data_7T3C # _model_server_result.job_id qx8nyXL4MhzXlzIRFcWPIw _model_server_result.datetime_utc '2025-07-05 06:48:36' _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 7t3c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":501}' # _entry.id 7T3C # _exptl.entry_id 7T3C _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 12 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 7T3C _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7T3C _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details heptadecameric _pdbx_struct_assembly.oligomeric_count 17 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 12 R N N ? 12 T N N ? 12 V N 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 86 n n PB O2B GDP sing 87 n n PB O3B GDP sing 88 n n PB O3A GDP sing 89 n n O2B HOB2 GDP sing 90 n n O3B HOB3 GDP sing 91 n n O3A PA GDP sing 92 n n PA O1A GDP doub 93 n n PA O2A GDP sing 94 n n PA O5' GDP sing 95 n n O2A HOA2 GDP sing 96 n n O5' C5' GDP sing 97 n n C5' C4' GDP sing 98 n n C5' H5' GDP sing 99 n n C5' "H5''" GDP sing 100 n n C4' O4' GDP sing 101 n n C4' C3' GDP sing 102 n n C4' H4' GDP sing 103 n n O4' C1' GDP sing 104 n n C3' O3' GDP sing 105 n n C3' C2' GDP sing 106 n n C3' H3' GDP sing 107 n n O3' HO3' GDP sing 108 n n C2' O2' GDP sing 109 n n C2' C1' GDP sing 110 n n C2' H2' GDP sing 111 n n O2' HO2' GDP sing 112 n n C1' N9 GDP sing 113 n n C1' H1' GDP sing 114 n n N9 C8 GDP sing 115 n y N9 C4 GDP sing 116 n y C8 N7 GDP doub 117 n y C8 H8 GDP sing 118 n n N7 C5 GDP sing 119 n y C5 C6 GDP sing 120 n n C5 C4 GDP doub 121 n y C6 O6 GDP doub 122 n n C6 N1 GDP sing 123 n n N1 C2 GDP sing 124 n n N1 HN1 GDP sing 125 n n C2 N2 GDP sing 126 n n C2 N3 GDP doub 127 n n N2 HN21 GDP sing 128 n n N2 HN22 GDP sing 129 n n N3 C4 GDP sing 130 n n # _atom_sites.entry_id 7T3C _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 # 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 R 12 GDP D 1 501 501 GDP GDP . S 13 AF3 D 1 502 601 AF3 AF3 . T 12 GDP E 1 501 501 GDP GDP . U 13 AF3 E 1 502 601 AF3 AF3 . V 12 GDP K 1 501 501 GDP GDP . W 13 AF3 K 1 502 601 AF3 AF3 . # 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 . . . R 12 202.283 195.037 136.954 1 220.41 ? PB GDP 501 D 1 HETATM 2 O O1B GDP . . . R 12 202.5 195.897 135.742 1 220.41 ? O1B GDP 501 D 1 HETATM 3 O O2B GDP . . . R 12 201.007 194.254 136.829 1 220.41 ? O2B GDP 501 D 1 HETATM 4 O O3B GDP . . . R 12 203.452 194.105 137.162 1 220.41 ? O3B GDP 501 D 1 HETATM 5 O O3A GDP . . . R 12 202.192 195.918 138.289 1 220.41 ? O3A GDP 501 D 1 HETATM 6 P PA GDP . . . R 12 203.312 197.036 138.523 1 220.41 ? PA GDP 501 D 1 HETATM 7 O O1A GDP . . . R 12 204.482 196.822 137.606 1 220.41 ? O1A GDP 501 D 1 HETATM 8 O O2A GDP . . . R 12 202.524 198.274 138.349 1 220.41 ? O2A GDP 501 D 1 HETATM 9 O O5' GDP . . . R 12 203.829 197.007 140.041 1 220.41 ? O5' GDP 501 D 1 HETATM 10 C C5' GDP . . . R 12 204.452 198.199 140.54 1 220.41 ? C5' GDP 501 D 1 HETATM 11 C C4' GDP . . . R 12 205.866 197.942 141.077 1 220.41 ? C4' GDP 501 D 1 HETATM 12 O O4' GDP . . . R 12 206.854 198.401 140.144 1 220.41 ? O4' GDP 501 D 1 HETATM 13 C C3' GDP . . . R 12 206.153 198.675 142.387 1 220.41 ? C3' GDP 501 D 1 HETATM 14 O O3' GDP . . . R 12 206.445 197.779 143.463 1 220.41 ? O3' GDP 501 D 1 HETATM 15 C C2' GDP . . . R 12 207.375 199.535 142.147 1 220.41 ? C2' GDP 501 D 1 HETATM 16 O O2' GDP . . . R 12 208.296 199.366 143.222 1 220.41 ? O2' GDP 501 D 1 HETATM 17 C C1' GDP . . . R 12 207.953 198.987 140.857 1 220.41 ? C1' GDP 501 D 1 HETATM 18 N N9 GDP . . . R 12 208.774 199.914 140.013 1 220.41 ? N9 GDP 501 D 1 HETATM 19 C C8 GDP . . . R 12 209.601 199.409 139.085 1 220.41 ? C8 GDP 501 D 1 HETATM 20 N N7 GDP . . . R 12 210.267 200.37 138.418 1 220.41 ? N7 GDP 501 D 1 HETATM 21 C C5 GDP . . . R 12 209.864 201.543 138.912 1 220.41 ? C5 GDP 501 D 1 HETATM 22 C C6 GDP . . . R 12 210.198 202.95 138.619 1 220.41 ? C6 GDP 501 D 1 HETATM 23 O O6 GDP . . . R 12 211.023 203.253 137.745 1 220.41 ? O6 GDP 501 D 1 HETATM 24 N N1 GDP . . . R 12 209.592 203.902 139.301 1 220.41 ? N1 GDP 501 D 1 HETATM 25 C C2 GDP . . . R 12 208.706 203.613 140.264 1 220.41 ? C2 GDP 501 D 1 HETATM 26 N N2 GDP . . . R 12 208.156 204.661 140.92 1 220.41 ? N2 GDP 501 D 1 HETATM 27 N N3 GDP . . . R 12 208.337 202.337 140.583 1 220.41 ? N3 GDP 501 D 1 HETATM 28 C C4 GDP . . . R 12 208.879 201.259 139.965 1 220.41 ? C4 GDP 501 D 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 56 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #