data_2K5U # _model_server_result.job_id Hyh8g35BMwoN8UfUaSPPfg _model_server_result.datetime_utc '2025-03-06 02:45:29' _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 2k5u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":182}' # _entry.id 2K5U # _exptl.entry_id 2K5U _exptl.method 'SOLUTION NMR' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id C1 _struct_conn.ptnr1_label_comp_id MYR _struct_conn.ptnr1_label_seq_id 1 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id MYR _struct_conn.ptnr1_auth_seq_id 1 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id N _struct_conn.ptnr2_label_comp_id GLY _struct_conn.ptnr2_label_seq_id 2 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id GLY _struct_conn.ptnr2_auth_seq_id 2 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.328 _struct_conn.pdbx_value_order ? # _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 ? # _atom_sites.entry_id 2K5U _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 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id GDP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 182 _pdbx_nonpoly_scheme.auth_seq_num 182 _pdbx_nonpoly_scheme.pdb_mon_id GDP _pdbx_nonpoly_scheme.auth_mon_id GDP _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . B 2 -0.644 3.592 11.24 1 0 ? PB GDP 182 A 1 HETATM 2 O O1B GDP . . . B 2 -0.353 3.543 9.675 1 0 ? O1B GDP 182 A 1 HETATM 3 O O2B GDP . . . B 2 -1.583 2.4 11.721 1 0 ? O2B GDP 182 A 1 HETATM 4 O O3B GDP . . . B 2 0.69 3.7 12.105 1 0 ? O3B GDP 182 A 1 HETATM 5 O O3A GDP . . . B 2 -1.457 4.954 11.502 1 0 ? O3A GDP 182 A 1 HETATM 6 P PA GDP . . . B 2 -2.606 5.003 12.624 1 0 ? PA GDP 182 A 1 HETATM 7 O O1A GDP . . . B 2 -2.055 4.353 13.97 1 0 ? O1A GDP 182 A 1 HETATM 8 O O2A GDP . . . B 2 -3.927 4.324 12.048 1 0 ? O2A GDP 182 A 1 HETATM 9 O O5' GDP . . . B 2 -2.879 6.553 12.871 1 0 ? O5' GDP 182 A 1 HETATM 10 C C5' GDP . . . B 2 -1.801 7.464 13.062 1 0 ? C5' GDP 182 A 1 HETATM 11 C C4' GDP . . . B 2 -2.215 8.571 14.003 1 0 ? C4' GDP 182 A 1 HETATM 12 O O4' GDP . . . B 2 -3.108 9.473 13.293 1 0 ? O4' GDP 182 A 1 HETATM 13 C C3' GDP . . . B 2 -2.994 8.116 15.231 1 0 ? C3' GDP 182 A 1 HETATM 14 O O3' GDP . . . B 2 -2.756 8.969 16.343 1 0 ? O3' GDP 182 A 1 HETATM 15 C C2' GDP . . . B 2 -4.441 8.178 14.759 1 0 ? C2' GDP 182 A 1 HETATM 16 O O2' GDP . . . B 2 -5.322 8.434 15.835 1 0 ? O2' GDP 182 A 1 HETATM 17 C C1' GDP . . . B 2 -4.404 9.41 13.857 1 0 ? C1' GDP 182 A 1 HETATM 18 N N9 GDP . . . B 2 -5.377 9.373 12.771 1 0 ? N9 GDP 182 A 1 HETATM 19 C C8 GDP . . . B 2 -5.783 8.271 12.062 1 0 ? C8 GDP 182 A 1 HETATM 20 N N7 GDP . . . B 2 -6.668 8.546 11.144 1 0 ? N7 GDP 182 A 1 HETATM 21 C C5 GDP . . . B 2 -6.861 9.916 11.254 1 0 ? C5 GDP 182 A 1 HETATM 22 C C6 GDP . . . B 2 -7.707 10.788 10.52 1 0 ? C6 GDP 182 A 1 HETATM 23 O O6 GDP . . . B 2 -8.483 10.511 9.597 1 0 ? O6 GDP 182 A 1 HETATM 24 N N1 GDP . . . B 2 -7.589 12.103 10.958 1 0 ? N1 GDP 182 A 1 HETATM 25 C C2 GDP . . . B 2 -6.767 12.526 11.972 1 0 ? C2 GDP 182 A 1 HETATM 26 N N2 GDP . . . B 2 -6.8 13.839 12.248 1 0 ? N2 GDP 182 A 1 HETATM 27 N N3 GDP . . . B 2 -5.974 11.725 12.664 1 0 ? N3 GDP 182 A 1 HETATM 28 C C4 GDP . . . B 2 -6.07 10.443 12.254 1 0 ? C4 GDP 182 A 1 HETATM 29 H H5' GDP . . . B 2 -1.511 7.898 12.104 1 0 ? H5' GDP 182 A 1 HETATM 30 H "H5''" GDP . . . B 2 -0.945 6.94 13.486 1 0 ? "H5''" GDP 182 A 1 HETATM 31 H H4' GDP . . . B 2 -1.306 9.052 14.367 1 0 ? H4' GDP 182 A 1 HETATM 32 H H3' GDP . . . B 2 -2.699 7.117 15.549 1 0 ? H3' GDP 182 A 1 HETATM 33 H HO3' GDP . . . B 2 -3.513 9.552 16.422 1 0 ? HO3' GDP 182 A 1 HETATM 34 H H2' GDP . . . B 2 -4.705 7.277 14.2 1 0 ? H2' GDP 182 A 1 HETATM 35 H HO2' GDP . . . B 2 -6.147 8.743 15.461 1 0 ? HO2' GDP 182 A 1 HETATM 36 H H1' GDP . . . B 2 -4.555 10.333 14.417 1 0 ? H1' GDP 182 A 1 HETATM 37 H H8 GDP . . . B 2 -5.407 7.275 12.244 1 0 ? H8 GDP 182 A 1 HETATM 38 H HN1 GDP . . . B 2 -8.15 12.802 10.494 1 0 ? HN1 GDP 182 A 1 HETATM 39 H HN21 GDP . . . B 2 -6.219 14.215 12.984 1 0 ? HN21 GDP 182 A 1 HETATM 40 H HN22 GDP . . . B 2 -7.406 14.45 11.721 1 0 ? HN22 GDP 182 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 57 _model_server_stats.query_time_ms 5028 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #