data_3AF1 # _model_server_result.job_id nsinfdACyhG1Qg6ssDylJA _model_server_result.datetime_utc '2024-11-29 14:52:07' _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 3af1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":313}' # _entry.id 3AF1 # _exptl.entry_id 3AF1 _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 120 _cell.entry_id 3AF1 _cell.length_a 103.9 _cell.length_b 103.9 _cell.length_c 90.21 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AF1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,H,I,J,K,L,M,N,O,P,Q,R,S,T _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 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 100 n n PB O2B GDP sing 101 n n PB O3B GDP sing 102 n n PB O3A GDP sing 103 n n O2B HOB2 GDP sing 104 n n O3B HOB3 GDP sing 105 n n O3A PA GDP sing 106 n n PA O1A GDP doub 107 n n PA O2A GDP sing 108 n n PA O5' GDP sing 109 n n O2A HOA2 GDP sing 110 n n O5' C5' GDP sing 111 n n C5' C4' GDP sing 112 n n C5' H5' GDP sing 113 n n C5' "H5''" GDP sing 114 n n C4' O4' GDP sing 115 n n C4' C3' GDP sing 116 n n C4' H4' GDP sing 117 n n O4' C1' GDP sing 118 n n C3' O3' GDP sing 119 n n C3' C2' GDP sing 120 n n C3' H3' GDP sing 121 n n O3' HO3' GDP sing 122 n n C2' O2' GDP sing 123 n n C2' C1' GDP sing 124 n n C2' H2' GDP sing 125 n n O2' HO2' GDP sing 126 n n C1' N9 GDP sing 127 n n C1' H1' GDP sing 128 n n N9 C8 GDP sing 129 n y N9 C4 GDP sing 130 n y C8 N7 GDP doub 131 n y C8 H8 GDP sing 132 n n N7 C5 GDP sing 133 n y C5 C6 GDP sing 134 n n C5 C4 GDP doub 135 n y C6 O6 GDP doub 136 n n C6 N1 GDP sing 137 n n N1 C2 GDP sing 138 n n N1 HN1 GDP sing 139 n n C2 N2 GDP sing 140 n n C2 N3 GDP doub 141 n n N2 HN21 GDP sing 142 n n N2 HN22 GDP sing 143 n n N3 C4 GDP sing 144 n n # _atom_sites.entry_id 3AF1 _atom_sites.fract_transf_matrix[1][1] 0.009625 _atom_sites.fract_transf_matrix[1][2] 0.005557 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011114 _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] 0.011085 _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 1 313 313 GDP GDP . C 3 FLC A 1 314 314 FLC FLC . D 4 CL A 1 315 315 CL CL . E 4 CL A 1 316 316 CL CL . F 4 CL A 1 317 317 CL CL . G 5 GOL A 1 318 318 GOL GOL . H 5 GOL A 1 319 319 GOL GOL . I 5 GOL A 1 320 320 GOL GOL . J 5 GOL A 1 321 321 GOL GOL . K 5 GOL A 1 322 322 GOL GOL . L 5 GOL A 1 323 323 GOL GOL . M 5 GOL A 1 324 324 GOL GOL . N 5 GOL A 1 325 325 GOL GOL . O 5 GOL A 1 326 326 GOL GOL . P 5 GOL A 1 327 327 GOL GOL . Q 5 GOL A 1 328 328 GOL GOL . R 5 GOL A 1 329 329 GOL GOL . S 5 GOL A 1 330 330 GOL GOL . T 6 HOH A 1 331 331 HOH HOH . T 6 HOH A 2 332 332 HOH HOH . T 6 HOH A 3 333 333 HOH HOH . T 6 HOH A 4 334 334 HOH HOH . T 6 HOH A 5 335 335 HOH HOH . T 6 HOH A 6 336 336 HOH HOH . T 6 HOH A 7 337 337 HOH HOH . T 6 HOH A 8 338 338 HOH HOH . T 6 HOH A 9 339 339 HOH HOH . T 6 HOH A 10 340 340 HOH HOH . T 6 HOH A 11 341 341 HOH HOH . T 6 HOH A 12 342 342 HOH HOH . T 6 HOH A 13 343 343 HOH HOH . T 6 HOH A 14 344 344 HOH HOH . T 6 HOH A 15 345 345 HOH HOH . T 6 HOH A 16 346 346 HOH HOH . T 6 HOH A 17 347 347 HOH HOH . T 6 HOH A 18 348 348 HOH HOH . T 6 HOH A 19 349 349 HOH HOH . T 6 HOH A 20 350 350 HOH HOH . T 6 HOH A 21 351 351 HOH HOH . T 6 HOH A 22 352 352 HOH HOH . T 6 HOH A 23 353 353 HOH HOH . T 6 HOH A 24 354 354 HOH HOH . T 6 HOH A 25 355 355 HOH HOH . T 6 HOH A 26 356 356 HOH HOH . T 6 HOH A 27 357 357 HOH HOH . T 6 HOH A 28 358 358 HOH HOH . T 6 HOH A 29 359 359 HOH HOH . T 6 HOH A 30 360 360 HOH HOH . T 6 HOH A 31 361 361 HOH HOH . T 6 HOH A 32 362 362 HOH HOH . T 6 HOH A 33 363 363 HOH HOH . T 6 HOH A 34 364 364 HOH HOH . T 6 HOH A 35 365 365 HOH HOH . T 6 HOH A 36 366 366 HOH HOH . T 6 HOH A 37 367 367 HOH HOH . T 6 HOH A 38 368 368 HOH HOH . T 6 HOH A 39 369 369 HOH HOH . T 6 HOH A 40 370 370 HOH HOH . T 6 HOH A 41 371 371 HOH HOH . T 6 HOH A 42 372 372 HOH HOH . T 6 HOH A 43 373 373 HOH HOH . T 6 HOH A 44 374 374 HOH HOH . T 6 HOH A 45 375 375 HOH HOH . T 6 HOH A 46 376 376 HOH HOH . T 6 HOH A 47 377 377 HOH HOH . T 6 HOH A 48 378 378 HOH HOH . T 6 HOH A 49 379 379 HOH HOH . T 6 HOH A 50 380 380 HOH HOH . T 6 HOH A 51 381 381 HOH HOH . T 6 HOH A 52 382 382 HOH HOH . T 6 HOH A 53 383 383 HOH HOH . T 6 HOH A 54 384 384 HOH HOH . T 6 HOH A 55 385 385 HOH HOH . T 6 HOH A 56 386 386 HOH HOH . T 6 HOH A 57 387 387 HOH HOH . T 6 HOH A 58 388 388 HOH HOH . T 6 HOH A 59 389 389 HOH HOH . T 6 HOH A 60 390 390 HOH HOH . T 6 HOH A 61 391 391 HOH HOH . T 6 HOH A 62 392 392 HOH HOH . T 6 HOH A 63 393 393 HOH HOH . T 6 HOH A 64 394 394 HOH HOH . T 6 HOH A 65 395 395 HOH HOH . T 6 HOH A 66 396 396 HOH HOH . T 6 HOH A 67 397 397 HOH HOH . T 6 HOH A 68 398 398 HOH HOH . T 6 HOH A 69 399 399 HOH HOH . T 6 HOH A 70 400 400 HOH HOH . T 6 HOH A 71 401 401 HOH HOH . T 6 HOH A 72 402 402 HOH HOH . T 6 HOH A 73 403 403 HOH HOH . T 6 HOH A 74 404 404 HOH HOH . T 6 HOH A 75 405 405 HOH HOH . T 6 HOH A 76 406 406 HOH HOH . T 6 HOH A 77 407 407 HOH HOH . T 6 HOH A 78 408 408 HOH HOH . T 6 HOH A 79 409 409 HOH HOH . T 6 HOH A 80 410 410 HOH HOH . T 6 HOH A 81 411 411 HOH HOH . T 6 HOH A 82 412 412 HOH HOH . T 6 HOH A 83 413 413 HOH HOH . T 6 HOH A 84 414 414 HOH HOH . T 6 HOH A 85 415 415 HOH HOH . T 6 HOH A 86 416 416 HOH HOH . T 6 HOH A 87 417 417 HOH HOH . T 6 HOH A 88 418 418 HOH HOH . T 6 HOH A 89 419 419 HOH HOH . T 6 HOH A 90 420 420 HOH HOH . T 6 HOH A 91 421 421 HOH HOH . T 6 HOH A 92 422 422 HOH HOH . T 6 HOH A 93 423 423 HOH HOH . T 6 HOH A 94 424 424 HOH HOH . T 6 HOH A 95 425 425 HOH HOH . T 6 HOH A 96 426 426 HOH HOH . T 6 HOH A 97 427 427 HOH HOH . T 6 HOH A 98 428 428 HOH HOH . T 6 HOH A 99 429 429 HOH HOH . T 6 HOH A 100 430 430 HOH HOH . T 6 HOH A 101 431 431 HOH HOH . T 6 HOH A 102 432 432 HOH HOH . T 6 HOH A 103 433 433 HOH HOH . T 6 HOH A 104 434 434 HOH HOH . T 6 HOH A 105 435 435 HOH HOH . T 6 HOH A 106 436 436 HOH HOH . T 6 HOH A 107 437 437 HOH HOH . T 6 HOH A 108 438 438 HOH HOH . T 6 HOH A 109 439 439 HOH HOH . T 6 HOH A 110 440 440 HOH HOH . T 6 HOH A 111 441 441 HOH HOH . T 6 HOH A 112 442 442 HOH HOH . T 6 HOH A 113 443 443 HOH HOH . T 6 HOH A 114 444 444 HOH HOH . T 6 HOH A 115 445 445 HOH HOH . T 6 HOH A 116 446 446 HOH HOH . T 6 HOH A 117 447 447 HOH HOH . T 6 HOH A 118 448 448 HOH HOH . T 6 HOH A 119 449 449 HOH HOH . T 6 HOH A 120 450 450 HOH HOH . T 6 HOH A 121 451 451 HOH HOH . T 6 HOH A 122 452 452 HOH HOH . T 6 HOH A 123 453 453 HOH HOH . T 6 HOH A 124 454 454 HOH HOH . T 6 HOH A 125 455 455 HOH HOH . T 6 HOH A 126 456 456 HOH HOH . T 6 HOH A 127 457 457 HOH HOH . T 6 HOH A 128 458 458 HOH HOH . T 6 HOH A 129 459 459 HOH HOH . T 6 HOH A 130 460 460 HOH HOH . T 6 HOH A 131 461 461 HOH HOH . T 6 HOH A 132 462 462 HOH HOH . T 6 HOH A 133 463 463 HOH HOH . T 6 HOH A 134 464 464 HOH HOH . T 6 HOH A 135 465 465 HOH HOH . T 6 HOH A 136 466 466 HOH HOH . T 6 HOH A 137 467 467 HOH HOH . T 6 HOH A 138 468 468 HOH HOH . T 6 HOH A 139 469 469 HOH HOH . T 6 HOH A 140 470 470 HOH HOH . T 6 HOH A 141 471 471 HOH HOH . T 6 HOH A 142 472 472 HOH HOH . T 6 HOH A 143 473 473 HOH HOH . T 6 HOH A 144 474 474 HOH HOH . T 6 HOH A 145 475 475 HOH HOH . T 6 HOH A 146 476 476 HOH HOH . T 6 HOH A 147 477 477 HOH HOH . T 6 HOH A 148 478 478 HOH HOH . T 6 HOH A 149 479 479 HOH HOH . T 6 HOH A 150 480 480 HOH HOH . T 6 HOH A 151 481 481 HOH HOH . T 6 HOH A 152 482 482 HOH HOH . T 6 HOH A 153 483 483 HOH HOH . T 6 HOH A 154 484 484 HOH HOH . T 6 HOH A 155 485 485 HOH HOH . T 6 HOH A 156 486 486 HOH HOH . T 6 HOH A 157 487 487 HOH HOH . T 6 HOH A 158 488 488 HOH HOH . T 6 HOH A 159 489 489 HOH HOH . T 6 HOH A 160 490 490 HOH HOH . T 6 HOH A 161 491 491 HOH HOH . T 6 HOH A 162 492 492 HOH HOH . T 6 HOH A 163 493 493 HOH HOH . T 6 HOH A 164 494 494 HOH HOH . T 6 HOH A 165 495 495 HOH HOH . T 6 HOH A 166 496 496 HOH HOH . T 6 HOH A 167 497 497 HOH HOH . T 6 HOH A 168 498 498 HOH HOH . T 6 HOH A 169 499 499 HOH HOH . T 6 HOH A 170 500 500 HOH HOH . T 6 HOH A 171 501 501 HOH HOH . T 6 HOH A 172 502 502 HOH HOH . T 6 HOH A 173 503 503 HOH HOH . T 6 HOH A 174 504 504 HOH HOH . T 6 HOH A 175 505 505 HOH HOH . T 6 HOH A 176 506 506 HOH HOH . T 6 HOH A 177 507 507 HOH HOH . T 6 HOH A 178 508 508 HOH HOH . T 6 HOH A 179 509 509 HOH HOH . T 6 HOH A 180 510 510 HOH HOH . T 6 HOH A 181 511 511 HOH HOH . T 6 HOH A 182 512 512 HOH HOH . T 6 HOH A 183 513 513 HOH HOH . T 6 HOH A 184 514 514 HOH HOH . T 6 HOH A 185 515 515 HOH HOH . T 6 HOH A 186 516 516 HOH HOH . T 6 HOH A 187 517 517 HOH HOH . T 6 HOH A 188 518 518 HOH HOH . T 6 HOH A 189 519 519 HOH HOH . T 6 HOH A 190 520 520 HOH HOH . T 6 HOH A 191 521 521 HOH HOH . T 6 HOH A 192 522 522 HOH HOH . T 6 HOH A 193 523 523 HOH HOH . T 6 HOH A 194 524 524 HOH HOH . T 6 HOH A 195 525 525 HOH HOH . T 6 HOH A 196 526 526 HOH HOH . T 6 HOH A 197 527 527 HOH HOH . T 6 HOH A 198 528 528 HOH HOH . T 6 HOH A 199 529 529 HOH HOH . T 6 HOH A 200 530 530 HOH HOH . T 6 HOH A 201 531 531 HOH HOH . T 6 HOH A 202 532 532 HOH HOH . T 6 HOH A 203 533 533 HOH HOH . T 6 HOH A 204 534 534 HOH HOH . T 6 HOH A 205 535 535 HOH HOH . T 6 HOH A 206 536 536 HOH HOH . T 6 HOH A 207 537 537 HOH HOH . T 6 HOH A 208 538 538 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 36.687 31.057 16.941 1 32.18 ? PB GDP 313 A 1 HETATM 2 O O1B GDP . . . B 2 37.266 31.404 18.397 1 36.43 ? O1B GDP 313 A 1 HETATM 3 O O2B GDP . . . B 2 36.642 29.463 16.774 1 35.7 ? O2B GDP 313 A 1 HETATM 4 O O3B GDP . . . B 2 35.33 31.614 16.716 1 36.05 ? O3B GDP 313 A 1 HETATM 5 O O3A GDP . . . B 2 37.81 31.535 15.879 1 33.95 ? O3A GDP 313 A 1 HETATM 6 P PA GDP . . . B 2 39.258 32.201 16.164 1 34.28 ? PA GDP 313 A 1 HETATM 7 O O1A GDP . . . B 2 39.936 32.58 14.911 1 38.67 ? O1A GDP 313 A 1 HETATM 8 O O2A GDP . . . B 2 39.182 33.234 17.226 1 36.3 ? O2A GDP 313 A 1 HETATM 9 O O5' GDP . . . B 2 40.007 30.897 16.692 1 39.91 ? O5' GDP 313 A 1 HETATM 10 C C5' GDP . . . B 2 40.2 29.774 15.832 1 42.01 ? C5' GDP 313 A 1 HETATM 11 C C4' GDP . . . B 2 41.242 28.828 16.422 1 41.72 ? C4' GDP 313 A 1 HETATM 12 O O4' GDP . . . B 2 42.489 29.454 16.088 1 43.76 ? O4' GDP 313 A 1 HETATM 13 C C3' GDP . . . B 2 41.122 28.901 17.95 1 46.42 ? C3' GDP 313 A 1 HETATM 14 O O3' GDP . . . B 2 40.653 27.649 18.451 1 52.03 ? O3' GDP 313 A 1 HETATM 15 C C2' GDP . . . B 2 42.548 29.036 18.45 1 48.9 ? C2' GDP 313 A 1 HETATM 16 O O2' GDP . . . B 2 42.924 27.752 18.938 1 62.78 ? O2' GDP 313 A 1 HETATM 17 C C1' GDP . . . B 2 43.386 29.291 17.201 1 45.41 ? C1' GDP 313 A 1 HETATM 18 N N9 GDP . . . B 2 44.008 30.607 17.4 1 40.62 ? N9 GDP 313 A 1 HETATM 19 C C8 GDP . . . B 2 43.408 31.797 17.475 1 36.49 ? C8 GDP 313 A 1 HETATM 20 N N7 GDP . . . B 2 44.346 32.735 17.624 1 34.78 ? N7 GDP 313 A 1 HETATM 21 C C5 GDP . . . B 2 45.536 32.135 17.604 1 32.27 ? C5 GDP 313 A 1 HETATM 22 C C6 GDP . . . B 2 46.842 32.602 17.654 1 33.75 ? C6 GDP 313 A 1 HETATM 23 O O6 GDP . . . B 2 47.055 33.805 17.815 1 40.51 ? O6 GDP 313 A 1 HETATM 24 N N1 GDP . . . B 2 47.892 31.67 17.61 1 30.96 ? N1 GDP 313 A 1 HETATM 25 C C2 GDP . . . B 2 47.594 30.3 17.477 1 33.44 ? C2 GDP 313 A 1 HETATM 26 N N2 GDP . . . B 2 48.568 29.391 17.405 1 33.88 ? N2 GDP 313 A 1 HETATM 27 N N3 GDP . . . B 2 46.317 29.88 17.435 1 33.19 ? N3 GDP 313 A 1 HETATM 28 C C4 GDP . . . B 2 45.317 30.771 17.472 1 33.16 ? C4 GDP 313 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #