data_3J8X # _model_server_result.job_id UBRp9zL2lerc-VQxh_rNRA _model_server_result.datetime_utc '2024-10-20 20:02:40' _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 3j8x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 3J8X # _exptl.entry_id 3J8X _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 90 _cell.entry_id 3J8X _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3J8X _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 3J8X _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 D 4 GTP A 1 600 600 GTP GTP . E 5 GDP B 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 . . . E 5 -48.523 108.414 3.03 1 0 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . E 5 -48.406 109.591 2.143 1 0 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . E 5 -48.926 108.744 4.467 1 0 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . E 5 -47.31 107.437 3.095 1 0 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . E 5 -49.876 107.669 2.516 1 0 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . E 5 -49.84 106.102 2.545 1 0 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . E 5 -49.121 105.573 1.372 1 0 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . E 5 -49.596 105.538 3.91 1 0 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . E 5 -51.384 105.844 2.327 1 0 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . E 5 -51.816 104.684 1.568 1 0 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . E 5 -53.317 104.576 1.499 1 0 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . E 5 -53.703 103.267 0.888 1 0 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . E 5 -53.908 104.342 2.913 1 0 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . E 5 -55.247 104.921 2.977 1 0 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . E 5 -53.656 102.813 3.157 1 0 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . E 5 -54.629 102.097 4.03 1 0 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . E 5 -53.782 102.24 1.851 1 0 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . E 5 -52.768 101.074 1.62 1 0 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . E 5 -51.647 100.623 2.399 1 0 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . E 5 -50.921 99.718 1.854 1 0 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . E 5 -51.462 99.569 0.572 1 0 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . E 5 -51.029 98.786 -0.556 1 0 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . E 5 -50.052 98.126 -0.712 1 0 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . E 5 -51.842 98.991 -1.614 1 0 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . E 5 -52.983 99.744 -1.727 1 0 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . E 5 -53.662 99.71 -2.822 1 0 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . E 5 -53.404 100.457 -0.705 1 0 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . E 5 -52.622 100.36 0.431 1 0 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #