data_4G5O # _model_server_result.job_id Rf1_SGcukPi5uBice4JjWQ _model_server_result.datetime_utc '2024-11-22 13:23:57' _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 4g5o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 4G5O # _exptl.entry_id 4G5O _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 4 _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 120 _cell.entry_id 4G5O _cell.length_a 207.326 _cell.length_b 207.326 _cell.length_c 236.545 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4G5O _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # 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 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I,J,K,L,M,N,O,HA 1 1 B,F,P,Q,R,S,T,IA,LA 2 1 C,G,U,V,W,X,Y,Z,JA,MA 3 1 D,H,AA,BA,CA,DA,EA,FA,GA,KA 4 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 I N N ? 3 P N N ? 3 U N N ? 3 AA 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 103 n n PB O2B GDP sing 104 n n PB O3B GDP sing 105 n n PB O3A GDP sing 106 n n O2B HOB2 GDP sing 107 n n O3B HOB3 GDP sing 108 n n O3A PA GDP sing 109 n n PA O1A GDP doub 110 n n PA O2A GDP sing 111 n n PA O5' GDP sing 112 n n O2A HOA2 GDP sing 113 n n O5' C5' GDP sing 114 n n C5' C4' GDP sing 115 n n C5' H5' GDP sing 116 n n C5' "H5''" GDP sing 117 n n C4' O4' GDP sing 118 n n C4' C3' GDP sing 119 n n C4' H4' GDP sing 120 n n O4' C1' GDP sing 121 n n C3' O3' GDP sing 122 n n C3' C2' GDP sing 123 n n C3' H3' GDP sing 124 n n O3' HO3' GDP sing 125 n n C2' O2' GDP sing 126 n n C2' C1' GDP sing 127 n n C2' H2' GDP sing 128 n n O2' HO2' GDP sing 129 n n C1' N9 GDP sing 130 n n C1' H1' GDP sing 131 n n N9 C8 GDP sing 132 n y N9 C4 GDP sing 133 n y C8 N7 GDP doub 134 n y C8 H8 GDP sing 135 n n N7 C5 GDP sing 136 n y C5 C6 GDP sing 137 n n C5 C4 GDP doub 138 n y C6 O6 GDP doub 139 n n C6 N1 GDP sing 140 n n N1 C2 GDP sing 141 n n N1 HN1 GDP sing 142 n n C2 N2 GDP sing 143 n n C2 N3 GDP doub 144 n n N2 HN21 GDP sing 145 n n N2 HN22 GDP sing 146 n n N3 C4 GDP sing 147 n n # _atom_sites.entry_id 4G5O _atom_sites.fract_transf_matrix[1][1] 0.004823 _atom_sites.fract_transf_matrix[1][2] 0.002785 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005569 _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] 0.004228 _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 I 3 GDP A 1 401 1 GDP GDP . J 4 CIT A 1 402 2 CIT CIT . K 4 CIT A 1 403 4 CIT CIT . L 5 SO4 A 1 404 3 SO4 SO4 . M 5 SO4 A 1 405 5 SO4 SO4 . N 5 SO4 A 1 406 7 SO4 SO4 . O 5 SO4 A 1 407 16 SO4 SO4 . P 3 GDP B 1 401 2 GDP GDP . Q 5 SO4 B 1 402 1 SO4 SO4 . R 5 SO4 B 1 403 4 SO4 SO4 . S 5 SO4 B 1 404 8 SO4 SO4 . T 5 SO4 B 1 405 18 SO4 SO4 . U 3 GDP C 1 401 3 GDP GDP . V 4 CIT C 1 402 1 CIT CIT . W 5 SO4 C 1 403 2 SO4 SO4 . X 5 SO4 C 1 404 6 SO4 SO4 . Y 5 SO4 C 1 405 11 SO4 SO4 . Z 5 SO4 C 1 406 13 SO4 SO4 . AA 3 GDP D 1 401 4 GDP GDP . BA 4 CIT D 1 402 3 CIT CIT . CA 5 SO4 D 1 403 9 SO4 SO4 . DA 5 SO4 D 1 404 10 SO4 SO4 . EA 5 SO4 D 1 405 15 SO4 SO4 . FA 5 SO4 D 1 406 17 SO4 SO4 . GA 5 SO4 D 1 407 19 SO4 SO4 . HA 6 HOH A 1 501 14 HOH HOH . HA 6 HOH A 2 502 37 HOH HOH . IA 6 HOH B 1 501 11 HOH HOH . JA 6 HOH C 1 501 2 HOH HOH . JA 6 HOH C 2 502 8 HOH HOH . JA 6 HOH C 3 503 25 HOH HOH . JA 6 HOH C 4 504 34 HOH HOH . KA 6 HOH D 1 501 5 HOH HOH . KA 6 HOH D 2 502 7 HOH HOH . KA 6 HOH D 3 503 12 HOH HOH . LA 6 HOH F 1 701 10 HOH HOH . MA 6 HOH G 1 701 16 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 . . . I 3 55.655 -51.538 37.818 1 50.38 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . I 3 55.373 -52.783 38.617 1 49.39 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . I 3 56.97 -51.538 37.064 1 49.34 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . I 3 54.493 -51.071 36.977 1 48.35 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . I 3 55.819 -50.512 39.06 1 50.25 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . I 3 54.714 -49.407 39.501 1 49.94 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . I 3 53.361 -49.98 39.806 1 46.04 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . I 3 54.751 -48.304 38.484 1 50.07 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . I 3 55.359 -48.894 40.879 1 51.79 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . I 3 55.65 -49.777 41.956 1 53.46 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . I 3 55.241 -49.126 43.281 1 58.67 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . I 3 56.21 -48.172 43.732 1 57.31 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . I 3 53.946 -48.343 43.187 1 58.18 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . I 3 53.354 -48.391 44.483 1 56.77 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . I 3 54.403 -46.929 42.873 1 59.64 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . I 3 53.393 -45.948 43.162 1 59.21 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . I 3 55.68 -46.837 43.705 1 59.72 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . I 3 56.784 -46.046 43.118 1 61.87 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . I 3 57.208 -46.085 41.84 1 61.97 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . I 3 58.269 -45.27 41.647 1 59.37 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . I 3 58.552 -44.703 42.834 1 60.3 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . I 3 59.558 -43.742 43.342 1 59.41 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . I 3 60.407 -43.288 42.532 1 57.19 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . I 3 59.523 -43.403 44.656 1 57.99 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . I 3 58.599 -43.916 45.5 1 59.27 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . I 3 58.581 -43.568 46.811 1 57.15 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . I 3 57.656 -44.8 45.087 1 61.47 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . I 3 57.581 -45.223 43.801 1 61.38 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #