data_2FV8 # _model_server_result.job_id O0BSxsAzqgCEdoA_YEFNug _model_server_result.datetime_utc '2024-11-23 01:02:21' _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 2fv8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 2FV8 # _exptl.entry_id 2FV8 _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.58 _cell.angle_gamma 90 _cell.entry_id 2FV8 _cell.length_a 137.519 _cell.length_b 42.233 _cell.length_c 33.85 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2FV8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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,C _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 2FV8 _atom_sites.fract_transf_matrix[1][1] 0.007272 _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] 0.023678 _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] 0.029544 _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 B 2 GDP A 1 201 201 GDP GDP . C 3 HOH A 1 202 1 HOH HOH . C 3 HOH A 2 203 2 HOH HOH . C 3 HOH A 3 204 3 HOH HOH . C 3 HOH A 4 205 4 HOH HOH . C 3 HOH A 5 206 5 HOH HOH . C 3 HOH A 6 207 6 HOH HOH . C 3 HOH A 7 208 7 HOH HOH . C 3 HOH A 8 209 8 HOH HOH . C 3 HOH A 9 210 9 HOH HOH . C 3 HOH A 10 211 10 HOH HOH . C 3 HOH A 11 212 11 HOH HOH . C 3 HOH A 12 213 12 HOH HOH . C 3 HOH A 13 214 13 HOH HOH . C 3 HOH A 14 215 14 HOH HOH . C 3 HOH A 15 216 15 HOH HOH . C 3 HOH A 16 217 16 HOH HOH . C 3 HOH A 17 218 17 HOH HOH . C 3 HOH A 18 219 18 HOH HOH . C 3 HOH A 19 220 19 HOH HOH . C 3 HOH A 20 221 20 HOH HOH . C 3 HOH A 21 222 21 HOH HOH . C 3 HOH A 22 223 22 HOH HOH . C 3 HOH A 23 224 23 HOH HOH . C 3 HOH A 24 225 24 HOH HOH . C 3 HOH A 25 226 25 HOH HOH . C 3 HOH A 26 227 26 HOH HOH . C 3 HOH A 27 228 27 HOH HOH . C 3 HOH A 28 229 28 HOH HOH . C 3 HOH A 29 230 29 HOH HOH . C 3 HOH A 30 231 30 HOH HOH . C 3 HOH A 31 232 31 HOH HOH . C 3 HOH A 32 233 32 HOH HOH . C 3 HOH A 33 234 33 HOH HOH . C 3 HOH A 34 235 34 HOH HOH . C 3 HOH A 35 236 35 HOH HOH . C 3 HOH A 36 237 36 HOH HOH . C 3 HOH A 37 238 37 HOH HOH . C 3 HOH A 38 239 38 HOH HOH . C 3 HOH A 39 240 39 HOH HOH . C 3 HOH A 40 241 40 HOH HOH . C 3 HOH A 41 242 41 HOH HOH . C 3 HOH A 42 243 42 HOH HOH . C 3 HOH A 43 244 43 HOH HOH . C 3 HOH A 44 245 44 HOH HOH . C 3 HOH A 45 246 45 HOH HOH . C 3 HOH A 46 247 46 HOH HOH . C 3 HOH A 47 248 47 HOH HOH . C 3 HOH A 48 249 48 HOH HOH . C 3 HOH A 49 250 49 HOH HOH . C 3 HOH A 50 251 50 HOH HOH . C 3 HOH A 51 252 51 HOH HOH . C 3 HOH A 52 253 52 HOH HOH . C 3 HOH A 53 254 53 HOH HOH . C 3 HOH A 54 255 54 HOH HOH . C 3 HOH A 55 256 55 HOH HOH . C 3 HOH A 56 257 56 HOH HOH . C 3 HOH A 57 258 57 HOH HOH . C 3 HOH A 58 259 58 HOH HOH . C 3 HOH A 59 260 59 HOH HOH . C 3 HOH A 60 261 60 HOH HOH . C 3 HOH A 61 262 61 HOH HOH . C 3 HOH A 62 263 62 HOH HOH . C 3 HOH A 63 264 63 HOH HOH . C 3 HOH A 64 265 65 HOH HOH . C 3 HOH A 65 266 66 HOH HOH . C 3 HOH A 66 267 67 HOH HOH . C 3 HOH A 67 268 68 HOH HOH . C 3 HOH A 68 269 69 HOH HOH . C 3 HOH A 69 270 70 HOH HOH . C 3 HOH A 70 271 71 HOH HOH . C 3 HOH A 71 272 72 HOH HOH . C 3 HOH A 72 273 73 HOH HOH . C 3 HOH A 73 274 74 HOH HOH . C 3 HOH A 74 275 75 HOH HOH . C 3 HOH A 75 276 76 HOH HOH . C 3 HOH A 76 277 77 HOH HOH . C 3 HOH A 77 278 78 HOH HOH . C 3 HOH A 78 279 79 HOH HOH . C 3 HOH A 79 280 80 HOH HOH . C 3 HOH A 80 281 81 HOH HOH . C 3 HOH A 81 282 82 HOH HOH . C 3 HOH A 82 283 83 HOH HOH . C 3 HOH A 83 284 84 HOH HOH . C 3 HOH A 84 285 85 HOH HOH . C 3 HOH A 85 286 86 HOH HOH . C 3 HOH A 86 287 87 HOH HOH . C 3 HOH A 87 288 88 HOH HOH . C 3 HOH A 88 289 89 HOH HOH . C 3 HOH A 89 290 90 HOH HOH . C 3 HOH A 90 291 91 HOH HOH . C 3 HOH A 91 292 92 HOH HOH . C 3 HOH A 92 293 93 HOH HOH . C 3 HOH A 93 294 94 HOH HOH . C 3 HOH A 94 295 95 HOH HOH . C 3 HOH A 95 296 96 HOH HOH . C 3 HOH A 96 297 97 HOH HOH . C 3 HOH A 97 298 98 HOH HOH . C 3 HOH A 98 299 99 HOH HOH . C 3 HOH A 99 300 100 HOH HOH . C 3 HOH A 100 301 101 HOH HOH . C 3 HOH A 101 302 103 HOH HOH . C 3 HOH A 102 303 105 HOH HOH . C 3 HOH A 103 304 108 HOH HOH . C 3 HOH A 104 305 109 HOH HOH . C 3 HOH A 105 306 113 HOH HOH . C 3 HOH A 106 307 115 HOH HOH . C 3 HOH A 107 308 116 HOH HOH . C 3 HOH A 108 309 117 HOH HOH . C 3 HOH A 109 310 118 HOH HOH . C 3 HOH A 110 311 119 HOH HOH . C 3 HOH A 111 312 120 HOH HOH . C 3 HOH A 112 313 121 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 . . . B 2 52.864 30.657 1.396 1 29.78 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 52.874 32.026 1.995 1 30.65 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 53.438 30.824 0.012 1 29.41 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 51.495 29.99 1.408 1 28.37 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 53.905 29.724 2.223 1 29.93 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 53.772 28.183 2.68 1 33.9 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 53.53 27.314 1.483 1 34.8 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 52.79 27.936 3.802 1 31.53 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 55.225 27.906 3.317 1 35.11 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 56.4 28.164 2.549 1 36.45 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 57.521 27.243 2.994 1 37.75 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 57.811 27.458 4.374 1 37.25 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 57.129 25.796 2.873 1 37.95 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 58.266 24.992 2.574 1 41.01 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 56.646 25.431 4.245 1 37.77 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 56.77 24.038 4.51 1 36.6 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 57.527 26.274 5.122 1 36.74 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 56.861 26.68 6.378 1 37.52 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 55.601 27.154 6.544 1 37.47 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 55.348 27.414 7.848 1 36.93 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 56.475 27.131 8.526 1 36.97 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 56.923 27.185 9.935 1 37.51 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 56.181 27.584 10.869 1 36.76 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 58.181 26.779 10.192 1 37.81 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 59.037 26.341 9.248 1 37.2 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 60.28 25.957 9.617 1 37.1 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 58.698 26.261 7.936 1 37.5 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 57.459 26.642 7.544 1 37.69 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #