data_5TDH # _model_server_result.job_id 3-OWwXrnx03ZKAbqGHeu7Q _model_server_result.datetime_utc '2024-10-11 00:31:29' _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 5tdh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":401}' # _entry.id 5TDH # _exptl.entry_id 5TDH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 113.1 _cell.angle_gamma 90 _cell.entry_id 5TDH _cell.length_a 126.009 _cell.length_b 54.57 _cell.length_c 138.35 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TDH _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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,B,C,G 1 1 D,E,F,H 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 ? 4 G N N ? 4 H 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 5TDH _atom_sites.fract_transf_matrix[1][1] 0.007936 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003385 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018325 _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] 0.007858 _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 G 4 GDP A 1 401 355 GDP GDP . H 4 GDP H 1 401 355 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 . . . H 4 4.232 -22.136 59.117 1 37.51 ? PB GDP 401 H 1 HETATM 2 O O1B GDP . . . H 4 4.806 -22.605 57.799 1 36.66 ? O1B GDP 401 H 1 HETATM 3 O O2B GDP . . . H 4 4.349 -20.63 59.226 1 37.66 ? O2B GDP 401 H 1 HETATM 4 O O3B GDP . . . H 4 2.788 -22.567 59.227 1 38.3 ? O3B GDP 401 H 1 HETATM 5 O O3A GDP . . . H 4 5.075 -22.81 60.308 1 39.04 ? O3A GDP 401 H 1 HETATM 6 P PA GDP . . . H 4 5.062 -24.41 60.484 1 43.21 ? PA GDP 401 H 1 HETATM 7 O O1A GDP . . . H 4 4.934 -25.117 59.152 1 43.06 ? O1A GDP 401 H 1 HETATM 8 O O2A GDP . . . H 4 3.953 -24.813 61.425 1 42.35 ? O2A GDP 401 H 1 HETATM 9 O O5' GDP . . . H 4 6.497 -24.709 61.145 1 42.73 ? O5' GDP 401 H 1 HETATM 10 C C5' GDP . . . H 4 7.352 -25.667 60.527 1 42.55 ? C5' GDP 401 H 1 HETATM 11 C C4' GDP . . . H 4 8.091 -26.446 61.602 1 42.96 ? C4' GDP 401 H 1 HETATM 12 O O4' GDP . . . H 4 8.825 -25.562 62.454 1 42.01 ? O4' GDP 401 H 1 HETATM 13 C C3' GDP . . . H 4 7.1 -27.184 62.483 1 43.46 ? C3' GDP 401 H 1 HETATM 14 O O3' GDP . . . H 4 7.04 -28.573 62.155 1 44.71 ? O3' GDP 401 H 1 HETATM 15 C C2' GDP . . . H 4 7.607 -26.985 63.894 1 42.66 ? C2' GDP 401 H 1 HETATM 16 O O2' GDP . . . H 4 8.048 -28.208 64.466 1 42.61 ? O2' GDP 401 H 1 HETATM 17 C C1' GDP . . . H 4 8.777 -26.031 63.799 1 41.3 ? C1' GDP 401 H 1 HETATM 18 N N9 GDP . . . H 4 8.445 -24.951 64.75 1 39.03 ? N9 GDP 401 H 1 HETATM 19 C C8 GDP . . . H 4 7.488 -24.021 64.561 1 38.88 ? C8 GDP 401 H 1 HETATM 20 N N7 GDP . . . H 4 7.41 -23.176 65.622 1 37.81 ? N7 GDP 401 H 1 HETATM 21 C C5 GDP . . . H 4 8.334 -23.579 66.514 1 35.94 ? C5 GDP 401 H 1 HETATM 22 C C6 GDP . . . H 4 8.783 -23.133 67.851 1 32.91 ? C6 GDP 401 H 1 HETATM 23 O O6 GDP . . . H 4 8.251 -22.148 68.398 1 31.91 ? O6 GDP 401 H 1 HETATM 24 N N1 GDP . . . H 4 9.767 -23.806 68.456 1 32.13 ? N1 GDP 401 H 1 HETATM 25 C C2 GDP . . . H 4 10.352 -24.873 67.885 1 31.91 ? C2 GDP 401 H 1 HETATM 26 N N2 GDP . . . H 4 11.341 -25.497 68.571 1 30.86 ? N2 GDP 401 H 1 HETATM 27 N N3 GDP . . . H 4 9.995 -25.347 66.66 1 34.28 ? N3 GDP 401 H 1 HETATM 28 C C4 GDP . . . H 4 9.01 -24.752 65.943 1 36.34 ? C4 GDP 401 H 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #