data_9I8H # _model_server_result.job_id 0f6hVHw1nvZLsvjE80HQQA _model_server_result.datetime_utc '2025-09-08 16:48:40' _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 9i8h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"NA","auth_seq_id":501}' # _entry.id 9I8H # _exptl.entry_id 9I8H _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 14 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 33-meric _pdbx_struct_assembly.oligomeric_count 33 _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,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA _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 ? 10 IA N N ? 10 JA N N ? 10 KA N N ? 10 LA N N ? 10 MA N N ? 10 NA N N ? 10 OA N N ? 10 PA N N ? 10 QA N N ? 10 RA N N ? 10 SA N N ? 10 TA N N ? 10 UA N N ? 10 VA 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 127 n n PB O2B GDP sing 128 n n PB O3B GDP sing 129 n n PB O3A GDP sing 130 n n O2B HOB2 GDP sing 131 n n O3B HOB3 GDP sing 132 n n O3A PA GDP sing 133 n n PA O1A GDP doub 134 n n PA O2A GDP sing 135 n n PA O5' GDP sing 136 n n O2A HOA2 GDP sing 137 n n O5' C5' GDP sing 138 n n C5' C4' GDP sing 139 n n C5' H5' GDP sing 140 n n C5' "H5''" GDP sing 141 n n C4' O4' GDP sing 142 n n C4' C3' GDP sing 143 n n C4' H4' GDP sing 144 n n O4' C1' GDP sing 145 n n C3' O3' GDP sing 146 n n C3' C2' GDP sing 147 n n C3' H3' GDP sing 148 n n O3' HO3' GDP sing 149 n n C2' O2' GDP sing 150 n n C2' C1' GDP sing 151 n n C2' H2' GDP sing 152 n n O2' HO2' GDP sing 153 n n C1' N9 GDP sing 154 n n C1' H1' GDP sing 155 n n N9 C8 GDP sing 156 n y N9 C4 GDP sing 157 n y C8 N7 GDP doub 158 n y C8 H8 GDP sing 159 n n N7 C5 GDP sing 160 n y C5 C6 GDP sing 161 n n C5 C4 GDP doub 162 n y C6 O6 GDP doub 163 n n C6 N1 GDP sing 164 n n N1 C2 GDP sing 165 n n N1 HN1 GDP sing 166 n n C2 N2 GDP sing 167 n n C2 N3 GDP doub 168 n n N2 HN21 GDP sing 169 n n N2 HN22 GDP sing 170 n n N3 C4 GDP sing 171 n n # _atom_sites.entry_id 9I8H _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 HA 9 ADP U 1 800 800 ADP ADP . IA 10 GDP a 1 501 501 GDP GDP . JA 10 GDP b 1 501 501 GDP GDP . KA 10 GDP c 1 501 501 GDP GDP . LA 10 GDP d 1 501 501 GDP GDP . MA 10 GDP e 1 501 501 GDP GDP . NA 10 GDP f 1 501 501 GDP GDP . OA 10 GDP g 1 501 501 GDP GDP . PA 10 GDP h 1 501 501 GDP GDP . QA 10 GDP i 1 501 501 GDP GDP . RA 10 GDP j 1 501 501 GDP GDP . SA 10 GDP k 1 501 501 GDP GDP . TA 10 GDP l 1 501 501 GDP GDP . UA 10 GDP m 1 501 501 GDP GDP . VA 10 GDP t 1 501 501 GDP GDP . # 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 . . . NA 10 369.85 275.093 419.731 1 86.95 ? PB GDP 501 f 1 HETATM 2 O O1B GDP . . . NA 10 370.826 274.48 420.706 1 86.95 ? O1B GDP 501 f 1 HETATM 3 O O2B GDP . . . NA 10 370.471 276.05 418.742 1 86.95 ? O2B GDP 501 f 1 HETATM 4 O O3B GDP . . . NA 10 368.879 274.106 419.124 1 86.95 ? O3B GDP 501 f 1 HETATM 5 O O3A GDP . . . NA 10 368.927 276.033 420.655 1 86.95 ? O3A GDP 501 f 1 HETATM 6 P PA GDP . . . NA 10 367.491 276.535 420.134 1 86.95 ? PA GDP 501 f 1 HETATM 7 O O1A GDP . . . NA 10 367.689 277.233 418.809 1 86.95 ? O1A GDP 501 f 1 HETATM 8 O O2A GDP . . . NA 10 366.521 275.383 420.242 1 86.95 ? O2A GDP 501 f 1 HETATM 9 O O5' GDP . . . NA 10 367.088 277.642 421.231 1 86.95 ? O5' GDP 501 f 1 HETATM 10 C C5' GDP . . . NA 10 365.74 278.085 421.351 1 86.95 ? C5' GDP 501 f 1 HETATM 11 C C4' GDP . . . NA 10 365.705 279.4 422.119 1 86.95 ? C4' GDP 501 f 1 HETATM 12 O O4' GDP . . . NA 10 366.27 280.441 421.317 1 86.95 ? O4' GDP 501 f 1 HETATM 13 C C3' GDP . . . NA 10 364.28 279.809 422.455 1 86.95 ? C3' GDP 501 f 1 HETATM 14 O O3' GDP . . . NA 10 364.046 279.636 423.86 1 86.95 ? O3' GDP 501 f 1 HETATM 15 C C2' GDP . . . NA 10 364.147 281.26 422.009 1 86.95 ? C2' GDP 501 f 1 HETATM 16 O O2' GDP . . . NA 10 363.83 282.146 423.09 1 86.95 ? O2' GDP 501 f 1 HETATM 17 C C1' GDP . . . NA 10 365.493 281.638 421.413 1 86.95 ? C1' GDP 501 f 1 HETATM 18 N N9 GDP . . . NA 10 365.302 282.23 420.067 1 86.95 ? N9 GDP 501 f 1 HETATM 19 C C8 GDP . . . NA 10 365.24 281.546 418.908 1 86.95 ? C8 GDP 501 f 1 HETATM 20 N N7 GDP . . . NA 10 365.056 282.381 417.855 1 86.95 ? N7 GDP 501 f 1 HETATM 21 C C5 GDP . . . NA 10 364.998 283.633 418.338 1 86.95 ? C5 GDP 501 f 1 HETATM 22 C C6 GDP . . . NA 10 364.821 284.99 417.768 1 86.95 ? C6 GDP 501 f 1 HETATM 23 O O6 GDP . . . NA 10 364.677 285.159 416.538 1 86.95 ? O6 GDP 501 f 1 HETATM 24 N N1 GDP . . . NA 10 364.819 286.031 418.611 1 86.95 ? N1 GDP 501 f 1 HETATM 25 C C2 GDP . . . NA 10 364.971 285.878 419.942 1 86.95 ? C2 GDP 501 f 1 HETATM 26 N N2 GDP . . . NA 10 364.957 286.984 420.722 1 86.95 ? N2 GDP 501 f 1 HETATM 27 N N3 GDP . . . NA 10 365.139 284.668 420.531 1 86.95 ? N3 GDP 501 f 1 HETATM 28 C C4 GDP . . . NA 10 365.161 283.53 419.796 1 86.95 ? C4 GDP 501 f 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 140 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #