data_1DPF # _model_server_result.job_id xYZt-RctVoTYz6L8h0g-Vw _model_server_result.datetime_utc '2024-10-11 06:16:06' _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 1dpf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":200}' # _entry.id 1DPF # _exptl.entry_id 1DPF _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 _cell.angle_gamma 90 _cell.entry_id 1DPF _cell.length_a 91.2 _cell.length_b 91.2 _cell.length_c 56.5 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DPF _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _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 1DPF _atom_sites.fract_transf_matrix[1][1] 0.010965 _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] 0.010965 _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] 0.017699 _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 1 200 200 GDP GDP . C 3 HOH A 1 300 300 HOH TIP . C 3 HOH A 2 301 301 HOH TIP . C 3 HOH A 3 302 302 HOH TIP . C 3 HOH A 4 303 303 HOH TIP . C 3 HOH A 5 304 304 HOH TIP . C 3 HOH A 6 305 305 HOH TIP . C 3 HOH A 7 306 306 HOH TIP . C 3 HOH A 8 307 307 HOH TIP . C 3 HOH A 9 308 308 HOH TIP . C 3 HOH A 10 309 309 HOH TIP . C 3 HOH A 11 310 310 HOH TIP . C 3 HOH A 12 311 311 HOH TIP . C 3 HOH A 13 312 312 HOH TIP . C 3 HOH A 14 313 313 HOH TIP . C 3 HOH A 15 314 314 HOH TIP . C 3 HOH A 16 315 315 HOH TIP . C 3 HOH A 17 316 316 HOH TIP . C 3 HOH A 18 317 317 HOH TIP . C 3 HOH A 19 318 318 HOH TIP . C 3 HOH A 20 319 319 HOH TIP . C 3 HOH A 21 320 320 HOH TIP . C 3 HOH A 22 321 321 HOH TIP . C 3 HOH A 23 322 322 HOH TIP . C 3 HOH A 24 323 323 HOH TIP . C 3 HOH A 25 324 324 HOH TIP . C 3 HOH A 26 325 325 HOH TIP . C 3 HOH A 27 326 326 HOH TIP . C 3 HOH A 28 327 327 HOH TIP . C 3 HOH A 29 328 328 HOH TIP . C 3 HOH A 30 329 329 HOH TIP . C 3 HOH A 31 330 330 HOH TIP . C 3 HOH A 32 331 331 HOH TIP . C 3 HOH A 33 332 332 HOH TIP . C 3 HOH A 34 333 333 HOH TIP . C 3 HOH A 35 334 334 HOH TIP . C 3 HOH A 36 335 335 HOH TIP . C 3 HOH A 37 336 336 HOH TIP . C 3 HOH A 38 337 337 HOH TIP . C 3 HOH A 39 338 338 HOH TIP . C 3 HOH A 40 339 339 HOH TIP . C 3 HOH A 41 340 340 HOH TIP . C 3 HOH A 42 341 341 HOH TIP . C 3 HOH A 43 342 342 HOH TIP . C 3 HOH A 44 343 343 HOH TIP . C 3 HOH A 45 344 344 HOH TIP . C 3 HOH A 46 345 345 HOH TIP . C 3 HOH A 47 346 346 HOH TIP . C 3 HOH A 48 347 347 HOH TIP . C 3 HOH A 49 348 348 HOH TIP . C 3 HOH A 50 349 349 HOH TIP . C 3 HOH A 51 350 350 HOH TIP . C 3 HOH A 52 351 351 HOH TIP . C 3 HOH A 53 352 352 HOH TIP . C 3 HOH A 54 353 353 HOH TIP . C 3 HOH A 55 354 354 HOH TIP . C 3 HOH A 56 355 355 HOH TIP . C 3 HOH A 57 356 356 HOH TIP . C 3 HOH A 58 357 357 HOH TIP . C 3 HOH A 59 358 358 HOH TIP . C 3 HOH A 60 359 359 HOH TIP . C 3 HOH A 61 360 360 HOH TIP . C 3 HOH A 62 361 361 HOH TIP . C 3 HOH A 63 362 362 HOH TIP . C 3 HOH A 64 363 363 HOH TIP . C 3 HOH A 65 364 364 HOH TIP . C 3 HOH A 66 365 365 HOH TIP . C 3 HOH A 67 366 366 HOH TIP . C 3 HOH A 68 367 367 HOH TIP . C 3 HOH A 69 368 368 HOH TIP . C 3 HOH A 70 369 369 HOH TIP . C 3 HOH A 71 370 370 HOH TIP . C 3 HOH A 72 371 371 HOH TIP . C 3 HOH A 73 372 372 HOH TIP . C 3 HOH A 74 373 373 HOH TIP . C 3 HOH A 75 374 374 HOH TIP . C 3 HOH A 76 375 375 HOH TIP . C 3 HOH A 77 376 376 HOH TIP . C 3 HOH A 78 377 377 HOH TIP . C 3 HOH A 79 378 378 HOH TIP . C 3 HOH A 80 379 379 HOH TIP . C 3 HOH A 81 380 380 HOH TIP . C 3 HOH A 82 381 381 HOH TIP . C 3 HOH A 83 382 382 HOH TIP . C 3 HOH A 84 383 383 HOH TIP . C 3 HOH A 85 384 384 HOH TIP . C 3 HOH A 86 385 385 HOH TIP . C 3 HOH A 87 386 386 HOH TIP . C 3 HOH A 88 387 387 HOH TIP . C 3 HOH A 89 388 388 HOH TIP . C 3 HOH A 90 389 389 HOH TIP . C 3 HOH A 91 390 390 HOH TIP . C 3 HOH A 92 391 391 HOH TIP . C 3 HOH A 93 392 392 HOH TIP . C 3 HOH A 94 393 393 HOH TIP . C 3 HOH A 95 394 394 HOH TIP . C 3 HOH A 96 395 395 HOH TIP . C 3 HOH A 97 396 396 HOH TIP . C 3 HOH A 98 397 397 HOH TIP . C 3 HOH A 99 398 398 HOH TIP . C 3 HOH A 100 399 399 HOH TIP . C 3 HOH A 101 400 400 HOH TIP . C 3 HOH A 102 401 401 HOH TIP . C 3 HOH A 103 402 402 HOH TIP . C 3 HOH A 104 403 403 HOH TIP . C 3 HOH A 105 404 404 HOH TIP . C 3 HOH A 106 405 405 HOH TIP . C 3 HOH A 107 406 406 HOH TIP . C 3 HOH A 108 407 407 HOH TIP . C 3 HOH A 109 408 408 HOH TIP . C 3 HOH A 110 409 409 HOH TIP . C 3 HOH A 111 410 410 HOH TIP . C 3 HOH A 112 411 411 HOH TIP . C 3 HOH A 113 412 412 HOH TIP . C 3 HOH A 114 413 413 HOH TIP . C 3 HOH A 115 414 414 HOH TIP . C 3 HOH A 116 415 415 HOH TIP . C 3 HOH A 117 416 416 HOH TIP . C 3 HOH A 118 417 417 HOH TIP . C 3 HOH A 119 418 418 HOH TIP . C 3 HOH A 120 419 419 HOH TIP . C 3 HOH A 121 420 420 HOH TIP . C 3 HOH A 122 421 421 HOH TIP . C 3 HOH A 123 422 422 HOH TIP . C 3 HOH A 124 423 423 HOH TIP . C 3 HOH A 125 424 424 HOH TIP . C 3 HOH A 126 425 425 HOH TIP . C 3 HOH A 127 426 426 HOH TIP . C 3 HOH A 128 427 427 HOH TIP . C 3 HOH A 129 428 428 HOH TIP . C 3 HOH A 130 429 429 HOH TIP . C 3 HOH A 131 430 430 HOH TIP . C 3 HOH A 132 431 431 HOH TIP . C 3 HOH A 133 432 432 HOH TIP . C 3 HOH A 134 433 433 HOH TIP . C 3 HOH A 135 434 434 HOH TIP . C 3 HOH A 136 435 435 HOH TIP . C 3 HOH A 137 436 436 HOH TIP . C 3 HOH A 138 437 437 HOH TIP . C 3 HOH A 139 438 438 HOH TIP . C 3 HOH A 140 439 439 HOH TIP . C 3 HOH A 141 440 440 HOH TIP . C 3 HOH A 142 441 441 HOH TIP . C 3 HOH A 143 442 442 HOH TIP . C 3 HOH A 144 443 443 HOH TIP . C 3 HOH A 145 444 444 HOH TIP . C 3 HOH A 146 445 445 HOH TIP . C 3 HOH A 147 446 446 HOH TIP . C 3 HOH A 148 447 447 HOH TIP . C 3 HOH A 149 448 448 HOH TIP . C 3 HOH A 150 449 449 HOH TIP . C 3 HOH A 151 450 450 HOH TIP . C 3 HOH A 152 451 451 HOH TIP . C 3 HOH A 153 452 452 HOH TIP . C 3 HOH A 154 453 453 HOH TIP . C 3 HOH A 155 454 454 HOH TIP . C 3 HOH A 156 455 455 HOH TIP . C 3 HOH A 157 456 456 HOH TIP . C 3 HOH A 158 457 457 HOH TIP . C 3 HOH A 159 458 458 HOH TIP . C 3 HOH A 160 459 459 HOH TIP . C 3 HOH A 161 460 460 HOH TIP . C 3 HOH A 162 461 461 HOH TIP . C 3 HOH A 163 462 462 HOH TIP . C 3 HOH A 164 463 463 HOH TIP . C 3 HOH A 165 464 464 HOH TIP . C 3 HOH A 166 465 465 HOH TIP . C 3 HOH A 167 466 466 HOH TIP . C 3 HOH A 168 467 467 HOH TIP . C 3 HOH A 169 468 468 HOH TIP . C 3 HOH A 170 469 469 HOH TIP . C 3 HOH A 171 470 470 HOH TIP . C 3 HOH A 172 471 471 HOH TIP . C 3 HOH A 173 472 472 HOH TIP . C 3 HOH A 174 473 473 HOH TIP . C 3 HOH A 175 474 474 HOH TIP . C 3 HOH A 176 475 475 HOH TIP . C 3 HOH A 177 476 476 HOH TIP . C 3 HOH A 178 477 477 HOH TIP . C 3 HOH A 179 478 478 HOH TIP . C 3 HOH A 180 479 479 HOH TIP . C 3 HOH A 181 480 480 HOH TIP . C 3 HOH A 182 481 481 HOH TIP . C 3 HOH A 183 482 482 HOH TIP . C 3 HOH A 184 483 483 HOH TIP . C 3 HOH A 185 484 484 HOH TIP . C 3 HOH A 186 485 485 HOH TIP . C 3 HOH A 187 486 486 HOH TIP . # 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 5.509 18.053 18.403 1 23.98 ? PB GDP 200 A 1 HETATM 2 O O1B GDP . . . B 2 4.301 17.523 19.026 1 26.65 ? O1B GDP 200 A 1 HETATM 3 O O2B GDP . . . B 2 5.445 19.234 17.562 1 28.63 ? O2B GDP 200 A 1 HETATM 4 O O3B GDP . . . B 2 6.527 18.32 19.528 1 26.95 ? O3B GDP 200 A 1 HETATM 5 O O3A GDP . . . B 2 6.283 16.854 17.609 1 29.2 ? O3A GDP 200 A 1 HETATM 6 P PA GDP . . . B 2 7.008 16.705 16.152 1 24.31 ? PA GDP 200 A 1 HETATM 7 O O1A GDP . . . B 2 7.915 17.854 15.913 1 24.96 ? O1A GDP 200 A 1 HETATM 8 O O2A GDP . . . B 2 7.564 15.355 16.107 1 30.58 ? O2A GDP 200 A 1 HETATM 9 O O5' GDP . . . B 2 5.751 16.804 15.098 1 25.78 ? O5' GDP 200 A 1 HETATM 10 C C5' GDP . . . B 2 4.841 15.683 14.936 1 22.45 ? C5' GDP 200 A 1 HETATM 11 C C4' GDP . . . B 2 4.777 15.074 13.493 1 23.21 ? C4' GDP 200 A 1 HETATM 12 O O4' GDP . . . B 2 4.956 16.093 12.509 1 22.13 ? O4' GDP 200 A 1 HETATM 13 C C3' GDP . . . B 2 5.837 14.022 13.191 1 23.19 ? C3' GDP 200 A 1 HETATM 14 O O3' GDP . . . B 2 5.261 12.919 12.52 1 24.89 ? O3' GDP 200 A 1 HETATM 15 C C2' GDP . . . B 2 6.893 14.731 12.336 1 23 ? C2' GDP 200 A 1 HETATM 16 O O2' GDP . . . B 2 7.69 13.917 11.445 1 23.81 ? O2' GDP 200 A 1 HETATM 17 C C1' GDP . . . B 2 6.021 15.728 11.605 1 21.97 ? C1' GDP 200 A 1 HETATM 18 N N9 GDP . . . B 2 6.741 16.953 11.239 1 21.82 ? N9 GDP 200 A 1 HETATM 19 C C8 GDP . . . B 2 7.491 17.796 12.003 1 20.88 ? C8 GDP 200 A 1 HETATM 20 N N7 GDP . . . B 2 8 18.808 11.388 1 21.97 ? N7 GDP 200 A 1 HETATM 21 C C5 GDP . . . B 2 7.549 18.635 10.078 1 21.44 ? C5 GDP 200 A 1 HETATM 22 C C6 GDP . . . B 2 7.775 19.445 8.908 1 22.18 ? C6 GDP 200 A 1 HETATM 23 O O6 GDP . . . B 2 8.422 20.477 8.81 1 21.88 ? O6 GDP 200 A 1 HETATM 24 N N1 GDP . . . B 2 7.138 18.917 7.778 1 22.83 ? N1 GDP 200 A 1 HETATM 25 C C2 GDP . . . B 2 6.377 17.761 7.758 1 23.25 ? C2 GDP 200 A 1 HETATM 26 N N2 GDP . . . B 2 5.853 17.427 6.584 1 22.77 ? N2 GDP 200 A 1 HETATM 27 N N3 GDP . . . B 2 6.157 16.994 8.848 1 22.97 ? N3 GDP 200 A 1 HETATM 28 C C4 GDP . . . B 2 6.774 17.495 9.97 1 21.57 ? C4 GDP 200 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #