data_8DZN # _model_server_result.job_id HuGWBzNZSZZ4d9jPSr6_Ug _model_server_result.datetime_utc '2024-12-18 02:16:28' _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 8dzn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 8DZN # _exptl.entry_id 8DZN _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 105.95 _cell.angle_gamma 90 _cell.entry_id 8DZN _cell.length_a 57.172 _cell.length_b 63.97 _cell.length_c 62.233 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DZN _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,F 1 1 B,D,E,G 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 E 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 8DZN _atom_sites.fract_transf_matrix[1][1] 0.017491 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004998 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015632 _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] 0.016712 _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 1 201 1 GDP GDP . D 3 SO4 B 1 201 1 SO4 SO4 . E 2 GDP B 1 202 2 GDP GDP . F 4 HOH A 1 301 32 HOH HOH . F 4 HOH A 2 302 77 HOH HOH . F 4 HOH A 3 303 58 HOH HOH . F 4 HOH A 4 304 54 HOH HOH . F 4 HOH A 5 305 114 HOH HOH . F 4 HOH A 6 306 2 HOH HOH . F 4 HOH A 7 307 19 HOH HOH . F 4 HOH A 8 308 13 HOH HOH . F 4 HOH A 9 309 5 HOH HOH . F 4 HOH A 10 310 55 HOH HOH . F 4 HOH A 11 311 10 HOH HOH . F 4 HOH A 12 312 28 HOH HOH . F 4 HOH A 13 313 1 HOH HOH . F 4 HOH A 14 314 11 HOH HOH . F 4 HOH A 15 315 78 HOH HOH . F 4 HOH A 16 316 67 HOH HOH . F 4 HOH A 17 317 56 HOH HOH . F 4 HOH A 18 318 62 HOH HOH . F 4 HOH A 19 319 104 HOH HOH . F 4 HOH A 20 320 24 HOH HOH . F 4 HOH A 21 321 6 HOH HOH . F 4 HOH A 22 322 35 HOH HOH . F 4 HOH A 23 323 102 HOH HOH . F 4 HOH A 24 324 86 HOH HOH . F 4 HOH A 25 325 61 HOH HOH . F 4 HOH A 26 326 82 HOH HOH . F 4 HOH A 27 327 16 HOH HOH . F 4 HOH A 28 328 63 HOH HOH . F 4 HOH A 29 329 27 HOH HOH . F 4 HOH A 30 330 107 HOH HOH . F 4 HOH A 31 331 15 HOH HOH . F 4 HOH A 32 332 69 HOH HOH . F 4 HOH A 33 333 80 HOH HOH . F 4 HOH A 34 334 31 HOH HOH . F 4 HOH A 35 335 17 HOH HOH . F 4 HOH A 36 336 22 HOH HOH . F 4 HOH A 37 337 23 HOH HOH . F 4 HOH A 38 338 64 HOH HOH . F 4 HOH A 39 339 93 HOH HOH . F 4 HOH A 40 340 70 HOH HOH . F 4 HOH A 41 341 45 HOH HOH . F 4 HOH A 42 342 92 HOH HOH . F 4 HOH A 43 343 88 HOH HOH . F 4 HOH A 44 344 21 HOH HOH . F 4 HOH A 45 345 14 HOH HOH . F 4 HOH A 46 346 84 HOH HOH . F 4 HOH A 47 347 4 HOH HOH . F 4 HOH A 48 348 42 HOH HOH . F 4 HOH A 49 349 57 HOH HOH . F 4 HOH A 50 350 68 HOH HOH . F 4 HOH A 51 351 117 HOH HOH . F 4 HOH A 52 352 118 HOH HOH . F 4 HOH A 53 353 41 HOH HOH . F 4 HOH A 54 354 97 HOH HOH . F 4 HOH A 55 355 111 HOH HOH . F 4 HOH A 56 356 83 HOH HOH . F 4 HOH A 57 357 113 HOH HOH . F 4 HOH A 58 358 119 HOH HOH . F 4 HOH A 59 359 18 HOH HOH . F 4 HOH A 60 360 85 HOH HOH . F 4 HOH A 61 361 89 HOH HOH . F 4 HOH A 62 362 48 HOH HOH . F 4 HOH A 63 363 66 HOH HOH . G 4 HOH B 1 301 94 HOH HOH . G 4 HOH B 2 302 95 HOH HOH . G 4 HOH B 3 303 121 HOH HOH . G 4 HOH B 4 304 109 HOH HOH . G 4 HOH B 5 305 96 HOH HOH . G 4 HOH B 6 306 30 HOH HOH . G 4 HOH B 7 307 98 HOH HOH . G 4 HOH B 8 308 116 HOH HOH . G 4 HOH B 9 309 99 HOH HOH . G 4 HOH B 10 310 53 HOH HOH . G 4 HOH B 11 311 51 HOH HOH . G 4 HOH B 12 312 20 HOH HOH . G 4 HOH B 13 313 29 HOH HOH . G 4 HOH B 14 314 36 HOH HOH . G 4 HOH B 15 315 39 HOH HOH . G 4 HOH B 16 316 33 HOH HOH . G 4 HOH B 17 317 3 HOH HOH . G 4 HOH B 18 318 7 HOH HOH . G 4 HOH B 19 319 100 HOH HOH . G 4 HOH B 20 320 38 HOH HOH . G 4 HOH B 21 321 44 HOH HOH . G 4 HOH B 22 322 101 HOH HOH . G 4 HOH B 23 323 8 HOH HOH . G 4 HOH B 24 324 74 HOH HOH . G 4 HOH B 25 325 79 HOH HOH . G 4 HOH B 26 326 108 HOH HOH . G 4 HOH B 27 327 71 HOH HOH . G 4 HOH B 28 328 120 HOH HOH . G 4 HOH B 29 329 34 HOH HOH . G 4 HOH B 30 330 26 HOH HOH . G 4 HOH B 31 331 47 HOH HOH . G 4 HOH B 32 332 49 HOH HOH . G 4 HOH B 33 333 12 HOH HOH . G 4 HOH B 34 334 59 HOH HOH . G 4 HOH B 35 335 75 HOH HOH . G 4 HOH B 36 336 43 HOH HOH . G 4 HOH B 37 337 72 HOH HOH . G 4 HOH B 38 338 87 HOH HOH . G 4 HOH B 39 339 40 HOH HOH . G 4 HOH B 40 340 103 HOH HOH . G 4 HOH B 41 341 9 HOH HOH . G 4 HOH B 42 342 60 HOH HOH . G 4 HOH B 43 343 115 HOH HOH . G 4 HOH B 44 344 37 HOH HOH . G 4 HOH B 45 345 46 HOH HOH . G 4 HOH B 46 346 50 HOH HOH . G 4 HOH B 47 347 25 HOH HOH . G 4 HOH B 48 348 65 HOH HOH . G 4 HOH B 49 349 112 HOH HOH . G 4 HOH B 50 350 90 HOH HOH . G 4 HOH B 51 351 76 HOH HOH . G 4 HOH B 52 352 73 HOH HOH . G 4 HOH B 53 353 52 HOH HOH . G 4 HOH B 54 354 105 HOH HOH . G 4 HOH B 55 355 106 HOH HOH . G 4 HOH B 56 356 110 HOH HOH . G 4 HOH B 57 357 81 HOH HOH . G 4 HOH B 58 358 91 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 -68.057 6.178 -105.559 1 30.61 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . C 2 -66.896 6.617 -106.363 1 23.82 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . C 2 -69.1 7.271 -105.394 1 23.2 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . C 2 -67.601 5.701 -104.164 1 25.74 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . C 2 -68.7 4.992 -106.299 1 34.73 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . C 2 -69.926 5.046 -107.266 1 31.15 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . C 2 -69.712 6.079 -108.338 1 32.34 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . C 2 -71.237 5.262 -106.511 1 27.43 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . C 2 -70.044 3.6 -107.933 1 37.95 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . C 2 -68.928 2.997 -108.534 1 29.52 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . C 2 -69.379 1.872 -109.42 1 32.75 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . C 2 -69.58 0.796 -108.693 1 35.95 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . C 2 -70.813 2.258 -110.161 1 33.22 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . C 2 -70.782 1.699 -111.539 1 41.77 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . C 2 -71.724 1.702 -109.517 1 37.1 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . C 2 -72.898 1.37 -110.36 1 35.97 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . C 2 -70.971 0.356 -109.083 1 37.42 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . C 2 -71.608 -0.342 -108.187 1 42.43 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . C 2 -71.852 0.516 -107.147 1 34.9 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . C 2 -72.541 -0.186 -106.192 1 39.26 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . C 2 -72.709 -1.469 -106.635 1 40.14 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . C 2 -73.355 -2.739 -106.083 1 41.21 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . C 2 -73.901 -2.781 -105.001 1 36.14 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . C 2 -73.336 -3.91 -106.868 1 38.54 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . C 2 -72.714 -3.927 -108.14 1 35.2 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . C 2 -72.667 -5.078 -108.944 1 39.57 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . C 2 -72.094 -2.738 -108.643 1 40.37 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . C 2 -72.123 -1.53 -107.858 1 41.29 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 245 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #