data_8FPX # _model_server_result.job_id SGTNMZ6b5fzQx_TD0xOkCQ _model_server_result.datetime_utc '2024-11-22 00:40:17' _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 8fpx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 8FPX # _exptl.entry_id 8FPX _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 95.91 _cell.angle_gamma 90 _cell.entry_id 8FPX _cell.length_a 32.212 _cell.length_b 87.265 _cell.length_c 34.044 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8FPX _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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,D,E _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 # 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 metalc ? metalc1 A OG1 THR 21 A THR 19 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc2 A O PRO 38 A PRO 36 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc3 B O3B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc4 C MG MG . A MG 202 1_555 E O HOH . A HOH 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc5 C MG MG . A MG 202 1_555 E O HOH . A HOH 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc6 C MG MG . A MG 202 1_555 E O HOH . A HOH 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? # _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 97 n n PB O2B GDP sing 98 n n PB O3B GDP sing 99 n n PB O3A GDP sing 100 n n O2B HOB2 GDP sing 101 n n O3B HOB3 GDP sing 102 n n O3A PA GDP sing 103 n n PA O1A GDP doub 104 n n PA O2A GDP sing 105 n n PA O5' GDP sing 106 n n O2A HOA2 GDP sing 107 n n O5' C5' GDP sing 108 n n C5' C4' GDP sing 109 n n C5' H5' GDP sing 110 n n C5' "H5''" GDP sing 111 n n C4' O4' GDP sing 112 n n C4' C3' GDP sing 113 n n C4' H4' GDP sing 114 n n O4' C1' GDP sing 115 n n C3' O3' GDP sing 116 n n C3' C2' GDP sing 117 n n C3' H3' GDP sing 118 n n O3' HO3' GDP sing 119 n n C2' O2' GDP sing 120 n n C2' C1' GDP sing 121 n n C2' H2' GDP sing 122 n n O2' HO2' GDP sing 123 n n C1' N9 GDP sing 124 n n C1' H1' GDP sing 125 n n N9 C8 GDP sing 126 n y N9 C4 GDP sing 127 n y C8 N7 GDP doub 128 n y C8 H8 GDP sing 129 n n N7 C5 GDP sing 130 n y C5 C6 GDP sing 131 n n C5 C4 GDP doub 132 n y C6 O6 GDP doub 133 n n C6 N1 GDP sing 134 n n N1 C2 GDP sing 135 n n N1 HN1 GDP sing 136 n n C2 N2 GDP sing 137 n n C2 N3 GDP doub 138 n n N2 HN21 GDP sing 139 n n N2 HN22 GDP sing 140 n n N3 C4 GDP sing 141 n n # _atom_sites.entry_id 8FPX _atom_sites.fract_transf_matrix[1][1] 0.031044 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003211 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011459 _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] 0.029531 _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 MG A 1 202 202 MG MG . D 4 DIO A 1 203 203 DIO DIO . E 5 HOH A 1 301 518 HOH HOH . E 5 HOH A 2 302 467 HOH HOH . E 5 HOH A 3 303 363 HOH HOH . E 5 HOH A 4 304 419 HOH HOH . E 5 HOH A 5 305 503 HOH HOH . E 5 HOH A 6 306 489 HOH HOH . E 5 HOH A 7 307 383 HOH HOH . E 5 HOH A 8 308 431 HOH HOH . E 5 HOH A 9 309 506 HOH HOH . E 5 HOH A 10 310 451 HOH HOH . E 5 HOH A 11 311 380 HOH HOH . E 5 HOH A 12 312 414 HOH HOH . E 5 HOH A 13 313 364 HOH HOH . E 5 HOH A 14 314 411 HOH HOH . E 5 HOH A 15 315 476 HOH HOH . E 5 HOH A 16 316 412 HOH HOH . E 5 HOH A 17 317 401 HOH HOH . E 5 HOH A 18 318 444 HOH HOH . E 5 HOH A 19 319 405 HOH HOH . E 5 HOH A 20 320 302 HOH HOH . E 5 HOH A 21 321 340 HOH HOH . E 5 HOH A 22 322 390 HOH HOH . E 5 HOH A 23 323 382 HOH HOH . E 5 HOH A 24 324 338 HOH HOH . E 5 HOH A 25 325 361 HOH HOH . E 5 HOH A 26 326 398 HOH HOH . E 5 HOH A 27 327 330 HOH HOH . E 5 HOH A 28 328 370 HOH HOH . E 5 HOH A 29 329 341 HOH HOH . E 5 HOH A 30 330 327 HOH HOH . E 5 HOH A 31 331 329 HOH HOH . E 5 HOH A 32 332 430 HOH HOH . E 5 HOH A 33 333 519 HOH HOH . E 5 HOH A 34 334 317 HOH HOH . E 5 HOH A 35 335 377 HOH HOH . E 5 HOH A 36 336 301 HOH HOH . E 5 HOH A 37 337 304 HOH HOH . E 5 HOH A 38 338 402 HOH HOH . E 5 HOH A 39 339 417 HOH HOH . E 5 HOH A 40 340 326 HOH HOH . E 5 HOH A 41 341 442 HOH HOH . E 5 HOH A 42 342 400 HOH HOH . E 5 HOH A 43 343 446 HOH HOH . E 5 HOH A 44 344 344 HOH HOH . E 5 HOH A 45 345 315 HOH HOH . E 5 HOH A 46 346 455 HOH HOH . E 5 HOH A 47 347 360 HOH HOH . E 5 HOH A 48 348 342 HOH HOH . E 5 HOH A 49 349 352 HOH HOH . E 5 HOH A 50 350 305 HOH HOH . E 5 HOH A 51 351 339 HOH HOH . E 5 HOH A 52 352 325 HOH HOH . E 5 HOH A 53 353 306 HOH HOH . E 5 HOH A 54 354 343 HOH HOH . E 5 HOH A 55 355 408 HOH HOH . E 5 HOH A 56 356 526 HOH HOH . E 5 HOH A 57 357 310 HOH HOH . E 5 HOH A 58 358 312 HOH HOH . E 5 HOH A 59 359 334 HOH HOH . E 5 HOH A 60 360 369 HOH HOH . E 5 HOH A 61 361 514 HOH HOH . E 5 HOH A 62 362 379 HOH HOH . E 5 HOH A 63 363 410 HOH HOH . E 5 HOH A 64 364 319 HOH HOH . E 5 HOH A 65 365 391 HOH HOH . E 5 HOH A 66 366 365 HOH HOH . E 5 HOH A 67 367 349 HOH HOH . E 5 HOH A 68 368 359 HOH HOH . E 5 HOH A 69 369 311 HOH HOH . E 5 HOH A 70 370 321 HOH HOH . E 5 HOH A 71 371 357 HOH HOH . E 5 HOH A 72 372 393 HOH HOH . E 5 HOH A 73 373 308 HOH HOH . E 5 HOH A 74 374 428 HOH HOH . E 5 HOH A 75 375 496 HOH HOH . E 5 HOH A 76 376 345 HOH HOH . E 5 HOH A 77 377 493 HOH HOH . E 5 HOH A 78 378 484 HOH HOH . E 5 HOH A 79 379 461 HOH HOH . E 5 HOH A 80 380 407 HOH HOH . E 5 HOH A 81 381 309 HOH HOH . E 5 HOH A 82 382 452 HOH HOH . E 5 HOH A 83 383 501 HOH HOH . E 5 HOH A 84 384 404 HOH HOH . E 5 HOH A 85 385 441 HOH HOH . E 5 HOH A 86 386 462 HOH HOH . E 5 HOH A 87 387 322 HOH HOH . E 5 HOH A 88 388 314 HOH HOH . E 5 HOH A 89 389 492 HOH HOH . E 5 HOH A 90 390 320 HOH HOH . E 5 HOH A 91 391 465 HOH HOH . E 5 HOH A 92 392 416 HOH HOH . E 5 HOH A 93 393 303 HOH HOH . E 5 HOH A 94 394 396 HOH HOH . E 5 HOH A 95 395 336 HOH HOH . E 5 HOH A 96 396 440 HOH HOH . E 5 HOH A 97 397 351 HOH HOH . E 5 HOH A 98 398 366 HOH HOH . E 5 HOH A 99 399 504 HOH HOH . E 5 HOH A 100 400 438 HOH HOH . E 5 HOH A 101 401 481 HOH HOH . E 5 HOH A 102 402 313 HOH HOH . E 5 HOH A 103 403 475 HOH HOH . E 5 HOH A 104 404 434 HOH HOH . E 5 HOH A 105 405 406 HOH HOH . E 5 HOH A 106 406 307 HOH HOH . E 5 HOH A 107 407 425 HOH HOH . E 5 HOH A 108 408 353 HOH HOH . E 5 HOH A 109 409 368 HOH HOH . E 5 HOH A 110 410 480 HOH HOH . E 5 HOH A 111 411 509 HOH HOH . E 5 HOH A 112 412 331 HOH HOH . E 5 HOH A 113 413 337 HOH HOH . E 5 HOH A 114 414 512 HOH HOH . E 5 HOH A 115 415 468 HOH HOH . E 5 HOH A 116 416 421 HOH HOH . E 5 HOH A 117 417 498 HOH HOH . E 5 HOH A 118 418 422 HOH HOH . E 5 HOH A 119 419 427 HOH HOH . E 5 HOH A 120 420 372 HOH HOH . E 5 HOH A 121 421 335 HOH HOH . E 5 HOH A 122 422 433 HOH HOH . E 5 HOH A 123 423 358 HOH HOH . E 5 HOH A 124 424 435 HOH HOH . E 5 HOH A 125 425 413 HOH HOH . E 5 HOH A 126 426 516 HOH HOH . E 5 HOH A 127 427 524 HOH HOH . E 5 HOH A 128 428 508 HOH HOH . E 5 HOH A 129 429 387 HOH HOH . E 5 HOH A 130 430 436 HOH HOH . E 5 HOH A 131 431 316 HOH HOH . E 5 HOH A 132 432 347 HOH HOH . E 5 HOH A 133 433 323 HOH HOH . E 5 HOH A 134 434 502 HOH HOH . E 5 HOH A 135 435 513 HOH HOH . E 5 HOH A 136 436 367 HOH HOH . E 5 HOH A 137 437 482 HOH HOH . E 5 HOH A 138 438 374 HOH HOH . E 5 HOH A 139 439 474 HOH HOH . E 5 HOH A 140 440 483 HOH HOH . E 5 HOH A 141 441 457 HOH HOH . E 5 HOH A 142 442 521 HOH HOH . E 5 HOH A 143 443 399 HOH HOH . E 5 HOH A 144 444 378 HOH HOH . E 5 HOH A 145 445 362 HOH HOH . E 5 HOH A 146 446 439 HOH HOH . E 5 HOH A 147 447 389 HOH HOH . E 5 HOH A 148 448 463 HOH HOH . E 5 HOH A 149 449 437 HOH HOH . E 5 HOH A 150 450 479 HOH HOH . E 5 HOH A 151 451 346 HOH HOH . E 5 HOH A 152 452 418 HOH HOH . E 5 HOH A 153 453 373 HOH HOH . E 5 HOH A 154 454 415 HOH HOH . E 5 HOH A 155 455 491 HOH HOH . E 5 HOH A 156 456 511 HOH HOH . E 5 HOH A 157 457 348 HOH HOH . E 5 HOH A 158 458 354 HOH HOH . E 5 HOH A 159 459 333 HOH HOH . E 5 HOH A 160 460 375 HOH HOH . E 5 HOH A 161 461 356 HOH HOH . E 5 HOH A 162 462 376 HOH HOH . E 5 HOH A 163 463 499 HOH HOH . E 5 HOH A 164 464 424 HOH HOH . E 5 HOH A 165 465 392 HOH HOH . E 5 HOH A 166 466 448 HOH HOH . E 5 HOH A 167 467 460 HOH HOH . E 5 HOH A 168 468 450 HOH HOH . E 5 HOH A 169 469 403 HOH HOH . E 5 HOH A 170 470 497 HOH HOH . E 5 HOH A 171 471 386 HOH HOH . E 5 HOH A 172 472 423 HOH HOH . E 5 HOH A 173 473 458 HOH HOH . E 5 HOH A 174 474 487 HOH HOH . E 5 HOH A 175 475 453 HOH HOH . E 5 HOH A 176 476 456 HOH HOH . E 5 HOH A 177 477 371 HOH HOH . E 5 HOH A 178 478 432 HOH HOH . E 5 HOH A 179 479 394 HOH HOH . E 5 HOH A 180 480 328 HOH HOH . E 5 HOH A 181 481 420 HOH HOH . E 5 HOH A 182 482 318 HOH HOH . E 5 HOH A 183 483 409 HOH HOH . E 5 HOH A 184 484 388 HOH HOH . E 5 HOH A 185 485 350 HOH HOH . E 5 HOH A 186 486 384 HOH HOH . E 5 HOH A 187 487 395 HOH HOH . E 5 HOH A 188 488 515 HOH HOH . E 5 HOH A 189 489 324 HOH HOH . E 5 HOH A 190 490 381 HOH HOH . E 5 HOH A 191 491 355 HOH HOH . E 5 HOH A 192 492 397 HOH HOH . E 5 HOH A 193 493 485 HOH HOH . E 5 HOH A 194 494 332 HOH HOH . E 5 HOH A 195 495 525 HOH HOH . E 5 HOH A 196 496 454 HOH HOH . E 5 HOH A 197 497 449 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 -4.779 0.519 2.1 1 10.11 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -5.716 -0.269 1.211 1 10.25 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -3.358 0.354 1.654 1 11.23 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -5.168 1.982 2.226 1 11.07 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -4.847 -0.16 3.567 1 9.71 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -5.703 0.333 4.843 1 11.74 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -7.16 0.486 4.477 1 11.77 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -5.061 1.498 5.559 1 12.4 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -5.541 -0.949 5.799 1 10.08 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -6.038 -2.2 5.326 1 12.83 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -6.223 -3.169 6.493 1 12.7 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -5.003 -3.391 7.213 1 14.41 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -7.198 -2.591 7.492 1 14.84 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -7.958 -3.679 8.038 1 21.74 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -6.316 -2.048 8.589 1 17.94 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -7.004 -2.012 9.841 1 18.52 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -5.171 -3.037 8.594 1 14.43 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -3.911 -2.431 9.048 1 12.79 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -3.416 -1.232 8.679 1 15.11 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -2.213 -1.009 9.273 1 13.21 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -1.931 -2.097 10.03 1 14.53 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -0.822 -2.525 10.9 1 14.06 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 0.179 -1.797 11.102 1 12.57 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -0.917 -3.726 11.48 1 12.34 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -1.973 -4.547 11.294 1 13.51 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -1.988 -5.754 11.932 1 11.83 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -3.026 -4.224 10.506 1 11.94 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -3.045 -3.03 9.86 1 12.34 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #