data_2E1R # _model_server_result.job_id 7dkgLMwraUA3_jtX-UzzDg _model_server_result.datetime_utc '2024-11-08 19:12:50' _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 2e1r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":902}' # _entry.id 2E1R # _exptl.entry_id 2E1R _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 2E1R _cell.length_a 116.86 _cell.length_b 158.77 _cell.length_c 60.31 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2E1R _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2E1R _atom_sites.fract_transf_matrix[1][1] 0.008557 _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] 0.006298 _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] 0.016581 _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 B 2 SOD A 1 901 901 SOD SOR . C 3 GDP A 1 902 902 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 . . . C 3 30.791 -41.261 -12.374 1 78.64 ? PB GDP 902 A 1 HETATM 2 O O1B GDP . . . C 3 31.033 -42.339 -13.397 1 79.87 ? O1B GDP 902 A 1 HETATM 3 O O2B GDP . . . C 3 31.031 -39.912 -12.95 1 79.97 ? O2B GDP 902 A 1 HETATM 4 O O3B GDP . . . C 3 29.424 -41.428 -11.765 1 79.29 ? O3B GDP 902 A 1 HETATM 5 O O3A GDP . . . C 3 31.871 -41.526 -11.232 1 76.75 ? O3A GDP 902 A 1 HETATM 6 P PA GDP . . . C 3 31.728 -41.939 -9.678 1 73.62 ? PA GDP 902 A 1 HETATM 7 O O1A GDP . . . C 3 31.069 -40.813 -8.948 1 74.97 ? O1A GDP 902 A 1 HETATM 8 O O2A GDP . . . C 3 31.054 -43.253 -9.581 1 73.46 ? O2A GDP 902 A 1 HETATM 9 O O5' GDP . . . C 3 33.231 -42 -9.306 1 76.3 ? O5' GDP 902 A 1 HETATM 10 C C5' GDP . . . C 3 34.124 -42.965 -9.879 1 76.62 ? C5' GDP 902 A 1 HETATM 11 C C4' GDP . . . C 3 35.265 -43.248 -8.935 1 76.89 ? C4' GDP 902 A 1 HETATM 12 O O4' GDP . . . C 3 35.932 -42.001 -8.619 1 76.71 ? O4' GDP 902 A 1 HETATM 13 C C3' GDP . . . C 3 34.841 -43.849 -7.58 1 77.24 ? C3' GDP 902 A 1 HETATM 14 O O3' GDP . . . C 3 35.727 -44.896 -7.197 1 78.29 ? O3' GDP 902 A 1 HETATM 15 C C2' GDP . . . C 3 34.863 -42.667 -6.623 1 77.23 ? C2' GDP 902 A 1 HETATM 16 O O2' GDP . . . C 3 35.077 -43.014 -5.25 1 76.64 ? O2' GDP 902 A 1 HETATM 17 C C1' GDP . . . C 3 35.963 -41.783 -7.2 1 77.81 ? C1' GDP 902 A 1 HETATM 18 N N9 GDP . . . C 3 35.737 -40.346 -6.926 1 78.87 ? N9 GDP 902 A 1 HETATM 19 C C8 GDP . . . C 3 34.682 -39.538 -7.334 1 79.86 ? C8 GDP 902 A 1 HETATM 20 N N7 GDP . . . C 3 34.781 -38.293 -6.907 1 80.65 ? N7 GDP 902 A 1 HETATM 21 C C5 GDP . . . C 3 35.982 -38.262 -6.194 1 80.15 ? C5 GDP 902 A 1 HETATM 22 C C6 GDP . . . C 3 36.631 -37.22 -5.463 1 79.72 ? C6 GDP 902 A 1 HETATM 23 O O6 GDP . . . C 3 36.254 -36.043 -5.365 1 78.91 ? O6 GDP 902 A 1 HETATM 24 N N1 GDP . . . C 3 37.845 -37.595 -4.855 1 80.19 ? N1 GDP 902 A 1 HETATM 25 C C2 GDP . . . C 3 38.382 -38.892 -4.899 1 79.73 ? C2 GDP 902 A 1 HETATM 26 N N2 GDP . . . C 3 39.532 -39.091 -4.265 1 79.73 ? N2 GDP 902 A 1 HETATM 27 N N3 GDP . . . C 3 37.767 -39.892 -5.572 1 79.81 ? N3 GDP 902 A 1 HETATM 28 C C4 GDP . . . C 3 36.567 -39.532 -6.178 1 79.76 ? C4 GDP 902 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #