data_2NPF # _model_server_result.job_id eFe2Y-2HSkxBl39ER3XuNQ _model_server_result.datetime_utc '2024-12-02 16:49:22' _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 2npf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1902}' # _entry.id 2NPF # _exptl.entry_id 2NPF _exptl.method 'X-RAY DIFFRACTION' # _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.83 _cell.angle_gamma 90 _cell.entry_id 2NPF _cell.length_a 59.97 _cell.length_b 159.12 _cell.length_c 112.14 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2NPF _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D 1 1 B,E,F 2 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 D N N ? 3 F 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 2NPF _atom_sites.fract_transf_matrix[1][1] 0.016675 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002293 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006285 _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] 0.009001 _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 C 2 MOU A 1 901 901 MOU MOL . D 3 GDP A 1 902 902 GDP GDP . E 2 MOU B 1 1901 901 MOU MOL . F 3 GDP B 1 1902 902 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 . . . F 3 -31.932 25.566 111.626 1 108.03 ? PB GDP 1902 B 1 HETATM 2 O O1B GDP . . . F 3 -30.939 24.436 111.821 1 107.5 ? O1B GDP 1902 B 1 HETATM 3 O O2B GDP . . . F 3 -31.306 26.901 111.794 1 108.16 ? O2B GDP 1902 B 1 HETATM 4 O O3B GDP . . . F 3 -32.641 25.422 110.312 1 109.39 ? O3B GDP 1902 B 1 HETATM 5 O O3A GDP . . . F 3 -33.01 25.379 112.772 1 106.73 ? O3A GDP 1902 B 1 HETATM 6 P PA GDP . . . F 3 -34.464 24.704 112.747 1 106.62 ? PA GDP 1902 B 1 HETATM 7 O O1A GDP . . . F 3 -35.336 25.522 111.845 1 106.23 ? O1A GDP 1902 B 1 HETATM 8 O O2A GDP . . . F 3 -34.301 23.273 112.389 1 106.2 ? O2A GDP 1902 B 1 HETATM 9 O O5' GDP . . . F 3 -34.892 24.902 114.235 1 107.24 ? O5' GDP 1902 B 1 HETATM 10 C C5' GDP . . . F 3 -34.203 24.239 115.308 1 107.37 ? C5' GDP 1902 B 1 HETATM 11 C C4' GDP . . . F 3 -35.09 24.037 116.519 1 106.84 ? C4' GDP 1902 B 1 HETATM 12 O O4' GDP . . . F 3 -35.416 25.312 117.115 1 106.97 ? O4' GDP 1902 B 1 HETATM 13 C C3' GDP . . . F 3 -36.437 23.362 116.226 1 107.02 ? C3' GDP 1902 B 1 HETATM 14 O O3' GDP . . . F 3 -36.698 22.373 117.21 1 107.58 ? O3' GDP 1902 B 1 HETATM 15 C C2' GDP . . . F 3 -37.446 24.5 116.246 1 107.05 ? C2' GDP 1902 B 1 HETATM 16 O O2' GDP . . . F 3 -38.778 24.112 116.602 1 107.17 ? O2' GDP 1902 B 1 HETATM 17 C C1' GDP . . . F 3 -36.837 25.485 117.227 1 107.27 ? C1' GDP 1902 B 1 HETATM 18 N N9 GDP . . . F 3 -37.174 26.895 116.906 1 108.22 ? N9 GDP 1902 B 1 HETATM 19 C C8 GDP . . . F 3 -36.96 27.589 115.72 1 108.53 ? C8 GDP 1902 B 1 HETATM 20 N N7 GDP . . . F 3 -37.381 28.834 115.768 1 108.46 ? N7 GDP 1902 B 1 HETATM 21 C C5 GDP . . . F 3 -37.904 28.987 117.051 1 108.71 ? C5 GDP 1902 B 1 HETATM 22 C C6 GDP . . . F 3 -38.507 30.105 117.709 1 109.1 ? C6 GDP 1902 B 1 HETATM 23 O O6 GDP . . . F 3 -38.693 31.235 117.229 1 108.18 ? O6 GDP 1902 B 1 HETATM 24 N N1 GDP . . . F 3 -38.915 29.858 119.032 1 109.8 ? N1 GDP 1902 B 1 HETATM 25 C C2 GDP . . . F 3 -38.763 28.631 119.693 1 109.7 ? C2 GDP 1902 B 1 HETATM 26 N N2 GDP . . . F 3 -39.207 28.566 120.951 1 108.92 ? N2 GDP 1902 B 1 HETATM 27 N N3 GDP . . . F 3 -38.19 27.561 119.076 1 109.86 ? N3 GDP 1902 B 1 HETATM 28 C C4 GDP . . . F 3 -37.783 27.796 117.766 1 108.8 ? C4 GDP 1902 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #