data_3QBV # _model_server_result.job_id dnv56xa8n_kcVEXoqvFHMw _model_server_result.datetime_utc '2025-02-26 15:49:09' _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 3qbv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":200}' # _entry.id 3QBV # _exptl.entry_id 3QBV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 108.23 _cell.angle_gamma 90 _cell.entry_id 3QBV _cell.length_a 85.46 _cell.length_b 80.062 _cell.length_c 94.591 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QBV _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,G,H 1 1 C,D,F,I,J 2 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 ? 3 E N N ? 3 F 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 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 3QBV _atom_sites.fract_transf_matrix[1][1] 0.011701 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003854 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01249 _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] 0.01113 _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 E 3 GDP A 1 200 200 GDP GDP . F 3 GDP C 1 200 200 GDP GDP . G 4 HOH A 1 179 179 HOH HOH . G 4 HOH A 2 180 180 HOH HOH . G 4 HOH A 3 181 181 HOH HOH . G 4 HOH A 4 182 182 HOH HOH . G 4 HOH A 5 183 183 HOH HOH . G 4 HOH A 6 184 184 HOH HOH . G 4 HOH A 7 185 185 HOH HOH . G 4 HOH A 8 186 186 HOH HOH . G 4 HOH A 9 187 187 HOH HOH . G 4 HOH A 10 188 188 HOH HOH . G 4 HOH A 11 189 189 HOH HOH . G 4 HOH A 12 190 190 HOH HOH . G 4 HOH A 13 191 191 HOH HOH . G 4 HOH A 14 192 192 HOH HOH . G 4 HOH A 15 193 193 HOH HOH . G 4 HOH A 16 194 194 HOH HOH . G 4 HOH A 17 195 195 HOH HOH . G 4 HOH A 18 196 196 HOH HOH . G 4 HOH A 19 197 197 HOH HOH . G 4 HOH A 20 198 198 HOH HOH . G 4 HOH A 21 199 199 HOH HOH . H 4 HOH B 1 12 12 HOH HOH . H 4 HOH B 2 13 13 HOH HOH . H 4 HOH B 3 14 14 HOH HOH . H 4 HOH B 4 15 15 HOH HOH . H 4 HOH B 5 16 16 HOH HOH . H 4 HOH B 6 17 17 HOH HOH . H 4 HOH B 7 18 18 HOH HOH . H 4 HOH B 8 19 19 HOH HOH . H 4 HOH B 9 20 20 HOH HOH . H 4 HOH B 10 21 21 HOH HOH . H 4 HOH B 11 22 22 HOH HOH . H 4 HOH B 12 44 44 HOH HOH . H 4 HOH B 13 50 50 HOH HOH . H 4 HOH B 14 54 54 HOH HOH . H 4 HOH B 15 57 57 HOH HOH . H 4 HOH B 16 61 61 HOH HOH . H 4 HOH B 17 63 63 HOH HOH . H 4 HOH B 18 69 69 HOH HOH . H 4 HOH B 19 71 71 HOH HOH . H 4 HOH B 20 75 75 HOH HOH . H 4 HOH B 21 79 79 HOH HOH . H 4 HOH B 22 80 80 HOH HOH . H 4 HOH B 23 83 83 HOH HOH . H 4 HOH B 24 84 84 HOH HOH . H 4 HOH B 25 86 86 HOH HOH . H 4 HOH B 26 87 87 HOH HOH . H 4 HOH B 27 88 88 HOH HOH . H 4 HOH B 28 89 89 HOH HOH . H 4 HOH B 29 91 91 HOH HOH . H 4 HOH B 30 92 92 HOH HOH . H 4 HOH B 31 95 95 HOH HOH . H 4 HOH B 32 101 101 HOH HOH . H 4 HOH B 33 102 102 HOH HOH . H 4 HOH B 34 112 112 HOH HOH . I 4 HOH C 1 179 179 HOH HOH . I 4 HOH C 2 180 180 HOH HOH . I 4 HOH C 3 181 181 HOH HOH . I 4 HOH C 4 182 182 HOH HOH . I 4 HOH C 5 183 183 HOH HOH . I 4 HOH C 6 184 184 HOH HOH . I 4 HOH C 7 185 185 HOH HOH . I 4 HOH C 8 186 186 HOH HOH . I 4 HOH C 9 187 187 HOH HOH . I 4 HOH C 10 188 188 HOH HOH . I 4 HOH C 11 189 189 HOH HOH . I 4 HOH C 12 190 190 HOH HOH . I 4 HOH C 13 191 191 HOH HOH . I 4 HOH C 14 192 192 HOH HOH . I 4 HOH C 15 193 193 HOH HOH . I 4 HOH C 16 194 194 HOH HOH . I 4 HOH C 17 195 195 HOH HOH . I 4 HOH C 18 196 196 HOH HOH . J 4 HOH D 1 31 31 HOH HOH . J 4 HOH D 2 32 32 HOH HOH . J 4 HOH D 3 33 33 HOH HOH . J 4 HOH D 4 34 34 HOH HOH . J 4 HOH D 5 35 35 HOH HOH . J 4 HOH D 6 36 36 HOH HOH . J 4 HOH D 7 37 37 HOH HOH . J 4 HOH D 8 38 38 HOH HOH . J 4 HOH D 9 39 39 HOH HOH . J 4 HOH D 10 40 40 HOH HOH . J 4 HOH D 11 41 41 HOH HOH . J 4 HOH D 12 42 42 HOH HOH . J 4 HOH D 13 43 43 HOH HOH . J 4 HOH D 14 48 48 HOH HOH . J 4 HOH D 15 52 52 HOH HOH . J 4 HOH D 16 53 53 HOH HOH . J 4 HOH D 17 56 56 HOH HOH . J 4 HOH D 18 60 60 HOH HOH . J 4 HOH D 19 64 64 HOH HOH . J 4 HOH D 20 65 65 HOH HOH . J 4 HOH D 21 66 66 HOH HOH . J 4 HOH D 22 68 68 HOH HOH . J 4 HOH D 23 74 74 HOH HOH . J 4 HOH D 24 76 76 HOH HOH . J 4 HOH D 25 77 77 HOH HOH . J 4 HOH D 26 78 78 HOH HOH . J 4 HOH D 27 82 82 HOH HOH . J 4 HOH D 28 85 85 HOH HOH . J 4 HOH D 29 94 94 HOH HOH . J 4 HOH D 30 98 98 HOH HOH . J 4 HOH D 31 100 100 HOH HOH . J 4 HOH D 32 103 103 HOH HOH . J 4 HOH D 33 104 104 HOH HOH . J 4 HOH D 34 105 105 HOH HOH . J 4 HOH D 35 106 106 HOH HOH . J 4 HOH D 36 110 110 HOH HOH . J 4 HOH D 37 114 114 HOH HOH . J 4 HOH D 38 115 115 HOH HOH . J 4 HOH D 39 117 117 HOH HOH . J 4 HOH D 40 118 118 HOH HOH . J 4 HOH D 41 119 119 HOH HOH . J 4 HOH D 42 120 120 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 P PB GDP . . . E 3 38.092 6.47 34.055 1 39.98 ? PB GDP 200 A 1 HETATM 2 O O1B GDP . . . E 3 38.347 6.905 32.635 1 40.24 ? O1B GDP 200 A 1 HETATM 3 O O2B GDP . . . E 3 38.054 4.962 34.143 1 36.99 ? O2B GDP 200 A 1 HETATM 4 O O3B GDP . . . E 3 36.757 7.008 34.527 1 45.62 ? O3B GDP 200 A 1 HETATM 5 O O3A GDP . . . E 3 39.292 7.022 34.982 1 91.17 ? O3A GDP 200 A 1 HETATM 6 P PA GDP . . . E 3 39.03 7.955 36.275 1 98.76 ? PA GDP 200 A 1 HETATM 7 O O1A GDP . . . E 3 38.143 7.258 37.281 1 101.7 ? O1A GDP 200 A 1 HETATM 8 O O2A GDP . . . E 3 38.431 9.286 35.897 1 94.25 ? O2A GDP 200 A 1 HETATM 9 O O5' GDP . . . E 3 40.508 8.111 36.886 1 89.01 ? O5' GDP 200 A 1 HETATM 10 C C5' GDP . . . E 3 40.636 8.106 38.305 1 93.33 ? C5' GDP 200 A 1 HETATM 11 C C4' GDP . . . E 3 42.038 7.707 38.742 1 94.06 ? C4' GDP 200 A 1 HETATM 12 O O4' GDP . . . E 3 42.991 8.258 37.835 1 91.01 ? O4' GDP 200 A 1 HETATM 13 C C3' GDP . . . E 3 42.314 8.314 40.106 1 95.15 ? C3' GDP 200 A 1 HETATM 14 O O3' GDP . . . E 3 43.121 7.425 40.886 1 97.41 ? O3' GDP 200 A 1 HETATM 15 C C2' GDP . . . E 3 43.081 9.584 39.813 1 91.32 ? C2' GDP 200 A 1 HETATM 16 O O2' GDP . . . E 3 44.061 9.822 40.827 1 91.01 ? O2' GDP 200 A 1 HETATM 17 C C1' GDP . . . E 3 43.727 9.315 38.462 1 90.09 ? C1' GDP 200 A 1 HETATM 18 N N9 GDP . . . E 3 43.669 10.503 37.575 1 86.78 ? N9 GDP 200 A 1 HETATM 19 C C8 GDP . . . E 3 42.661 10.802 36.736 1 83.76 ? C8 GDP 200 A 1 HETATM 20 N N7 GDP . . . E 3 42.914 11.943 36.052 1 81.48 ? N7 GDP 200 A 1 HETATM 21 C C5 GDP . . . E 3 44.118 12.395 36.453 1 82.49 ? C5 GDP 200 A 1 HETATM 22 C C6 GDP . . . E 3 44.989 13.553 36.131 1 81.12 ? C6 GDP 200 A 1 HETATM 23 O O6 GDP . . . E 3 44.642 14.414 35.289 1 77.92 ? O6 GDP 200 A 1 HETATM 24 N N1 GDP . . . E 3 46.159 13.644 36.772 1 83.05 ? N1 GDP 200 A 1 HETATM 25 C C2 GDP . . . E 3 46.561 12.733 37.679 1 84.01 ? C2 GDP 200 A 1 HETATM 26 N N2 GDP . . . E 3 47.762 12.897 38.286 1 83.92 ? N2 GDP 200 A 1 HETATM 27 N N3 GDP . . . E 3 45.818 11.652 38.023 1 84.47 ? N3 GDP 200 A 1 HETATM 28 C C4 GDP . . . E 3 44.611 11.438 37.455 1 84.5 ? C4 GDP 200 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #