data_5YY1 # _model_server_result.job_id 057Rr5uj89m0iS437-xlRg _model_server_result.datetime_utc '2025-07-31 13:42:20' _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 5yy1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 5YY1 # _exptl.entry_id 5YY1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 _cell.angle_gamma 90 _cell.entry_id 5YY1 _cell.length_a 40.391 _cell.length_b 51.73 _cell.length_c 89.242 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YY1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,G _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A SG CYS 13 A CYS 12 1_555 D C14 94F . A 94F 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.617 ? metalc ? metalc1 A OG SER 18 A SER 17 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc2 B MG MG . A MG 201 1_555 C O3B GDP . A GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc3 B MG MG . A MG 201 1_555 G O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc4 B MG MG . A MG 201 1_555 G O HOH . A HOH 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc5 B MG MG . A MG 201 1_555 G O HOH . A HOH 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc6 B MG MG . A MG 201 1_555 G O HOH . A HOH 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? # _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 146 n n PB O2B GDP sing 147 n n PB O3B GDP sing 148 n n PB O3A GDP sing 149 n n O2B HOB2 GDP sing 150 n n O3B HOB3 GDP sing 151 n n O3A PA GDP sing 152 n n PA O1A GDP doub 153 n n PA O2A GDP sing 154 n n PA O5' GDP sing 155 n n O2A HOA2 GDP sing 156 n n O5' C5' GDP sing 157 n n C5' C4' GDP sing 158 n n C5' H5' GDP sing 159 n n C5' "H5''" GDP sing 160 n n C4' O4' GDP sing 161 n n C4' C3' GDP sing 162 n n C4' H4' GDP sing 163 n n O4' C1' GDP sing 164 n n C3' O3' GDP sing 165 n n C3' C2' GDP sing 166 n n C3' H3' GDP sing 167 n n O3' HO3' GDP sing 168 n n C2' O2' GDP sing 169 n n C2' C1' GDP sing 170 n n C2' H2' GDP sing 171 n n O2' HO2' GDP sing 172 n n C1' N9 GDP sing 173 n n C1' H1' GDP sing 174 n n N9 C8 GDP sing 175 n y N9 C4 GDP sing 176 n y C8 N7 GDP doub 177 n y C8 H8 GDP sing 178 n n N7 C5 GDP sing 179 n y C5 C6 GDP sing 180 n n C5 C4 GDP doub 181 n y C6 O6 GDP doub 182 n n C6 N1 GDP sing 183 n n N1 C2 GDP sing 184 n n N1 HN1 GDP sing 185 n n C2 N2 GDP sing 186 n n C2 N3 GDP doub 187 n n N2 HN21 GDP sing 188 n n N2 HN22 GDP sing 189 n n N3 C4 GDP sing 190 n n # _atom_sites.entry_id 5YY1 _atom_sites.fract_transf_matrix[1][1] 0.024758 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019331 _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] 0.011205 _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 MG A 1 201 199 MG MG . C 3 GDP A 1 202 200 GDP GDP . D 4 94F A 1 203 201 94F UNL . E 5 EDO A 1 204 1 EDO EDO . F 5 EDO A 1 205 2 EDO EDO . G 6 HOH A 1 301 138 HOH HOH . G 6 HOH A 2 302 94 HOH HOH . G 6 HOH A 3 303 74 HOH HOH . G 6 HOH A 4 304 92 HOH HOH . G 6 HOH A 5 305 41 HOH HOH . G 6 HOH A 6 306 32 HOH HOH . G 6 HOH A 7 307 100 HOH HOH . G 6 HOH A 8 308 33 HOH HOH . G 6 HOH A 9 309 36 HOH HOH . G 6 HOH A 10 310 133 HOH HOH . G 6 HOH A 11 311 76 HOH HOH . G 6 HOH A 12 312 68 HOH HOH . G 6 HOH A 13 313 46 HOH HOH . G 6 HOH A 14 314 31 HOH HOH . G 6 HOH A 15 315 40 HOH HOH . G 6 HOH A 16 316 13 HOH HOH . G 6 HOH A 17 317 29 HOH HOH . G 6 HOH A 18 318 89 HOH HOH . G 6 HOH A 19 319 47 HOH HOH . G 6 HOH A 20 320 10 HOH HOH . G 6 HOH A 21 321 86 HOH HOH . G 6 HOH A 22 322 126 HOH HOH . G 6 HOH A 23 323 83 HOH HOH . G 6 HOH A 24 324 70 HOH HOH . G 6 HOH A 25 325 20 HOH HOH . G 6 HOH A 26 326 3 HOH HOH . G 6 HOH A 27 327 71 HOH HOH . G 6 HOH A 28 328 51 HOH HOH . G 6 HOH A 29 329 19 HOH HOH . G 6 HOH A 30 330 18 HOH HOH . G 6 HOH A 31 331 135 HOH HOH . G 6 HOH A 32 332 25 HOH HOH . G 6 HOH A 33 333 131 HOH HOH . G 6 HOH A 34 334 121 HOH HOH . G 6 HOH A 35 335 5 HOH HOH . G 6 HOH A 36 336 102 HOH HOH . G 6 HOH A 37 337 79 HOH HOH . G 6 HOH A 38 338 49 HOH HOH . G 6 HOH A 39 339 7 HOH HOH . G 6 HOH A 40 340 48 HOH HOH . G 6 HOH A 41 341 67 HOH HOH . G 6 HOH A 42 342 134 HOH HOH . G 6 HOH A 43 343 87 HOH HOH . G 6 HOH A 44 344 35 HOH HOH . G 6 HOH A 45 345 16 HOH HOH . G 6 HOH A 46 346 113 HOH HOH . G 6 HOH A 47 347 45 HOH HOH . G 6 HOH A 48 348 108 HOH HOH . G 6 HOH A 49 349 61 HOH HOH . G 6 HOH A 50 350 140 HOH HOH . G 6 HOH A 51 351 12 HOH HOH . G 6 HOH A 52 352 2 HOH HOH . G 6 HOH A 53 353 30 HOH HOH . G 6 HOH A 54 354 78 HOH HOH . G 6 HOH A 55 355 4 HOH HOH . G 6 HOH A 56 356 14 HOH HOH . G 6 HOH A 57 357 91 HOH HOH . G 6 HOH A 58 358 1 HOH HOH . G 6 HOH A 59 359 60 HOH HOH . G 6 HOH A 60 360 66 HOH HOH . G 6 HOH A 61 361 24 HOH HOH . G 6 HOH A 62 362 72 HOH HOH . G 6 HOH A 63 363 95 HOH HOH . G 6 HOH A 64 364 97 HOH HOH . G 6 HOH A 65 365 9 HOH HOH . G 6 HOH A 66 366 28 HOH HOH . G 6 HOH A 67 367 129 HOH HOH . G 6 HOH A 68 368 96 HOH HOH . G 6 HOH A 69 369 137 HOH HOH . G 6 HOH A 70 370 62 HOH HOH . G 6 HOH A 71 371 17 HOH HOH . G 6 HOH A 72 372 99 HOH HOH . G 6 HOH A 73 373 114 HOH HOH . G 6 HOH A 74 374 116 HOH HOH . G 6 HOH A 75 375 54 HOH HOH . G 6 HOH A 76 376 58 HOH HOH . G 6 HOH A 77 377 69 HOH HOH . G 6 HOH A 78 378 122 HOH HOH . G 6 HOH A 79 379 82 HOH HOH . G 6 HOH A 80 380 84 HOH HOH . G 6 HOH A 81 381 27 HOH HOH . G 6 HOH A 82 382 98 HOH HOH . G 6 HOH A 83 383 50 HOH HOH . G 6 HOH A 84 384 77 HOH HOH . G 6 HOH A 85 385 136 HOH HOH . G 6 HOH A 86 386 26 HOH HOH . G 6 HOH A 87 387 123 HOH HOH . G 6 HOH A 88 388 57 HOH HOH . G 6 HOH A 89 389 6 HOH HOH . G 6 HOH A 90 390 128 HOH HOH . G 6 HOH A 91 391 55 HOH HOH . G 6 HOH A 92 392 107 HOH HOH . G 6 HOH A 93 393 65 HOH HOH . G 6 HOH A 94 394 11 HOH HOH . G 6 HOH A 95 395 75 HOH HOH . G 6 HOH A 96 396 139 HOH HOH . G 6 HOH A 97 397 124 HOH HOH . G 6 HOH A 98 398 53 HOH HOH . G 6 HOH A 99 399 23 HOH HOH . G 6 HOH A 100 400 111 HOH HOH . G 6 HOH A 101 401 15 HOH HOH . G 6 HOH A 102 402 63 HOH HOH . G 6 HOH A 103 403 130 HOH HOH . G 6 HOH A 104 404 88 HOH HOH . G 6 HOH A 105 405 34 HOH HOH . G 6 HOH A 106 406 22 HOH HOH . G 6 HOH A 107 407 119 HOH HOH . G 6 HOH A 108 408 39 HOH HOH . G 6 HOH A 109 409 8 HOH HOH . G 6 HOH A 110 410 38 HOH HOH . G 6 HOH A 111 411 21 HOH HOH . G 6 HOH A 112 412 109 HOH HOH . G 6 HOH A 113 413 37 HOH HOH . G 6 HOH A 114 414 125 HOH HOH . G 6 HOH A 115 415 110 HOH HOH . G 6 HOH A 116 416 85 HOH HOH . G 6 HOH A 117 417 106 HOH HOH . G 6 HOH A 118 418 105 HOH HOH . G 6 HOH A 119 419 127 HOH HOH . G 6 HOH A 120 420 59 HOH HOH . G 6 HOH A 121 421 90 HOH HOH . G 6 HOH A 122 422 132 HOH HOH . G 6 HOH A 123 423 73 HOH HOH . G 6 HOH A 124 424 93 HOH HOH . G 6 HOH A 125 425 112 HOH HOH . G 6 HOH A 126 426 56 HOH HOH . G 6 HOH A 127 427 44 HOH HOH . G 6 HOH A 128 428 81 HOH HOH . G 6 HOH A 129 429 52 HOH HOH . G 6 HOH A 130 430 80 HOH HOH . G 6 HOH A 131 431 42 HOH HOH . G 6 HOH A 132 432 64 HOH HOH . G 6 HOH A 133 433 101 HOH HOH . G 6 HOH A 134 434 43 HOH HOH . G 6 HOH A 135 435 104 HOH HOH . G 6 HOH A 136 436 118 HOH HOH . G 6 HOH A 137 437 117 HOH HOH . G 6 HOH A 138 438 103 HOH HOH . G 6 HOH A 139 439 115 HOH HOH . G 6 HOH A 140 440 120 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 3 28.108 3.349 15.694 1 22.13 ? PB GDP 202 A 1 HETATM 2 O O1B GDP . . . C 3 27.148 2.295 15.179 1 21.91 ? O1B GDP 202 A 1 HETATM 3 O O2B GDP . . . C 3 29.015 2.763 16.759 1 22.97 ? O2B GDP 202 A 1 HETATM 4 O O3B GDP . . . C 3 27.37 4.563 16.163 1 21.42 ? O3B GDP 202 A 1 HETATM 5 O O3A GDP . . . C 3 28.991 3.764 14.41 1 22.46 ? O3A GDP 202 A 1 HETATM 6 P PA GDP . . . C 3 29.6 5.217 14.117 1 23.34 ? PA GDP 202 A 1 HETATM 7 O O1A GDP . . . C 3 28.614 6.183 13.497 1 23.91 ? O1A GDP 202 A 1 HETATM 8 O O2A GDP . . . C 3 30.3 5.752 15.339 1 24.37 ? O2A GDP 202 A 1 HETATM 9 O O5' GDP . . . C 3 30.66 4.841 12.979 1 24.34 ? O5' GDP 202 A 1 HETATM 10 C C5' GDP . . . C 3 31.747 3.969 13.281 1 25.67 ? C5' GDP 202 A 1 HETATM 11 C C4' GDP . . . C 3 32.921 4.295 12.372 1 26.87 ? C4' GDP 202 A 1 HETATM 12 O O4' GDP . . . C 3 32.558 3.996 11.028 1 25.65 ? O4' GDP 202 A 1 HETATM 13 C C3' GDP . . . C 3 33.274 5.771 12.408 1 28.39 ? C3' GDP 202 A 1 HETATM 14 O O3' GDP . . . C 3 34.696 5.917 12.294 1 30.84 ? O3' GDP 202 A 1 HETATM 15 C C2' GDP . . . C 3 32.556 6.36 11.208 1 26.87 ? C2' GDP 202 A 1 HETATM 16 O O2' GDP . . . C 3 33.217 7.483 10.616 1 28.78 ? O2' GDP 202 A 1 HETATM 17 C C1' GDP . . . C 3 32.549 5.191 10.242 1 25.45 ? C1' GDP 202 A 1 HETATM 18 N N9 GDP . . . C 3 31.367 5.126 9.362 1 24.92 ? N9 GDP 202 A 1 HETATM 19 C C8 GDP . . . C 3 30.063 5.188 9.708 1 24.91 ? C8 GDP 202 A 1 HETATM 20 N N7 GDP . . . C 3 29.275 5.053 8.612 1 24.66 ? N7 GDP 202 A 1 HETATM 21 C C5 GDP . . . C 3 30.085 4.881 7.55 1 24.99 ? C5 GDP 202 A 1 HETATM 22 C C6 GDP . . . C 3 29.932 4.676 6.097 1 24.95 ? C6 GDP 202 A 1 HETATM 23 O O6 GDP . . . C 3 28.799 4.617 5.565 1 24.38 ? O6 GDP 202 A 1 HETATM 24 N N1 GDP . . . C 3 31.051 4.542 5.364 1 24.81 ? N1 GDP 202 A 1 HETATM 25 C C2 GDP . . . C 3 32.291 4.599 5.895 1 25.08 ? C2 GDP 202 A 1 HETATM 26 N N2 GDP . . . C 3 33.378 4.463 5.094 1 25.02 ? N2 GDP 202 A 1 HETATM 27 N N3 GDP . . . C 3 32.509 4.79 7.211 1 24.17 ? N3 GDP 202 A 1 HETATM 28 C C4 GDP . . . C 3 31.463 4.927 8.06 1 24.63 ? C4 GDP 202 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #