data_3J4S # _model_server_result.job_id 3plzgu72fnvO6pp-AkNwwA _model_server_result.datetime_utc '2024-10-13 16:26:32' _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 3j4s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":900}' # _entry.id 3J4S # _exptl.entry_id 3J4S _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 3J4S _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3J4S _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? helical 24 'representative helical assembly' 1 ? monomeric 1 'helical asymmetric unit' 2 ? monomeric 1 'helical asymmetric unit, std helical frame' 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B 1 (1-24) A,B 2 1 A,B 3 H # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] H 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'helical symmetry operation' ? ? 0 -1 0 1 0 0 0 0 1 0 0 0 3 'helical symmetry operation' ? ? -1 0 0 0 -1 0 0 0 1 0 0 0 4 'helical symmetry operation' ? ? 0 1 0 -1 0 0 0 0 1 0 0 0 5 'helical symmetry operation' ? ? 0.849999 -0.526784 0 0.526784 0.849999 0 0 0 1 0 0 43.54512 6 'helical symmetry operation' ? ? -0.526784 -0.849999 0 0.849999 -0.526784 0 0 0 1 0 0 43.54512 7 'helical symmetry operation' ? ? -0.849999 0.526784 0 -0.526784 -0.849999 0 0 0 1 0 0 43.54512 8 'helical symmetry operation' ? ? 0.526784 0.849999 0 -0.849999 0.526784 0 0 0 1 0 0 43.54512 9 'helical symmetry operation' ? ? 0.444997 -0.895532 0 0.895532 0.444997 0 0 0 1 0 0 87.09024 10 'helical symmetry operation' ? ? -0.895532 -0.444997 0 0.444997 -0.895532 0 0 0 1 0 0 87.09024 11 'helical symmetry operation' ? ? -0.444997 0.895532 0 -0.895532 -0.444997 0 0 0 1 0 0 87.09024 12 'helical symmetry operation' ? ? 0.895532 0.444997 0 -0.444997 0.895532 0 0 0 1 0 0 87.09024 13 'helical symmetry operation' ? ? -0.093505 -0.995619 0 0.995619 -0.093505 0 0 0 1 0 0 130.63536 14 'helical symmetry operation' ? ? -0.995619 0.093505 0 -0.093505 -0.995619 0 0 0 1 0 0 130.63536 15 'helical symmetry operation' ? ? 0.093505 0.995619 0 -0.995619 0.093505 0 0 0 1 0 0 130.63536 16 'helical symmetry operation' ? ? 0.995619 -0.093505 0 0.093505 0.995619 0 0 0 1 0 0 130.63536 17 'helical symmetry operation' ? ? -0.603956 -0.797018 0 0.797018 -0.603956 0 0 0 1 0 0 174.18048 18 'helical symmetry operation' ? ? -0.797018 0.603956 0 -0.603956 -0.797018 0 0 0 1 0 0 174.18048 19 'helical symmetry operation' ? ? 0.603956 0.797018 0 -0.797018 0.603956 0 0 0 1 0 0 174.18048 20 'helical symmetry operation' ? ? 0.797018 -0.603956 0 0.603956 0.797018 0 0 0 1 0 0 174.18048 21 'helical symmetry operation' ? ? -0.933218 -0.35931 0 0.35931 -0.933218 0 0 0 1 0 0 217.7256 22 'helical symmetry operation' ? ? -0.35931 0.933218 0 -0.933218 -0.35931 0 0 0 1 0 0 217.7256 23 'helical symmetry operation' ? ? 0.933218 0.35931 0 -0.35931 0.933218 0 0 0 1 0 0 217.7256 24 'helical symmetry operation' ? ? 0.35931 -0.933218 0 0.933218 0.35931 0 0 0 1 0 0 217.7256 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 3J4S _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 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id GDP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 900 _pdbx_nonpoly_scheme.auth_seq_num 900 _pdbx_nonpoly_scheme.pdb_mon_id GDP _pdbx_nonpoly_scheme.auth_mon_id GDP _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . B 2 -22.601 -29.824 -84.904 1 0 ? PB GDP 900 A 1 HETATM 2 O O1B GDP . . . B 2 -23.768 -30.703 -85.313 1 0 ? O1B GDP 900 A 1 HETATM 3 O O2B GDP . . . B 2 -21.738 -30.422 -83.816 1 0 ? O2B GDP 900 A 1 HETATM 4 O O3B GDP . . . B 2 -22.955 -28.369 -84.628 1 0 ? O3B GDP 900 A 1 HETATM 5 O O3A GDP . . . B 2 -21.639 -29.774 -86.266 1 0 ? O3A GDP 900 A 1 HETATM 6 P PA GDP . . . B 2 -20.48 -28.782 -86.674 1 0 ? PA GDP 900 A 1 HETATM 7 O O1A GDP . . . B 2 -20.927 -27.858 -87.732 1 0 ? O1A GDP 900 A 1 HETATM 8 O O2A GDP . . . B 2 -20.004 -28.207 -85.416 1 0 ? O2A GDP 900 A 1 HETATM 9 O O5' GDP . . . B 2 -19.37 -29.709 -87.239 1 0 ? O5' GDP 900 A 1 HETATM 10 C C5' GDP . . . B 2 -19.549 -30.515 -88.404 1 0 ? C5' GDP 900 A 1 HETATM 11 C C4' GDP . . . B 2 -18.55 -30.087 -89.458 1 0 ? C4' GDP 900 A 1 HETATM 12 O O4' GDP . . . B 2 -18.741 -28.724 -89.796 1 0 ? O4' GDP 900 A 1 HETATM 13 C C3' GDP . . . B 2 -17.073 -30.184 -89.055 1 0 ? C3' GDP 900 A 1 HETATM 14 O O3' GDP . . . B 2 -16.292 -30.59 -90.185 1 0 ? O3' GDP 900 A 1 HETATM 15 C C2' GDP . . . B 2 -16.746 -28.777 -88.653 1 0 ? C2' GDP 900 A 1 HETATM 16 O O2' GDP . . . B 2 -15.397 -28.426 -88.809 1 0 ? O2' GDP 900 A 1 HETATM 17 C C1' GDP . . . B 2 -17.522 -28.099 -89.671 1 0 ? C1' GDP 900 A 1 HETATM 18 N N9 GDP . . . B 2 -17.71 -26.785 -89.334 1 0 ? N9 GDP 900 A 1 HETATM 19 C C8 GDP . . . B 2 -18.321 -26.273 -88.256 1 0 ? C8 GDP 900 A 1 HETATM 20 N N7 GDP . . . B 2 -18.398 -25 -88.337 1 0 ? N7 GDP 900 A 1 HETATM 21 C C5 GDP . . . B 2 -17.806 -24.694 -89.492 1 0 ? C5 GDP 900 A 1 HETATM 22 C C6 GDP . . . B 2 -17.817 -23.494 -90.163 1 0 ? C6 GDP 900 A 1 HETATM 23 O O6 GDP . . . B 2 -18.41 -22.501 -89.763 1 0 ? O6 GDP 900 A 1 HETATM 24 N N1 GDP . . . B 2 -17.02 -23.559 -91.31 1 0 ? N1 GDP 900 A 1 HETATM 25 C C2 GDP . . . B 2 -16.383 -24.713 -91.766 1 0 ? C2 GDP 900 A 1 HETATM 26 N N2 GDP . . . B 2 -15.525 -24.548 -92.8 1 0 ? N2 GDP 900 A 1 HETATM 27 N N3 GDP . . . B 2 -16.63 -25.911 -91.218 1 0 ? N3 GDP 900 A 1 HETATM 28 C C4 GDP . . . B 2 -17.295 -25.794 -90.081 1 0 ? C4 GDP 900 A 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #