data_2LKD # _model_server_result.job_id RFLqhhAlLivRxgrFhnJhvA _model_server_result.datetime_utc '2024-12-06 02:21:34' _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 2lkd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":179}' # _entry.id 2LKD # _exptl.entry_id 2LKD _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 # _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 2LKD _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 179 _pdbx_nonpoly_scheme.auth_seq_num 179 _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 -8.754 -3.245 15.263 1 0.68 ? PB GDP 179 A 1 HETATM 2 O O1B GDP . . . B 2 -8.576 -4.641 15.764 1 1.61 ? O1B GDP 179 A 1 HETATM 3 O O2B GDP . . . B 2 -10.051 -3.033 14.498 1 1.63 ? O2B GDP 179 A 1 HETATM 4 O O3B GDP . . . B 2 -7.519 -2.635 14.568 1 1.65 ? O3B GDP 179 A 1 HETATM 5 O O3A GDP . . . B 2 -8.946 -2.335 16.648 1 0.68 ? O3A GDP 179 A 1 HETATM 6 P PA GDP . . . B 2 -9.804 -1.048 16.904 1 0.75 ? PA GDP 179 A 1 HETATM 7 O O1A GDP . . . B 2 -10.36 -1.024 18.278 1 0.87 ? O1A GDP 179 A 1 HETATM 8 O O2A GDP . . . B 2 -10.748 -0.738 15.765 1 0.88 ? O2A GDP 179 A 1 HETATM 9 O O5' GDP . . . B 2 -8.661 0.083 16.817 1 0.69 ? O5' GDP 179 A 1 HETATM 10 C C5' GDP . . . B 2 -7.412 -0.106 17.477 1 0.65 ? C5' GDP 179 A 1 HETATM 11 C C4' GDP . . . B 2 -6.758 1.223 17.777 1 0.66 ? C4' GDP 179 A 1 HETATM 12 O O4' GDP . . . B 2 -6.315 1.831 16.544 1 0.63 ? O4' GDP 179 A 1 HETATM 13 C C3' GDP . . . B 2 -7.656 2.286 18.403 1 0.75 ? C3' GDP 179 A 1 HETATM 14 O O3' GDP . . . B 2 -7.572 2.24 19.822 1 0.96 ? O3' GDP 179 A 1 HETATM 15 C C2' GDP . . . B 2 -7.131 3.617 17.849 1 0.75 ? C2' GDP 179 A 1 HETATM 16 O O2' GDP . . . B 2 -6.507 4.392 18.855 1 0.95 ? O2' GDP 179 A 1 HETATM 17 C C1' GDP . . . B 2 -6.077 3.191 16.825 1 0.62 ? C1' GDP 179 A 1 HETATM 18 N N9 GDP . . . B 2 -6.12 3.945 15.576 1 0.55 ? N9 GDP 179 A 1 HETATM 19 C C8 GDP . . . B 2 -6.924 3.705 14.491 1 0.62 ? C8 GDP 179 A 1 HETATM 20 N N7 GDP . . . B 2 -6.728 4.538 13.506 1 0.61 ? N7 GDP 179 A 1 HETATM 21 C C5 GDP . . . B 2 -5.731 5.386 13.969 1 0.49 ? C5 GDP 179 A 1 HETATM 22 C C6 GDP . . . B 2 -5.099 6.492 13.34 1 0.45 ? C6 GDP 179 A 1 HETATM 23 O O6 GDP . . . B 2 -5.292 6.951 12.208 1 0.55 ? O6 GDP 179 A 1 HETATM 24 N N1 GDP . . . B 2 -4.136 7.075 14.16 1 0.37 ? N1 GDP 179 A 1 HETATM 25 C C2 GDP . . . B 2 -3.831 6.64 15.429 1 0.4 ? C2 GDP 179 A 1 HETATM 26 N N2 GDP . . . B 2 -2.88 7.329 16.076 1 0.46 ? N2 GDP 179 A 1 HETATM 27 N N3 GDP . . . B 2 -4.411 5.614 16.027 1 0.45 ? N3 GDP 179 A 1 HETATM 28 C C4 GDP . . . B 2 -5.346 5.034 15.245 1 0.46 ? C4 GDP 179 A 1 HETATM 29 H H5' GDP . . . B 2 -6.75 -0.697 16.845 1 0.79 ? H5' GDP 179 A 1 HETATM 30 H "H5''" GDP . . . B 2 -7.569 -0.638 18.415 1 0.71 ? "H5''" GDP 179 A 1 HETATM 31 H H4' GDP . . . B 2 -5.949 1.038 18.484 1 0.74 ? H4' GDP 179 A 1 HETATM 32 H H3' GDP . . . B 2 -8.703 2.119 18.163 1 0.85 ? H3' GDP 179 A 1 HETATM 33 H HO3' GDP . . . B 2 -6.946 2.917 20.091 1 1.25 ? HO3' GDP 179 A 1 HETATM 34 H H2' GDP . . . B 2 -7.945 4.161 17.364 1 0.85 ? H2' GDP 179 A 1 HETATM 35 H HO2' GDP . . . B 2 -5.743 3.899 19.16 1 1.35 ? HO2' GDP 179 A 1 HETATM 36 H H1' GDP . . . B 2 -5.065 3.262 17.227 1 0.67 ? H1' GDP 179 A 1 HETATM 37 H H8 GDP . . . B 2 -7.638 2.897 14.451 1 0.71 ? H8 GDP 179 A 1 HETATM 38 H HN1 GDP . . . B 2 -3.618 7.856 13.785 1 0.36 ? HN1 GDP 179 A 1 HETATM 39 H HN21 GDP . . . B 2 -2.608 7.06 17.013 1 0.55 ? HN21 GDP 179 A 1 HETATM 40 H HN22 GDP . . . B 2 -2.437 8.121 15.63 1 0.45 ? HN22 GDP 179 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 432 _model_server_stats.query_time_ms 9586 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 40 #