data_3JD0 # _model_server_result.job_id 2ELYDuJEkJ51wNLmPjLPnQ _model_server_result.datetime_utc '2024-11-29 14:12:48' _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 3jd0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":601}' # _entry.id 3JD0 # _exptl.entry_id 3JD0 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.18 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _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 3JD0 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JD0 _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _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 PG O1G GTP doub 129 n n PG O2G GTP sing 130 n n PG O3G GTP sing 131 n n PG O3B GTP sing 132 n n O2G HOG2 GTP sing 133 n n O3G HOG3 GTP sing 134 n n O3B PB GTP sing 135 n n PB O1B GTP doub 136 n n PB O2B GTP sing 137 n n PB O3A GTP sing 138 n n O2B HOB2 GTP sing 139 n n O3A PA GTP sing 140 n n PA O1A GTP doub 141 n n PA O2A GTP sing 142 n n PA O5' GTP sing 143 n n O2A HOA2 GTP sing 144 n n O5' C5' GTP sing 145 n n C5' C4' GTP sing 146 n n C5' H5' GTP sing 147 n n C5' "H5''" GTP sing 148 n n C4' O4' GTP sing 149 n n C4' C3' GTP sing 150 n n C4' H4' GTP sing 151 n n O4' C1' GTP sing 152 n n C3' O3' GTP sing 153 n n C3' C2' GTP sing 154 n n C3' H3' GTP sing 155 n n O3' HO3' GTP sing 156 n n C2' O2' GTP sing 157 n n C2' C1' GTP sing 158 n n C2' H2' GTP sing 159 n n O2' HO2' GTP sing 160 n n C1' N9 GTP sing 161 n n C1' H1' GTP sing 162 n n N9 C8 GTP sing 163 n y N9 C4 GTP sing 164 n y C8 N7 GTP doub 165 n y C8 H8 GTP sing 166 n n N7 C5 GTP sing 167 n y C5 C6 GTP sing 168 n n C5 C4 GTP doub 169 n y C6 O6 GTP doub 170 n n C6 N1 GTP sing 171 n n N1 C2 GTP sing 172 n n N1 HN1 GTP sing 173 n n C2 N2 GTP sing 174 n n C2 N3 GTP doub 175 n n N2 HN21 GTP sing 176 n n N2 HN22 GTP sing 177 n n N3 C4 GTP sing 178 n n # _atom_sites.entry_id 3JD0 _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 G 2 GTP A 1 601 503 GTP GTP . H 2 GTP B 1 601 503 GTP GTP . I 2 GTP C 1 601 503 GTP GTP . J 2 GTP D 1 601 503 GTP GTP . K 2 GTP E 1 601 503 GTP GTP . L 2 GTP F 1 601 503 GTP GTP . # 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 PG GTP . . . L 2 63.484 65.235 118.495 1 21.31 ? PG GTP 601 F 1 HETATM 2 O O1G GTP . . . L 2 63.558 65.429 117.004 1 21.22 ? O1G GTP 601 F 1 HETATM 3 O O2G GTP . . . L 2 63.824 63.821 118.889 1 13.22 ? O2G GTP 601 F 1 HETATM 4 O O3G GTP . . . L 2 62.079 65.526 118.954 1 16.62 ? O3G GTP 601 F 1 HETATM 5 O O3B GTP . . . L 2 64.496 66.258 119.201 1 25.78 ? O3B GTP 601 F 1 HETATM 6 P PB GTP . . . L 2 66.083 66.188 118.953 1 25.81 ? PB GTP 601 F 1 HETATM 7 O O1B GTP . . . L 2 66.391 66.848 117.636 1 23.12 ? O1B GTP 601 F 1 HETATM 8 O O2B GTP . . . L 2 66.814 66.859 120.085 1 21.25 ? O2B GTP 601 F 1 HETATM 9 O O3A GTP . . . L 2 66.483 64.631 118.879 1 17.09 ? O3A GTP 601 F 1 HETATM 10 P PA GTP . . . L 2 66.995 63.925 117.526 1 23.93 ? PA GTP 601 F 1 HETATM 11 O O1A GTP . . . L 2 68.136 64.695 116.931 1 20.63 ? O1A GTP 601 F 1 HETATM 12 O O2A GTP . . . L 2 67.385 62.492 117.767 1 27.04 ? O2A GTP 601 F 1 HETATM 13 O O5' GTP . . . L 2 65.749 63.999 116.533 1 17.92 ? O5' GTP 601 F 1 HETATM 14 C C5' GTP . . . L 2 65.081 62.806 116.215 1 12.02 ? C5' GTP 601 F 1 HETATM 15 C C4' GTP . . . L 2 64.857 62.754 114.72 1 2.85 ? C4' GTP 601 F 1 HETATM 16 O O4' GTP . . . L 2 64.064 61.626 114.428 1 8.57 ? O4' GTP 601 F 1 HETATM 17 C C3' GTP . . . L 2 64.092 63.972 114.247 1 5.16 ? C3' GTP 601 F 1 HETATM 18 O O3' GTP . . . L 2 64.96 64.901 113.65 1 4.24 ? O3' GTP 601 F 1 HETATM 19 C C2' GTP . . . L 2 63.147 63.431 113.205 1 7.39 ? C2' GTP 601 F 1 HETATM 20 O O2' GTP . . . L 2 63.646 63.773 111.935 1 2 ? O2' GTP 601 F 1 HETATM 21 C C1' GTP . . . L 2 63.155 61.923 113.393 1 13.6 ? C1' GTP 601 F 1 HETATM 22 N N9 GTP . . . L 2 61.823 61.465 113.801 1 22.89 ? N9 GTP 601 F 1 HETATM 23 C C8 GTP . . . L 2 60.938 60.755 113.036 1 20.3 ? C8 GTP 601 F 1 HETATM 24 N N7 GTP . . . L 2 59.827 60.525 113.767 1 30.17 ? N7 GTP 601 F 1 HETATM 25 C C5 GTP . . . L 2 60.002 61.077 114.987 1 33.02 ? C5 GTP 601 F 1 HETATM 26 C C6 GTP . . . L 2 59.185 61.134 116.101 1 34.48 ? C6 GTP 601 F 1 HETATM 27 O O6 GTP . . . L 2 58.079 60.606 116.066 1 37.56 ? O6 GTP 601 F 1 HETATM 28 N N1 GTP . . . L 2 59.622 61.772 117.238 1 33.91 ? N1 GTP 601 F 1 HETATM 29 C C2 GTP . . . L 2 60.868 62.354 117.257 1 34.61 ? C2 GTP 601 F 1 HETATM 30 N N2 GTP . . . L 2 61.286 62.968 118.357 1 41.83 ? N2 GTP 601 F 1 HETATM 31 N N3 GTP . . . L 2 61.679 62.298 116.144 1 34.29 ? N3 GTP 601 F 1 HETATM 32 C C4 GTP . . . L 2 61.253 61.667 115.026 1 29.47 ? C4 GTP 601 F 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 32 #