data_7EM5 # _model_server_result.job_id wRaVSLLFEmHbTODJUwWZBw _model_server_result.datetime_utc '2024-11-14 23:43:29' _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":"C","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 . A . C 2 46.024 57.836 -1.39 0.5 121.86 ? C1 CZC 501 A 1 HETATM 2 C C1 CZC . B . C 2 43.025 59.279 -0.247 0.5 121.78 ? C1 CZC 501 A 1 HETATM 3 C C2 CZC . A . C 2 45.194 59.814 -2.479 0.5 127.89 ? C2 CZC 501 A 1 HETATM 4 C C2 CZC . B . C 2 44.222 60.092 -2.179 0.5 126.13 ? C2 CZC 501 A 1 HETATM 5 C C3 CZC . A . C 2 44.169 59.841 -1.622 0.5 136.74 ? C3 CZC 501 A 1 HETATM 6 C C3 CZC . B . C 2 45.156 59.157 -1.974 0.5 135.2 ? C3 CZC 501 A 1 HETATM 7 C C4 CZC . A . C 2 45.901 61.323 -4.453 0.5 145.07 ? C4 CZC 501 A 1 HETATM 8 C C4 CZC . B . C 2 43.954 61.945 -3.979 0.5 142.74 ? C4 CZC 501 A 1 HETATM 9 C C5 CZC . A . C 2 45.296 60.982 -5.803 0.5 154.71 ? C5 CZC 501 A 1 HETATM 10 C C5 CZC . B . C 2 44.745 63.226 -3.802 0.5 149.5 ? C5 CZC 501 A 1 HETATM 11 C C6 CZC . A . C 2 46.011 61.982 -6.656 0.5 157.38 ? C6 CZC 501 A 1 HETATM 12 C C6 CZC . B . C 2 44.339 63.982 -5.043 0.5 156.75 ? C6 CZC 501 A 1 HETATM 13 C C7 CZC . A . C 2 45.665 63.202 -5.819 0.5 156.2 ? C7 CZC 501 A 1 HETATM 14 C C7 CZC . B . C 2 44.657 62.871 -6.02 0.5 155.74 ? C7 CZC 501 A 1 HETATM 15 C C8 CZC . A . C 2 44.163 63.501 -5.905 0.5 156.61 ? C8 CZC 501 A 1 HETATM 16 C C8 CZC . B . C 2 46.169 62.619 -6.064 0.5 154.55 ? C8 CZC 501 A 1 HETATM 17 C C9 CZC . A . C 2 44.024 58.925 -0.664 0.5 121.12 ? C9 CZC 501 A 1 HETATM 18 C C9 CZC . B . C 2 45.084 58.293 -0.966 0.5 120.86 ? C9 CZC 501 A 1 HETATM 19 C C10 CZC . A . C 2 43.963 61.511 -2.963 0.5 134.32 ? C10 CZC 501 A 1 HETATM 20 C C10 CZC . B . C 2 45.722 60.29 -3.706 0.5 131.33 ? C10 CZC 501 A 1 HETATM 21 N N1 CZC . A . C 2 44.947 57.895 -0.52 0.5 121.82 ? N1 CZC 501 A 1 HETATM 22 N N1 CZC . B . C 2 44.019 58.326 -0.07 0.5 121.77 ? N1 CZC 501 A 1 HETATM 23 N N2 CZC . A . C 2 46.157 58.805 -2.386 0.5 123.74 ? N2 CZC 501 A 1 HETATM 24 N N2 CZC . B . C 2 43.122 60.176 -1.316 0.5 123.98 ? N2 CZC 501 A 1 HETATM 25 N N3 CZC . A . C 2 43.414 60.888 -1.929 0.5 130.37 ? N3 CZC 501 A 1 HETATM 26 N N3 CZC . B . C 2 46.078 59.285 -2.918 0.5 129.53 ? N3 CZC 501 A 1 HETATM 27 N N4 CZC . A . C 2 45.063 60.853 -3.308 0.5 128.4 ? N4 CZC 501 A 1 HETATM 28 N N4 CZC . B . C 2 44.579 60.795 -3.258 0.5 128.42 ? N4 CZC 501 A 1 HETATM 29 O O1 CZC . A . C 2 46.845 56.934 -1.273 0.5 121.49 ? O1 CZC 501 A 1 HETATM 30 O O1 CZC . B . C 2 42.076 59.322 0.532 0.5 123.13 ? O1 CZC 501 A 1 HETATM 31 O O2 CZC . A . C 2 45.627 59.639 -6.196 0.5 157.28 ? O2 CZC 501 A 1 HETATM 32 O O2 CZC . B . C 2 44.352 63.905 -2.599 0.5 153.5 ? O2 CZC 501 A 1 HETATM 33 O O3 CZC . A . C 2 47.422 61.738 -6.624 0.5 163.54 ? O3 CZC 501 A 1 HETATM 34 O O3 CZC . B . C 2 42.928 64.252 -5.056 0.5 164.37 ? O3 CZC 501 A 1 HETATM 35 O O4 CZC . A . C 2 45.987 62.781 -4.466 0.5 152.43 ? O4 CZC 501 A 1 HETATM 36 O O4 CZC . B . C 2 43.958 61.738 -5.43 0.5 152.62 ? O4 CZC 501 A 1 HETATM 37 O O5 CZC . A . C 2 43.88 64.703 -5.18 0.5 159.17 ? O5 CZC 501 A 1 HETATM 38 O O5 CZC . B . C 2 46.499 61.905 -7.259 0.5 158.8 ? O5 CZC 501 A 1 HETATM 39 O O6 CZC . A . C 2 43.07 58.974 0.109 0.5 121.76 ? O6 CZC 501 A 1 HETATM 40 O O6 CZC . B . C 2 45.964 57.45 -0.813 0.5 121.59 ? O6 CZC 501 A 1 HETATM 41 O O7 CZC . A . C 2 41.928 65.066 -6.877 0.5 179.24 ? O7 CZC 501 A 1 HETATM 42 O O7 CZC . B . C 2 47.621 63.368 -9.11 0.5 178.72 ? O7 CZC 501 A 1 HETATM 43 O O8 CZC . A . C 2 41.454 65.193 -4.412 0.5 168.43 ? O8 CZC 501 A 1 HETATM 44 O O8 CZC . B . C 2 48.868 62.906 -6.984 0.5 168.43 ? O8 CZC 501 A 1 HETATM 45 O O9 CZC . A . C 2 42.845 67.057 -5.533 0.5 175.66 ? O9 CZC 501 A 1 HETATM 46 O O9 CZC . B . C 2 48.491 60.983 -8.625 0.5 175.66 ? O9 CZC 501 A 1 HETATM 47 O O10 CZC . A . C 2 43.899 66.279 -8.036 0.5 191.09 ? O10 CZC 501 A 1 HETATM 48 O O10 CZC . B . C 2 46.309 61.536 -10.327 0.5 190.12 ? O10 CZC 501 A 1 HETATM 49 O O11 CZC . A . C 2 41.489 66.738 -8.798 0.5 190.18 ? O11 CZC 501 A 1 HETATM 50 O O11 CZC . B . C 2 47.589 63.28 -11.674 0.5 189.17 ? O11 CZC 501 A 1 HETATM 51 O O12 CZC . A . C 2 42.6 64.463 -9.283 0.5 190.65 ? O12 CZC 501 A 1 HETATM 52 O O12 CZC . B . C 2 45.454 63.959 -10.378 0.5 190.65 ? O12 CZC 501 A 1 HETATM 53 P P1 CZC . A . C 2 42.575 65.597 -5.502 0.5 170.26 ? P1 CZC 501 A 1 HETATM 54 P P1 CZC . B . C 2 47.881 62.196 -8.034 0.5 170.26 ? P1 CZC 501 A 1 HETATM 55 P P2 CZC . A . C 2 42.476 65.56 -8.296 0.5 187.12 ? P2 CZC 501 A 1 HETATM 56 P P2 CZC . B . C 2 46.67 63.107 -10.357 0.5 186.94 ? P2 CZC 501 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 56 #