data_5IZK # _model_server_result.job_id wT_OFNoUH_w3a9VOgoBWUw _model_server_result.datetime_utc '2024-11-22 09:07:47' _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 5izk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 5IZK # _exptl.entry_id 5IZK _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 90.25 _cell.angle_gamma 90 _cell.entry_id 5IZK _cell.length_a 58.691 _cell.length_b 96.861 _cell.length_c 125.408 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IZK _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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,E 1 1 B,D,F 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 ? 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 5IZK _atom_sites.fract_transf_matrix[1][1] 0.017038 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000074 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010324 _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] 0.007974 _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 1001 1001 GDP GDP . D 2 GDP B 1 1001 1001 GDP GDP . E 3 HOH A 1 1101 9 HOH HOH . E 3 HOH A 2 1102 4 HOH HOH . E 3 HOH A 3 1103 19 HOH HOH . E 3 HOH A 4 1104 10 HOH HOH . E 3 HOH A 5 1105 14 HOH HOH . E 3 HOH A 6 1106 11 HOH HOH . E 3 HOH A 7 1107 3 HOH HOH . E 3 HOH A 8 1108 6 HOH HOH . E 3 HOH A 9 1109 5 HOH HOH . E 3 HOH A 10 1110 7 HOH HOH . E 3 HOH A 11 1111 1 HOH HOH . E 3 HOH A 12 1112 20 HOH HOH . E 3 HOH A 13 1113 2 HOH HOH . E 3 HOH A 14 1114 8 HOH HOH . E 3 HOH A 15 1115 15 HOH HOH . F 3 HOH B 1 1101 17 HOH HOH . F 3 HOH B 2 1102 12 HOH HOH . F 3 HOH B 3 1103 21 HOH HOH . F 3 HOH B 4 1104 13 HOH HOH . F 3 HOH B 5 1105 16 HOH HOH . F 3 HOH B 6 1106 18 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 10.994 9.488 112.169 1 113.92 ? PB GDP 1001 A 1 HETATM 2 O O1B GDP . . . C 2 12.372 9.637 111.681 1 84.75 ? O1B GDP 1001 A 1 HETATM 3 O O2B GDP . . . C 2 10.407 8.146 112.056 1 129.48 ? O2B GDP 1001 A 1 HETATM 4 O O3B GDP . . . C 2 10.719 10.173 113.451 1 102.51 ? O3B GDP 1001 A 1 HETATM 5 O O3A GDP . . . C 2 10.136 10.365 111.161 1 105.31 ? O3A GDP 1001 A 1 HETATM 6 P PA GDP . . . C 2 10.691 11.791 110.66 1 81.9 ? PA GDP 1001 A 1 HETATM 7 O O1A GDP . . . C 2 12.018 11.577 110.044 1 110.4 ? O1A GDP 1001 A 1 HETATM 8 O O2A GDP . . . C 2 10.549 12.755 111.772 1 72.93 ? O2A GDP 1001 A 1 HETATM 9 O O5' GDP . . . C 2 9.637 12.167 109.508 1 87.52 ? O5' GDP 1001 A 1 HETATM 10 C C5' GDP . . . C 2 10.057 12.215 108.142 1 106.06 ? C5' GDP 1001 A 1 HETATM 11 C C4' GDP . . . C 2 8.991 12.925 107.305 1 96.33 ? C4' GDP 1001 A 1 HETATM 12 O O4' GDP . . . C 2 8.985 14.323 107.624 1 96.67 ? O4' GDP 1001 A 1 HETATM 13 C C3' GDP . . . C 2 9.387 12.884 105.838 1 93.68 ? C3' GDP 1001 A 1 HETATM 14 O O3' GDP . . . C 2 8.66 11.84 105.174 1 99.63 ? O3' GDP 1001 A 1 HETATM 15 C C2' GDP . . . C 2 8.944 14.234 105.297 1 82.38 ? C2' GDP 1001 A 1 HETATM 16 O O2' GDP . . . C 2 7.938 14.041 104.292 1 109.9 ? O2' GDP 1001 A 1 HETATM 17 C C1' GDP . . . C 2 8.333 14.932 106.5 1 82.94 ? C1' GDP 1001 A 1 HETATM 18 N N9 GDP . . . C 2 8.632 16.381 106.482 1 84.21 ? N9 GDP 1001 A 1 HETATM 19 C C8 GDP . . . C 2 9.585 16.988 107.183 1 83.67 ? C8 GDP 1001 A 1 HETATM 20 N N7 GDP . . . C 2 9.537 18.285 106.896 1 79.98 ? N7 GDP 1001 A 1 HETATM 21 C C5 GDP . . . C 2 8.556 18.481 106.02 1 89.35 ? C5 GDP 1001 A 1 HETATM 22 C C6 GDP . . . C 2 8.115 19.591 105.432 1 83.94 ? C6 GDP 1001 A 1 HETATM 23 O O6 GDP . . . C 2 8.636 20.679 105.672 1 78.95 ? O6 GDP 1001 A 1 HETATM 24 N N1 GDP . . . C 2 7.048 19.52 104.533 1 86.66 ? N1 GDP 1001 A 1 HETATM 25 C C2 GDP . . . C 2 6.479 18.272 104.282 1 105.34 ? C2 GDP 1001 A 1 HETATM 26 N N2 GDP . . . C 2 5.461 18.156 103.433 1 108.56 ? N2 GDP 1001 A 1 HETATM 27 N N3 GDP . . . C 2 6.966 17.191 104.904 1 115.74 ? N3 GDP 1001 A 1 HETATM 28 C C4 GDP . . . C 2 7.993 17.299 105.762 1 99.18 ? C4 GDP 1001 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #