data_7THY # _model_server_result.job_id DLI5ADE_sR-on7-xC9gcmg _model_server_result.datetime_utc '2024-11-27 01:59:37' _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 7thy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2601}' # _entry.id 7THY # _exptl.entry_id 7THY _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 7THY _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 2 151.726 143.027 189.007 1 198.55 ? PB GDP 2601 A 1 HETATM 2 O O1B GDP . . . B 2 152.731 144.164 188.454 1 205.22 ? O1B GDP 2601 A 1 HETATM 3 O O2B GDP . . . B 2 150.389 143.697 189.603 1 202.64 ? O2B GDP 2601 A 1 HETATM 4 O O3B GDP . . . B 2 152.493 142.366 190.071 1 201.02 ? O3B GDP 2601 A 1 HETATM 5 O O3A GDP . . . B 2 151.337 141.986 187.862 1 194.99 ? O3A GDP 2601 A 1 HETATM 6 P PA GDP . . . B 2 151.14 140.421 187.983 1 186.8 ? PA GDP 2601 A 1 HETATM 7 O O1A GDP . . . B 2 152.467 139.876 188.379 1 195.76 ? O1A GDP 2601 A 1 HETATM 8 O O2A GDP . . . B 2 150.079 140.067 189.144 1 188.75 ? O2A GDP 2601 A 1 HETATM 9 O O5' GDP . . . B 2 150.656 139.647 186.625 1 193.72 ? O5' GDP 2601 A 1 HETATM 10 C C5' GDP . . . B 2 149.378 138.953 186.398 1 198.55 ? C5' GDP 2601 A 1 HETATM 11 C C4' GDP . . . B 2 149.579 137.472 185.92 1 201.72 ? C4' GDP 2601 A 1 HETATM 12 O O4' GDP . . . B 2 149.825 136.586 187.028 1 199.62 ? O4' GDP 2601 A 1 HETATM 13 C C3' GDP . . . B 2 148.289 136.835 185.338 1 209.13 ? C3' GDP 2601 A 1 HETATM 14 O O3' GDP . . . B 2 148.12 137.185 183.951 1 215.79 ? O3' GDP 2601 A 1 HETATM 15 C C2' GDP . . . B 2 148.519 135.3 185.482 1 207.73 ? C2' GDP 2601 A 1 HETATM 16 O O2' GDP . . . B 2 148.997 134.83 184.218 1 207.14 ? O2' GDP 2601 A 1 HETATM 17 C C1' GDP . . . B 2 149.601 135.176 186.621 1 207.6 ? C1' GDP 2601 A 1 HETATM 18 N N9 GDP . . . B 2 149.161 134.3 187.786 1 211.32 ? N9 GDP 2601 A 1 HETATM 19 C C8 GDP . . . B 2 149.093 134.786 189.067 1 206.13 ? C8 GDP 2601 A 1 HETATM 20 N N7 GDP . . . B 2 149.363 133.897 189.974 1 210.63 ? N7 GDP 2601 A 1 HETATM 21 C C5 GDP . . . B 2 149.571 132.715 189.38 1 212.42 ? C5 GDP 2601 A 1 HETATM 22 C C6 GDP . . . B 2 149.875 131.359 189.862 1 213.47 ? C6 GDP 2601 A 1 HETATM 23 O O6 GDP . . . B 2 150.179 131.145 191.043 1 208.37 ? O6 GDP 2601 A 1 HETATM 24 N N1 GDP . . . B 2 149.837 130.301 188.959 1 213.68 ? N1 GDP 2601 A 1 HETATM 25 C C2 GDP . . . B 2 149.753 130.552 187.577 1 219.36 ? C2 GDP 2601 A 1 HETATM 26 N N2 GDP . . . B 2 149.87 129.511 186.715 1 221.32 ? N2 GDP 2601 A 1 HETATM 27 N N3 GDP . . . B 2 149.557 131.816 187.092 1 219.32 ? N3 GDP 2601 A 1 HETATM 28 C C4 GDP . . . B 2 149.423 132.928 187.949 1 214.61 ? C4 GDP 2601 A 1 HETATM 29 H H5' GDP . . . B 2 148.754 138.937 187.301 1 238.26 ? H5' GDP 2601 A 1 HETATM 30 H "H5''" GDP . . . B 2 148.84 139.516 185.632 1 238.26 ? "H5''" GDP 2601 A 1 HETATM 31 H H4' GDP . . . B 2 150.406 137.433 185.198 1 242.06 ? H4' GDP 2601 A 1 HETATM 32 H H3' GDP . . . B 2 147.412 137.129 185.924 1 250.96 ? H3' GDP 2601 A 1 HETATM 33 H HO3' GDP . . . B 2 147.735 138.097 183.831 1 258.95 ? HO3' GDP 2601 A 1 HETATM 34 H H2' GDP . . . B 2 147.591 134.785 185.757 1 249.27 ? H2' GDP 2601 A 1 HETATM 35 H HO2' GDP . . . B 2 148.851 135.486 183.505 1 248.57 ? HO2' GDP 2601 A 1 HETATM 36 H H1' GDP . . . B 2 150.528 134.775 186.201 1 249.11 ? H1' GDP 2601 A 1 HETATM 37 H H8 GDP . . . B 2 148.858 135.813 189.294 1 247.36 ? H8 GDP 2601 A 1 HETATM 38 H HN1 GDP . . . B 2 149.985 129.386 189.296 1 256.41 ? HN1 GDP 2601 A 1 HETATM 39 H HN21 GDP . . . B 2 149.825 128.594 187.065 1 265.58 ? HN21 GDP 2601 A 1 HETATM 40 H HN22 GDP . . . B 2 150.239 129.671 185.845 1 265.58 ? HN22 GDP 2601 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 1432 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 40 #