data_2EFG # _model_server_result.job_id pyO5CxR6VG-rUn1B9FJF9Q _model_server_result.datetime_utc '2024-11-06 15:34:22' _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 2efg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":900}' # _entry.id 2EFG # _exptl.entry_id 2EFG _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 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 2EFG _cell.length_a 77.269 _cell.length_b 106.224 _cell.length_c 115.447 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2EFG _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 3 _struct_asym.id C _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 2EFG _atom_sites.fract_transf_matrix[1][1] 0.012942 _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] 0.009414 _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] 0.008662 _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 3 GDP A 1 900 900 GDP GDP . D 4 HOH A 1 901 1 HOH HOH . D 4 HOH A 2 902 2 HOH HOH . D 4 HOH A 3 903 3 HOH HOH . D 4 HOH A 4 904 4 HOH HOH . D 4 HOH A 5 905 5 HOH HOH . D 4 HOH A 6 906 6 HOH HOH . D 4 HOH A 7 907 7 HOH HOH . D 4 HOH A 8 908 8 HOH HOH . D 4 HOH A 9 909 9 HOH HOH . D 4 HOH A 10 910 10 HOH HOH . D 4 HOH A 11 911 11 HOH HOH . D 4 HOH A 12 912 12 HOH HOH . D 4 HOH A 13 913 13 HOH HOH . D 4 HOH A 14 914 14 HOH HOH . D 4 HOH A 15 915 15 HOH HOH . D 4 HOH A 16 916 16 HOH HOH . D 4 HOH A 17 917 17 HOH HOH . D 4 HOH A 18 918 18 HOH HOH . D 4 HOH A 19 919 19 HOH HOH . D 4 HOH A 20 920 20 HOH HOH . D 4 HOH A 21 921 21 HOH HOH . # 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 . . . C 3 -2.585 21.398 20.443 1 53.55 ? PB GDP 900 A 1 HETATM 2 O O1B GDP . . . C 3 -1.12 21.757 20.361 1 58.63 ? O1B GDP 900 A 1 HETATM 3 O O2B GDP . . . C 3 -3.159 20.245 19.666 1 41.98 ? O2B GDP 900 A 1 HETATM 4 O O3B GDP . . . C 3 -3.023 21.11 21.854 1 61.69 ? O3B GDP 900 A 1 HETATM 5 O O3A GDP . . . C 3 -3.251 22.682 20.099 1 45.19 ? O3A GDP 900 A 1 HETATM 6 P PA GDP . . . C 3 -3.542 23.949 20.886 1 58.34 ? PA GDP 900 A 1 HETATM 7 O O1A GDP . . . C 3 -4.98 23.931 21.371 1 52.42 ? O1A GDP 900 A 1 HETATM 8 O O2A GDP . . . C 3 -2.455 24.066 21.932 1 56.99 ? O2A GDP 900 A 1 HETATM 9 O O5' GDP . . . C 3 -3.436 25.182 20.002 1 52.37 ? O5' GDP 900 A 1 HETATM 10 C C5' GDP . . . C 3 -2.327 25.406 19.132 1 51.34 ? C5' GDP 900 A 1 HETATM 11 C C4' GDP . . . C 3 -2.403 26.794 18.524 1 47.57 ? C4' GDP 900 A 1 HETATM 12 O O4' GDP . . . C 3 -3.53 26.786 17.626 1 46.81 ? O4' GDP 900 A 1 HETATM 13 C C3' GDP . . . C 3 -2.662 27.948 19.509 1 47.19 ? C3' GDP 900 A 1 HETATM 14 O O3' GDP . . . C 3 -1.888 29.051 19.137 1 54.83 ? O3' GDP 900 A 1 HETATM 15 C C2' GDP . . . C 3 -4.151 28.258 19.387 1 50.68 ? C2' GDP 900 A 1 HETATM 16 O O2' GDP . . . C 3 -4.416 29.542 19.959 1 49.7 ? O2' GDP 900 A 1 HETATM 17 C C1' GDP . . . C 3 -4.409 27.905 17.896 1 48.15 ? C1' GDP 900 A 1 HETATM 18 N N9 GDP . . . C 3 -5.778 27.472 17.485 1 38.66 ? N9 GDP 900 A 1 HETATM 19 C C8 GDP . . . C 3 -6.481 26.433 18.051 1 43.14 ? C8 GDP 900 A 1 HETATM 20 N N7 GDP . . . C 3 -7.733 26.319 17.656 1 46 ? N7 GDP 900 A 1 HETATM 21 C C5 GDP . . . C 3 -7.869 27.351 16.724 1 49.35 ? C5 GDP 900 A 1 HETATM 22 C C6 GDP . . . C 3 -9.058 27.837 15.867 1 46.56 ? C6 GDP 900 A 1 HETATM 23 O O6 GDP . . . C 3 -10.188 27.335 15.841 1 57.3 ? O6 GDP 900 A 1 HETATM 24 N N1 GDP . . . C 3 -8.808 29.012 15.132 1 40.86 ? N1 GDP 900 A 1 HETATM 25 C C2 GDP . . . C 3 -7.569 29.646 15.01 1 45.12 ? C2 GDP 900 A 1 HETATM 26 N N2 GDP . . . C 3 -7.491 30.771 14.266 1 40.58 ? N2 GDP 900 A 1 HETATM 27 N N3 GDP . . . C 3 -6.443 29.119 15.631 1 37.22 ? N3 GDP 900 A 1 HETATM 28 C C4 GDP . . . C 3 -6.671 28.033 16.594 1 43.05 ? C4 GDP 900 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #