data_9HXC # _model_server_result.job_id BTK4oxsn8yegI-gA9czgDw _model_server_result.datetime_utc '2025-04-10 11:30:08' _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 9hxc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"OA","auth_seq_id":501}' # _entry.id 9HXC # _exptl.entry_id 9HXC _exptl.method 'ELECTRON MICROSCOPY' # _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 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 28-meric _pdbx_struct_assembly.oligomeric_count 28 _pdbx_struct_assembly.details author_and_software_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 _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 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 CA N N ? 3 DA N N ? 3 EA N N ? 3 FA N N ? 3 GA N N ? 3 HA N N ? 3 IA N N ? 3 JA N N ? 3 KA N N ? 3 LA N N ? 3 MA N N ? 3 NA N N ? 3 OA N N ? 3 PA 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 9HXC _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 CA 3 GDP A 1 501 501 GDP GDP . DA 3 GDP B 1 501 501 GDP GDP . EA 3 GDP E 1 501 501 GDP GDP . FA 3 GDP G 1 501 501 GDP GDP . GA 3 GDP I 1 501 501 GDP GDP . HA 3 GDP K 1 501 501 GDP GDP . IA 3 GDP M 1 501 501 GDP GDP . JA 3 GDP O 1 501 501 GDP GDP . KA 3 GDP Q 1 501 501 GDP GDP . LA 3 GDP S 1 501 501 GDP GDP . MA 3 GDP U 1 501 501 GDP GDP . NA 3 GDP W 1 501 501 GDP GDP . OA 3 GDP Y 1 501 501 GDP GDP . PA 3 GDP a 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 . . . OA 3 93.512 156.493 209.841 1 51.88 ? PB GDP 501 Y 1 HETATM 2 O O1B GDP . . . OA 3 93.671 155.013 209.786 1 44.58 ? O1B GDP 501 Y 1 HETATM 3 O O2B GDP . . . OA 3 92.491 156.956 211.016 1 42.93 ? O2B GDP 501 Y 1 HETATM 4 O O3B GDP . . . OA 3 92.84 157.106 208.522 1 37.86 ? O3B GDP 501 Y 1 HETATM 5 O O3A GDP . . . OA 3 94.911 157.133 210.169 1 42.35 ? O3A GDP 501 Y 1 HETATM 6 P PA GDP . . . OA 3 95.852 158.054 209.298 1 52.33 ? PA GDP 501 Y 1 HETATM 7 O O1A GDP . . . OA 3 96.776 157.222 208.51 1 44.81 ? O1A GDP 501 Y 1 HETATM 8 O O2A GDP . . . OA 3 95.015 159.017 208.312 1 44.2 ? O2A GDP 501 Y 1 HETATM 9 O O5' GDP . . . OA 3 96.722 158.977 210.3 1 39.73 ? O5' GDP 501 Y 1 HETATM 10 C C5' GDP . . . OA 3 96.364 160.264 210.88 1 39.01 ? C5' GDP 501 Y 1 HETATM 11 C C4' GDP . . . OA 3 97.635 160.963 211.415 1 38.53 ? C4' GDP 501 Y 1 HETATM 12 O O4' GDP . . . OA 3 98.269 160.125 212.392 1 37.29 ? O4' GDP 501 Y 1 HETATM 13 C C3' GDP . . . OA 3 98.699 161.17 210.327 1 39.52 ? C3' GDP 501 Y 1 HETATM 14 O O3' GDP . . . OA 3 98.386 162.345 209.573 1 43.44 ? O3' GDP 501 Y 1 HETATM 15 C C2' GDP . . . OA 3 100.006 161.303 211.156 1 37.49 ? C2' GDP 501 Y 1 HETATM 16 O O2' GDP . . . OA 3 100.237 162.667 211.56 1 36.85 ? O2' GDP 501 Y 1 HETATM 17 C C1' GDP . . . OA 3 99.711 160.388 212.4 1 35.26 ? C1' GDP 501 Y 1 HETATM 18 N N9 GDP . . . OA 3 100.49 159.107 212.369 1 35.34 ? N9 GDP 501 Y 1 HETATM 19 C C8 GDP . . . OA 3 100.313 158.054 211.496 1 36.54 ? C8 GDP 501 Y 1 HETATM 20 N N7 GDP . . . OA 3 100.963 156.999 211.889 1 31.15 ? N7 GDP 501 Y 1 HETATM 21 C C5 GDP . . . OA 3 101.608 157.278 213.04 1 33.49 ? C5 GDP 501 Y 1 HETATM 22 C C6 GDP . . . OA 3 102.474 156.543 213.961 1 35.91 ? C6 GDP 501 Y 1 HETATM 23 O O6 GDP . . . OA 3 102.883 155.416 213.723 1 40.23 ? O6 GDP 501 Y 1 HETATM 24 N N1 GDP . . . OA 3 102.851 157.152 215.153 1 34.61 ? N1 GDP 501 Y 1 HETATM 25 C C2 GDP . . . OA 3 102.61 158.509 215.376 1 35.86 ? C2 GDP 501 Y 1 HETATM 26 N N2 GDP . . . OA 3 103.123 159.119 216.466 1 39.19 ? N2 GDP 501 Y 1 HETATM 27 N N3 GDP . . . OA 3 101.873 159.23 214.509 1 39.16 ? N3 GDP 501 Y 1 HETATM 28 C C4 GDP . . . OA 3 101.32 158.653 213.359 1 37.04 ? C4 GDP 501 Y 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 99 _model_server_stats.query_time_ms 214 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 28 #