data_7THZ # _model_server_result.job_id qCSiEZVZjYwPruepdOLFzg _model_server_result.datetime_utc '2024-11-26 23:39:52' _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 7thz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2601}' # _entry.id 7THZ # _exptl.entry_id 7THZ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B _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 ? _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 B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # 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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 7THZ _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id GDP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 2601 _pdbx_nonpoly_scheme.auth_seq_num 2601 _pdbx_nonpoly_scheme.pdb_mon_id GDP _pdbx_nonpoly_scheme.auth_mon_id GDP _pdbx_nonpoly_scheme.pdb_ins_code . # 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 P PB GDP . . . B 2 159.615 134.7 151.877 1 198.31 ? PB GDP 2601 A 1 HETATM 2 O O1B GDP . . . B 2 159.709 134.02 150.579 1 205.37 ? O1B GDP 2601 A 1 HETATM 3 O O2B GDP . . . B 2 160.175 133.741 153.055 1 201.55 ? O2B GDP 2601 A 1 HETATM 4 O O3B GDP . . . B 2 160.487 136.044 151.85 1 201.08 ? O3B GDP 2601 A 1 HETATM 5 O O3A GDP . . . B 2 158.111 135.095 152.188 1 194.73 ? O3A GDP 2601 A 1 HETATM 6 P PA GDP . . . B 2 156.706 134.439 151.859 1 191.47 ? PA GDP 2601 A 1 HETATM 7 O O1A GDP . . . B 2 155.936 135.325 150.937 1 196.11 ? O1A GDP 2601 A 1 HETATM 8 O O2A GDP . . . B 2 156.766 133.016 151.132 1 200.87 ? O2A GDP 2601 A 1 HETATM 9 O O5' GDP . . . B 2 155.783 134.271 153.208 1 193.39 ? O5' GDP 2601 A 1 HETATM 10 C C5' GDP . . . B 2 154.847 133.164 153.467 1 194.51 ? C5' GDP 2601 A 1 HETATM 11 C C4' GDP . . . B 2 154.038 133.309 154.808 1 199.18 ? C4' GDP 2601 A 1 HETATM 12 O O4' GDP . . . B 2 152.82 134.045 154.519 1 203.36 ? O4' GDP 2601 A 1 HETATM 13 C C3' GDP . . . B 2 153.575 131.937 155.408 1 203.9 ? C3' GDP 2601 A 1 HETATM 14 O O3' GDP . . . B 2 153.567 131.873 156.847 1 199.16 ? O3' GDP 2601 A 1 HETATM 15 C C2' GDP . . . B 2 152.132 131.808 154.877 1 209.69 ? C2' GDP 2601 A 1 HETATM 16 O O2' GDP . . . B 2 151.272 131.009 155.703 1 211.7 ? O2' GDP 2601 A 1 HETATM 17 C C1' GDP . . . B 2 151.629 133.278 154.909 1 210.36 ? C1' GDP 2601 A 1 HETATM 18 N N9 GDP . . . B 2 150.454 133.456 153.988 1 215.17 ? N9 GDP 2601 A 1 HETATM 19 C C8 GDP . . . B 2 150.453 134.23 152.854 1 211.85 ? C8 GDP 2601 A 1 HETATM 20 N N7 GDP . . . B 2 149.479 133.907 152.05 1 210.61 ? N7 GDP 2601 A 1 HETATM 21 C C5 GDP . . . B 2 148.708 132.956 152.633 1 217.44 ? C5 GDP 2601 A 1 HETATM 22 C C6 GDP . . . B 2 147.456 132.25 152.311 1 221.12 ? C6 GDP 2601 A 1 HETATM 23 O O6 GDP . . . B 2 147.056 132.107 151.159 1 217.85 ? O6 GDP 2601 A 1 HETATM 24 N N1 GDP . . . B 2 146.702 131.746 153.391 1 223.24 ? N1 GDP 2601 A 1 HETATM 25 C C2 GDP . . . B 2 147.429 131.266 154.503 1 224.05 ? C2 GDP 2601 A 1 HETATM 26 N N2 GDP . . . B 2 146.86 130.354 155.331 1 225.76 ? N2 GDP 2601 A 1 HETATM 27 N N3 GDP . . . B 2 148.698 131.705 154.763 1 222.48 ? N3 GDP 2601 A 1 HETATM 28 C C4 GDP . . . B 2 149.316 132.654 153.912 1 219.73 ? C4 GDP 2601 A 1 HETATM 29 H H5' GDP . . . B 2 154.121 133.101 152.657 1 233.41 ? H5' GDP 2601 A 1 HETATM 30 H "H5''" GDP . . . B 2 155.415 132.222 153.474 1 233.41 ? "H5''" GDP 2601 A 1 HETATM 31 H H4' GDP . . . B 2 154.627 133.85 155.55 1 239.02 ? H4' GDP 2601 A 1 HETATM 32 H H3' GDP . . . B 2 154.188 131.126 155.021 1 244.68 ? H3' GDP 2601 A 1 HETATM 33 H HO3' GDP . . . B 2 153.385 130.952 157.189 1 239 ? HO3' GDP 2601 A 1 HETATM 34 H H2' GDP . . . B 2 152.143 131.424 153.854 1 251.62 ? H2' GDP 2601 A 1 HETATM 35 H HO2' GDP . . . B 2 150.317 131.251 155.593 1 254.03 ? HO2' GDP 2601 A 1 HETATM 36 H H1' GDP . . . B 2 151.333 133.557 155.927 1 252.43 ? H1' GDP 2601 A 1 HETATM 37 H H8 GDP . . . B 2 151.186 134.998 152.653 1 254.22 ? H8 GDP 2601 A 1 HETATM 38 H HN1 GDP . . . B 2 145.921 132.319 153.598 1 267.89 ? HN1 GDP 2601 A 1 HETATM 39 H HN21 GDP . . . B 2 147.335 130.106 156.134 1 270.91 ? HN21 GDP 2601 A 1 HETATM 40 H HN22 GDP . . . B 2 146.128 129.806 155.014 1 270.91 ? HN22 GDP 2601 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 1279 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 40 #