC . B . C 2 42.967 64.112 -4.856 0.5 122.31 ? O3 CZC 501 A 1 HETATM 35 O O4 CZC . A . C 2 45.806 62.688 -4.501 0.5 111.65 ? O4 CZC 501 A 1 HETATM 36 O O4 CZC . B . C 2 44.272 61.716 -5.468 0.5 111.84 ? O4 CZC 501 A 1 HETATM 37 O O5 CZC . A . C 2 43.7 64.615 -5.407 0.5 120.33 ? O5 CZC 501 A 1 HETATM 38 O O5 CZC . B . C 2 46.576 61.927 -7.217 0.5 116.46 ? O5 CZC 501 A 1 HETATM 39 O O6 CZC . A . C 2 43.042 58.841 0.133 0.5 86.92 ? O6 CZC 501 A 1 HETATM 40 O O6 CZC . B . C 2 45.986 57.283 -0.944 0.5 84.06 ? O6 CZC 501 A 1 HETATM 41 O O7 CZC . A . C 2 41.81 64.652 -7.168 0.5 134.62 ? O7 CZC 501 A 1 HETATM 42 O O7 CZC . B . C 2 47.55 63.361 -9.177 0.5 129.63 ? O7 CZC 501 A 1 HETATM 43 O O8 CZC . A . C 2 41.212 64.74 -4.656 0.5 125.19 ? O8 CZC 501 A 1 HETATM 44 O O8 CZC . B . C 2 48.985 62.843 -7.16 0.5 118.14 ? O8 CZC 501 A 1 HETATM 45 O O9 CZC . A . C 2 42.308 66.766 -5.801 0.5 128.16 ? O9 CZC 501 A 1 HETATM 46 O O9 CZC . B . C 2 48.396 60.93 -8.769 0.5 125.37 ? O9 CZC 501 A 1 HETATM 47 O O10 CZC . A . C 2 43.878 65.881 -8.129 0.5 142.47 ? O10 CZC 501 A 1 HETATM 48 O O10 CZC . B . C 2 46.101 61.598 -10.357 0.5 139.83 ? O10 CZC 501 A 1 HETATM 49 O O11 CZC . A . C 2 41.546 66.415 -9.039 0.5 145.99 ? O11 CZC 501 A 1 HETATM 50 O O11 CZC . B . C 2 47.364 63.338 -11.735 0.5 141.06 ? O11 CZC 501 A 1 HETATM 51 O O12 CZC . A . C 2 42.669 64.153 -9.568 0.5 141.9 ? O12 CZC 501 A 1 HETATM 52 O O12 CZC . B . C 2 45.323 64.04 -10.306 0.5 140.36 ? O12 CZC 501 A 1 HETATM 53 P P1 CZC . A . C 2 42.276 65.284 -5.75 0.5 126.46 ? P1 CZC 501 A 1 HETATM 54 P P1 CZC . B . C 2 47.883 62.164 -8.127 0.5 119.97 ? P1 CZC 501 A 1 HETATM 55 P P2 CZC . A . C 2 42.475 65.193 -8.53 0.5 141.05 ? P2 CZC 501 A 1 HETATM 56 P P2 CZC . B . C 2 46.512 63.152 -10.371 0.5 136.65 ? P2 CZC 501 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 56 #