data_3T5D # _model_server_result.job_id 7-Q-BXwrCp5VYVzsrmeZqA _model_server_result.datetime_utc '2024-11-22 22:41:24' _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 3t5d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1}' # _entry.id 3T5D # _exptl.entry_id 3T5D _exptl.method 'X-RAY DIFFRACTION' # _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 2 _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 120 _cell.entry_id 3T5D _cell.length_a 82.363 _cell.length_b 82.363 _cell.length_c 210.598 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3T5D _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D 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 3T5D _atom_sites.fract_transf_matrix[1][1] 0.012141 _atom_sites.fract_transf_matrix[1][2] 0.00701 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01402 _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] 0.004748 _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 2 GDP A 1 1 1 GDP GDP . D 2 GDP C 1 1 1 GDP GDP . E 3 HOH A 1 2 2 HOH HOH . F 3 HOH C 1 298 1 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 2 31.183 -26.003 -8.247 1 96.88 ? PB GDP 1 A 1 HETATM 2 O O1B GDP . . . C 2 30.603 -27.282 -8.802 1 96.96 ? O1B GDP 1 A 1 HETATM 3 O O2B GDP . . . C 2 30.655 -24.825 -9.029 1 96.84 ? O2B GDP 1 A 1 HETATM 4 O O3B GDP . . . C 2 30.787 -25.856 -6.799 1 96.99 ? O3B GDP 1 A 1 HETATM 5 O O3A GDP . . . C 2 32.788 -26.038 -8.349 1 96.95 ? O3A GDP 1 A 1 HETATM 6 P PA GDP . . . C 2 33.529 -26.694 -9.618 1 96.98 ? PA GDP 1 A 1 HETATM 7 O O1A GDP . . . C 2 33.338 -28.191 -9.633 1 96.99 ? O1A GDP 1 A 1 HETATM 8 O O2A GDP . . . C 2 33.017 -26.083 -10.901 1 97.03 ? O2A GDP 1 A 1 HETATM 9 O O5' GDP . . . C 2 35.075 -26.316 -9.37 1 97.05 ? O5' GDP 1 A 1 HETATM 10 C C5' GDP . . . C 2 35.538 -24.986 -9.609 1 97.32 ? C5' GDP 1 A 1 HETATM 11 C C4' GDP . . . C 2 37.064 -24.926 -9.601 1 97.51 ? C4' GDP 1 A 1 HETATM 12 O O4' GDP . . . C 2 37.571 -25.407 -8.352 1 97.56 ? O4' GDP 1 A 1 HETATM 13 C C3' GDP . . . C 2 37.69 -25.767 -10.705 1 97.64 ? C3' GDP 1 A 1 HETATM 14 O O3' GDP . . . C 2 38.644 -24.975 -11.42 1 97.73 ? O3' GDP 1 A 1 HETATM 15 C C2' GDP . . . C 2 38.373 -26.921 -9.994 1 97.63 ? C2' GDP 1 A 1 HETATM 16 O O2' GDP . . . C 2 39.639 -27.236 -10.579 1 97.67 ? O2' GDP 1 A 1 HETATM 17 C C1' GDP . . . C 2 38.537 -26.441 -8.559 1 97.56 ? C1' GDP 1 A 1 HETATM 18 N N9 GDP . . . C 2 38.317 -27.538 -7.579 1 97.55 ? N9 GDP 1 A 1 HETATM 19 C C8 GDP . . . C 2 37.422 -28.541 -7.678 1 97.54 ? C8 GDP 1 A 1 HETATM 20 N N7 GDP . . . C 2 37.487 -29.367 -6.603 1 97.53 ? N7 GDP 1 A 1 HETATM 21 C C5 GDP . . . C 2 38.444 -28.888 -5.788 1 97.5 ? C5 GDP 1 A 1 HETATM 22 C C6 GDP . . . C 2 39.031 -29.275 -4.483 1 97.52 ? C6 GDP 1 A 1 HETATM 23 O O6 GDP . . . C 2 38.623 -30.282 -3.872 1 97.52 ? O6 GDP 1 A 1 HETATM 24 N N1 GDP . . . C 2 40.008 -28.508 -3.975 1 97.55 ? N1 GDP 1 A 1 HETATM 25 C C2 GDP . . . C 2 40.469 -27.411 -4.61 1 97.51 ? C2 GDP 1 A 1 HETATM 26 N N2 GDP . . . C 2 41.46 -26.692 -4.032 1 97.49 ? N2 GDP 1 A 1 HETATM 27 N N3 GDP . . . C 2 39.978 -26.999 -5.81 1 97.51 ? N3 GDP 1 A 1 HETATM 28 C C4 GDP . . . C 2 38.986 -27.683 -6.434 1 97.51 ? C4 GDP 1 A 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #