data_2NPF # _model_server_result.job_id bHpWIOgGQi5HOs5NrxxffQ _model_server_result.datetime_utc '2024-11-08 18:42:15' _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":"D","auth_seq_id":902}' # _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 . . . D 3 40.272 -1.941 57.744 1 51.76 ? PB GDP 902 A 1 HETATM 2 O O1B GDP . . . D 3 39.302 -0.775 57.868 1 50.97 ? O1B GDP 902 A 1 HETATM 3 O O2B GDP . . . D 3 39.602 -3.232 58.071 1 50.75 ? O2B GDP 902 A 1 HETATM 4 O O3B GDP . . . D 3 40.941 -1.956 56.397 1 48.91 ? O3B GDP 902 A 1 HETATM 5 O O3A GDP . . . D 3 41.396 -1.658 58.819 1 51.85 ? O3A GDP 902 A 1 HETATM 6 P PA GDP . . . D 3 42.929 -1.191 58.692 1 53.41 ? PA GDP 902 A 1 HETATM 7 O O1A GDP . . . D 3 43.706 -2.272 58.015 1 54.15 ? O1A GDP 902 A 1 HETATM 8 O O2A GDP . . . D 3 42.997 0.142 58.045 1 53.85 ? O2A GDP 902 A 1 HETATM 9 O O5' GDP . . . D 3 43.263 -1.159 60.212 1 55.43 ? O5' GDP 902 A 1 HETATM 10 C C5' GDP . . . D 3 42.523 -0.358 61.168 1 54.5 ? C5' GDP 902 A 1 HETATM 11 C C4' GDP . . . D 3 43.404 0.037 62.347 1 53.91 ? C4' GDP 902 A 1 HETATM 12 O O4' GDP . . . D 3 43.866 -1.176 62.978 1 54.66 ? O4' GDP 902 A 1 HETATM 13 C C3' GDP . . . D 3 44.691 0.794 61.96 1 52.63 ? C3' GDP 902 A 1 HETATM 14 O O3' GDP . . . D 3 45 1.743 62.973 1 52.35 ? O3' GDP 902 A 1 HETATM 15 C C2' GDP . . . D 3 45.725 -0.294 61.855 1 52 ? C2' GDP 902 A 1 HETATM 16 O O2' GDP . . . D 3 47.07 0.15 61.95 1 49.79 ? O2' GDP 902 A 1 HETATM 17 C C1' GDP . . . D 3 45.301 -1.227 62.976 1 55.43 ? C1' GDP 902 A 1 HETATM 18 N N9 GDP . . . D 3 45.672 -2.62 62.74 1 58.05 ? N9 GDP 902 A 1 HETATM 19 C C8 GDP . . . D 3 45.498 -3.387 61.586 1 59.89 ? C8 GDP 902 A 1 HETATM 20 N N7 GDP . . . D 3 45.937 -4.615 61.71 1 61.22 ? N7 GDP 902 A 1 HETATM 21 C C5 GDP . . . D 3 46.432 -4.669 63.013 1 60.47 ? C5 GDP 902 A 1 HETATM 22 C C6 GDP . . . D 3 47.021 -5.727 63.75 1 60.51 ? C6 GDP 902 A 1 HETATM 23 O O6 GDP . . . D 3 47.232 -6.865 63.329 1 60.51 ? O6 GDP 902 A 1 HETATM 24 N N1 GDP . . . D 3 47.398 -5.394 65.064 1 61.39 ? N1 GDP 902 A 1 HETATM 25 C C2 GDP . . . D 3 47.202 -4.125 65.638 1 60.14 ? C2 GDP 902 A 1 HETATM 26 N N2 GDP . . . D 3 47.612 -3.962 66.894 1 60.34 ? N2 GDP 902 A 1 HETATM 27 N N3 GDP . . . D 3 46.634 -3.112 64.948 1 58.4 ? N3 GDP 902 A 1 HETATM 28 C C4 GDP . . . D 3 46.261 -3.44 63.656 1 59.05 ? C4 GDP 902 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #