data_7AS4 # _model_server_result.job_id xf2gHmZuELZ057AGOPTuzw _model_server_result.datetime_utc '2025-04-04 17:26:24' _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 7as4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"SA","auth_seq_id":1501}' # _entry.id 7AS4 # _exptl.entry_id 7AS4 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 9 _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 _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 ? 9 HA N N ? 9 IA N N ? 9 JA N N ? 9 KA N N ? 9 LA N N ? 9 MA N N ? 9 NA N N ? 9 OA N N ? 9 PA N N ? 9 QA N N ? 9 RA N N ? 9 SA N N ? 9 TA N N ? 9 UA 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 7AS4 _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 GDP 1 1 1501 1501 GDP GDP . IA 9 GDP 2 1 1501 1501 GDP GDP . JA 9 GDP O 1 1501 1501 GDP GDP . KA 9 GDP P 1 1501 1501 GDP GDP . LA 9 GDP Q 1 1501 1501 GDP GDP . MA 9 GDP R 1 1501 1501 GDP GDP . NA 9 GDP S 1 1501 1501 GDP GDP . OA 9 GDP T 1 1501 1501 GDP GDP . PA 9 GDP U 1 1501 1501 GDP GDP . QA 9 GDP V 1 1501 1501 GDP GDP . RA 9 GDP W 1 1501 1501 GDP GDP . SA 9 GDP X 1 1501 1501 GDP GDP . TA 9 GDP Y 1 1501 1501 GDP GDP . UA 9 GDP Z 1 1501 1501 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 . . . SA 9 325.057 264.462 145.591 1 302.34 ? PB GDP 1501 X 1 HETATM 2 O O1B GDP . . . SA 9 325.268 264.5 144.103 1 297.87 ? O1B GDP 1501 X 1 HETATM 3 O O2B GDP . . . SA 9 324.418 263.223 146.138 1 303.48 -1 O2B GDP 1501 X 1 HETATM 4 O O3B GDP . . . SA 9 326.264 264.908 146.376 1 285.95 ? O3B GDP 1501 X 1 HETATM 5 O O3A GDP . . . SA 9 323.949 265.583 145.864 1 292.61 ? O3A GDP 1501 X 1 HETATM 6 P PA GDP . . . SA 9 324.499 267.055 146.14 1 287.68 ? PA GDP 1501 X 1 HETATM 7 O O1A GDP . . . SA 9 325.558 267.351 145.108 1 294.29 ? O1A GDP 1501 X 1 HETATM 8 O O2A GDP . . . SA 9 324.785 267.207 147.61 1 280.51 -1 O2A GDP 1501 X 1 HETATM 9 O O5' GDP . . . SA 9 323.243 267.975 145.795 1 281.07 ? O5' GDP 1501 X 1 HETATM 10 C C5' GDP . . . SA 9 323.509 269.354 145.599 1 276.58 ? C5' GDP 1501 X 1 HETATM 11 C C4' GDP . . . SA 9 322.38 270.148 146.214 1 281.62 ? C4' GDP 1501 X 1 HETATM 12 O O4' GDP . . . SA 9 322.115 269.689 147.529 1 284.41 ? O4' GDP 1501 X 1 HETATM 13 C C3' GDP . . . SA 9 322.72 271.617 146.311 1 280.3 ? C3' GDP 1501 X 1 HETATM 14 O O3' GDP . . . SA 9 321.804 272.311 145.479 1 269.97 ? O3' GDP 1501 X 1 HETATM 15 C C2' GDP . . . SA 9 322.543 271.99 147.761 1 282.81 ? C2' GDP 1501 X 1 HETATM 16 O O2' GDP . . . SA 9 321.716 273.139 147.926 1 282.32 ? O2' GDP 1501 X 1 HETATM 17 C C1' GDP . . . SA 9 321.829 270.809 148.353 1 275.09 ? C1' GDP 1501 X 1 HETATM 18 N N9 GDP . . . SA 9 322.217 270.444 149.732 1 270.9 ? N9 GDP 1501 X 1 HETATM 19 C C8 GDP . . . SA 9 323.312 269.768 150.113 1 274.31 ? C8 GDP 1501 X 1 HETATM 20 N N7 GDP . . . SA 9 323.31 269.584 151.459 1 252.91 ? N7 GDP 1501 X 1 HETATM 21 C C5 GDP . . . SA 9 322.184 270.13 151.946 1 256.32 ? C5 GDP 1501 X 1 HETATM 22 C C6 GDP . . . SA 9 321.537 270.305 153.26 1 262.65 ? C6 GDP 1501 X 1 HETATM 23 O O6 GDP . . . SA 9 322.076 269.864 154.29 1 268.95 ? O6 GDP 1501 X 1 HETATM 24 N N1 GDP . . . SA 9 320.366 270.946 153.318 1 263.67 ? N1 GDP 1501 X 1 HETATM 25 C C2 GDP . . . SA 9 319.765 271.432 152.222 1 256.87 ? C2 GDP 1501 X 1 HETATM 26 N N2 GDP . . . SA 9 318.577 272.076 152.331 1 253.47 ? N2 GDP 1501 X 1 HETATM 27 N N3 GDP . . . SA 9 320.302 271.312 150.992 1 248.56 ? N3 GDP 1501 X 1 HETATM 28 C C4 GDP . . . SA 9 321.485 270.697 150.804 1 258.29 ? C4 GDP 1501 X 1 # _model_server_stats.io_time_ms 147 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 209 _model_server_stats.query_time_ms 550 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #