data_3ORO # _model_server_result.job_id lXUPISesz5DFzfBRkjvGrg _model_server_result.datetime_utc '2024-12-08 11:13:25' _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 3oro # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":340}' # _entry.id 3ORO # _exptl.entry_id 3ORO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _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 3ORO _cell.length_a 40.598 _cell.length_b 51.423 _cell.length_c 135.327 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ORO _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 _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 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # 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 PG S1G AGS doub 1 n n PG O2G AGS sing 2 n n PG O3G AGS sing 3 n n PG O3B AGS sing 4 n n PB O1B AGS doub 5 n n PB O2B AGS sing 6 n n PB O3B AGS sing 7 n n PB O3A AGS sing 8 n n PA O1A AGS doub 9 n n PA O2A AGS sing 10 n n PA O3A AGS sing 11 n n PA O5' AGS sing 12 n n O5' C5' AGS sing 13 n n C5' C4' AGS sing 14 n n C4' O4' AGS sing 15 n n C4' C3' AGS sing 16 n n O4' C1' AGS sing 17 n n C3' O3' AGS sing 18 n n C3' C2' AGS sing 19 n n C2' O2' AGS sing 20 n n C2' C1' AGS sing 21 n n C1' N9 AGS sing 22 n n N9 C8 AGS sing 23 n y N9 C4 AGS sing 24 n y C8 N7 AGS doub 25 n y N7 C5 AGS sing 26 n y C5 C6 AGS sing 27 n y C5 C4 AGS doub 28 n y C6 N6 AGS sing 29 n n C6 N1 AGS doub 30 n y N1 C2 AGS sing 31 n y C2 N3 AGS doub 32 n y N3 C4 AGS sing 33 n y O2G HOG2 AGS sing 34 n n O3G H21 AGS sing 35 n n O2B HOB2 AGS sing 36 n n O2A HOA2 AGS sing 37 n n C5' "H5'1" AGS sing 38 n n C5' "H5'2" AGS sing 39 n n C4' H4' AGS sing 40 n n C3' H3' AGS sing 41 n n O3' HO3' AGS sing 42 n n C2' H2' AGS sing 43 n n O2' HO2' AGS sing 44 n n C1' H1' AGS sing 45 n n C8 H8 AGS sing 46 n n N6 HN61 AGS sing 47 n n N6 HN62 AGS sing 48 n n C2 H2 AGS sing 49 n n # _atom_sites.entry_id 3ORO _atom_sites.fract_transf_matrix[1][1] 0.024632 _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] 0.019447 _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] 0.00739 _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 AGS A 1 340 340 AGS AGS . C 3 NHE A 1 334 334 NHE NHE . D 4 HOH A 1 309 309 HOH HOH . D 4 HOH A 2 310 310 HOH HOH . D 4 HOH A 3 311 311 HOH HOH . D 4 HOH A 4 312 312 HOH HOH . D 4 HOH A 5 313 313 HOH HOH . D 4 HOH A 6 314 314 HOH HOH . D 4 HOH A 7 315 315 HOH HOH . D 4 HOH A 8 316 316 HOH HOH . D 4 HOH A 9 317 317 HOH HOH . D 4 HOH A 10 318 318 HOH HOH . D 4 HOH A 11 319 319 HOH HOH . D 4 HOH A 12 320 320 HOH HOH . D 4 HOH A 13 321 321 HOH HOH . D 4 HOH A 14 322 322 HOH HOH . D 4 HOH A 15 323 323 HOH HOH . D 4 HOH A 16 324 324 HOH HOH . D 4 HOH A 17 325 325 HOH HOH . D 4 HOH A 18 326 326 HOH HOH . D 4 HOH A 19 327 327 HOH HOH . D 4 HOH A 20 328 328 HOH HOH . D 4 HOH A 21 329 329 HOH HOH . D 4 HOH A 22 330 330 HOH HOH . D 4 HOH A 23 331 331 HOH HOH . D 4 HOH A 24 332 332 HOH HOH . D 4 HOH A 25 333 333 HOH HOH . D 4 HOH A 26 335 335 HOH HOH . D 4 HOH A 27 336 336 HOH HOH . D 4 HOH A 28 337 337 HOH HOH . D 4 HOH A 29 338 338 HOH HOH . D 4 HOH A 30 339 339 HOH HOH . D 4 HOH A 31 341 341 HOH HOH . D 4 HOH A 32 342 342 HOH HOH . D 4 HOH A 33 343 343 HOH HOH . D 4 HOH A 34 344 344 HOH HOH . D 4 HOH A 35 345 345 HOH HOH . D 4 HOH A 36 346 346 HOH HOH . D 4 HOH A 37 347 347 HOH HOH . D 4 HOH A 38 348 348 HOH HOH . D 4 HOH A 39 349 349 HOH HOH . D 4 HOH A 40 350 350 HOH HOH . D 4 HOH A 41 351 351 HOH HOH . D 4 HOH A 42 352 352 HOH HOH . D 4 HOH A 43 353 353 HOH HOH . D 4 HOH A 44 354 354 HOH HOH . D 4 HOH A 45 355 355 HOH HOH . D 4 HOH A 46 356 356 HOH HOH . D 4 HOH A 47 357 357 HOH HOH . D 4 HOH A 48 358 358 HOH HOH . D 4 HOH A 49 359 359 HOH HOH . D 4 HOH A 50 360 360 HOH HOH . D 4 HOH A 51 361 361 HOH HOH . D 4 HOH A 52 362 362 HOH HOH . D 4 HOH A 53 363 363 HOH HOH . D 4 HOH A 54 364 364 HOH HOH . D 4 HOH A 55 365 365 HOH HOH . D 4 HOH A 56 366 366 HOH HOH . D 4 HOH A 57 367 367 HOH HOH . D 4 HOH A 58 368 368 HOH HOH . D 4 HOH A 59 369 369 HOH HOH . D 4 HOH A 60 370 370 HOH HOH . D 4 HOH A 61 371 371 HOH HOH . D 4 HOH A 62 372 372 HOH HOH . D 4 HOH A 63 373 373 HOH HOH . D 4 HOH A 64 374 374 HOH HOH . D 4 HOH A 65 375 375 HOH HOH . D 4 HOH A 66 376 376 HOH HOH . D 4 HOH A 67 377 377 HOH HOH . D 4 HOH A 68 378 378 HOH HOH . D 4 HOH A 69 379 379 HOH HOH . D 4 HOH A 70 380 380 HOH HOH . D 4 HOH A 71 381 381 HOH HOH . D 4 HOH A 72 382 382 HOH HOH . D 4 HOH A 73 383 383 HOH HOH . D 4 HOH A 74 384 384 HOH HOH . D 4 HOH A 75 385 385 HOH HOH . D 4 HOH A 76 386 386 HOH HOH . D 4 HOH A 77 387 387 HOH HOH . D 4 HOH A 78 388 388 HOH HOH . D 4 HOH A 79 389 389 HOH HOH . D 4 HOH A 80 390 390 HOH HOH . D 4 HOH A 81 391 391 HOH HOH . D 4 HOH A 82 392 392 HOH HOH . D 4 HOH A 83 393 393 HOH HOH . D 4 HOH A 84 394 394 HOH HOH . D 4 HOH A 85 395 395 HOH HOH . D 4 HOH A 86 396 396 HOH HOH . D 4 HOH A 87 397 397 HOH HOH . D 4 HOH A 88 398 398 HOH HOH . D 4 HOH A 89 399 399 HOH HOH . D 4 HOH A 90 400 400 HOH HOH . D 4 HOH A 91 401 401 HOH HOH . D 4 HOH A 92 402 402 HOH HOH . D 4 HOH A 93 403 403 HOH HOH . D 4 HOH A 94 404 404 HOH HOH . D 4 HOH A 95 405 405 HOH HOH . D 4 HOH A 96 406 406 HOH HOH . D 4 HOH A 97 407 407 HOH HOH . D 4 HOH A 98 408 408 HOH HOH . D 4 HOH A 99 409 409 HOH HOH . D 4 HOH A 100 410 410 HOH HOH . D 4 HOH A 101 411 411 HOH HOH . D 4 HOH A 102 412 412 HOH HOH . D 4 HOH A 103 413 413 HOH HOH . D 4 HOH A 104 414 414 HOH HOH . D 4 HOH A 105 415 415 HOH HOH . D 4 HOH A 106 416 416 HOH HOH . D 4 HOH A 107 417 417 HOH HOH . D 4 HOH A 108 418 418 HOH HOH . D 4 HOH A 109 419 419 HOH HOH . D 4 HOH A 110 420 420 HOH HOH . D 4 HOH A 111 421 421 HOH HOH . D 4 HOH A 112 422 422 HOH HOH . D 4 HOH A 113 423 423 HOH HOH . D 4 HOH A 114 424 424 HOH HOH . D 4 HOH A 115 425 425 HOH HOH . D 4 HOH A 116 426 426 HOH HOH . D 4 HOH A 117 427 427 HOH HOH . D 4 HOH A 118 428 428 HOH HOH . D 4 HOH A 119 429 429 HOH HOH . D 4 HOH A 120 430 430 HOH HOH . D 4 HOH A 121 431 431 HOH HOH . D 4 HOH A 122 432 432 HOH HOH . D 4 HOH A 123 433 433 HOH HOH . D 4 HOH A 124 434 434 HOH HOH . D 4 HOH A 125 435 435 HOH HOH . D 4 HOH A 126 436 436 HOH HOH . D 4 HOH A 127 437 437 HOH HOH . D 4 HOH A 128 438 438 HOH HOH . D 4 HOH A 129 439 439 HOH HOH . D 4 HOH A 130 440 440 HOH HOH . D 4 HOH A 131 441 441 HOH HOH . D 4 HOH A 132 442 442 HOH HOH . D 4 HOH A 133 443 443 HOH HOH . D 4 HOH A 134 444 444 HOH HOH . D 4 HOH A 135 445 445 HOH HOH . D 4 HOH A 136 446 446 HOH HOH . D 4 HOH A 137 447 447 HOH HOH . D 4 HOH A 138 448 448 HOH HOH . D 4 HOH A 139 449 449 HOH HOH . D 4 HOH A 140 450 450 HOH HOH . D 4 HOH A 141 451 451 HOH HOH . D 4 HOH A 142 452 452 HOH HOH . D 4 HOH A 143 453 453 HOH HOH . D 4 HOH A 144 454 454 HOH HOH . D 4 HOH A 145 455 455 HOH HOH . D 4 HOH A 146 456 456 HOH HOH . D 4 HOH A 147 457 457 HOH HOH . D 4 HOH A 148 458 458 HOH HOH . D 4 HOH A 149 459 459 HOH HOH . D 4 HOH A 150 460 460 HOH HOH . D 4 HOH A 151 461 461 HOH HOH . D 4 HOH A 152 462 462 HOH HOH . D 4 HOH A 153 463 463 HOH HOH . D 4 HOH A 154 464 464 HOH HOH . D 4 HOH A 155 465 465 HOH HOH . D 4 HOH A 156 466 466 HOH HOH . D 4 HOH A 157 467 467 HOH HOH . D 4 HOH A 158 468 468 HOH HOH . D 4 HOH A 159 469 469 HOH HOH . D 4 HOH A 160 470 470 HOH HOH . D 4 HOH A 161 471 471 HOH HOH . D 4 HOH A 162 472 472 HOH HOH . D 4 HOH A 163 473 473 HOH HOH . D 4 HOH A 164 474 474 HOH HOH . D 4 HOH A 165 475 475 HOH HOH . D 4 HOH A 166 476 476 HOH HOH . D 4 HOH A 167 477 477 HOH HOH . D 4 HOH A 168 478 478 HOH HOH . D 4 HOH A 169 479 479 HOH HOH . D 4 HOH A 170 480 480 HOH HOH . D 4 HOH A 171 481 481 HOH HOH . D 4 HOH A 172 482 482 HOH HOH . D 4 HOH A 173 483 483 HOH HOH . D 4 HOH A 174 484 484 HOH HOH . D 4 HOH A 175 485 485 HOH HOH . D 4 HOH A 176 486 486 HOH HOH . D 4 HOH A 177 487 487 HOH HOH . D 4 HOH A 178 488 488 HOH HOH . D 4 HOH A 179 489 489 HOH HOH . D 4 HOH A 180 490 490 HOH HOH . D 4 HOH A 181 491 491 HOH HOH . D 4 HOH A 182 492 492 HOH HOH . D 4 HOH A 183 493 493 HOH HOH . D 4 HOH A 184 494 494 HOH HOH . D 4 HOH A 185 495 495 HOH HOH . D 4 HOH A 186 496 496 HOH HOH . D 4 HOH A 187 497 497 HOH HOH . D 4 HOH A 188 498 498 HOH HOH . D 4 HOH A 189 499 499 HOH HOH . D 4 HOH A 190 500 500 HOH HOH . D 4 HOH A 191 501 501 HOH HOH . D 4 HOH A 192 502 502 HOH HOH . D 4 HOH A 193 503 503 HOH HOH . D 4 HOH A 194 504 504 HOH HOH . D 4 HOH A 195 505 505 HOH HOH . D 4 HOH A 196 506 506 HOH HOH . D 4 HOH A 197 507 507 HOH HOH . D 4 HOH A 198 508 508 HOH HOH . D 4 HOH A 199 509 509 HOH HOH . D 4 HOH A 200 510 510 HOH HOH . D 4 HOH A 201 511 511 HOH HOH . D 4 HOH A 202 512 512 HOH HOH . D 4 HOH A 203 513 513 HOH HOH . D 4 HOH A 204 514 514 HOH HOH . D 4 HOH A 205 515 515 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 PG AGS . . . B 2 39.079 41.47 9.265 1 18.83 ? PG AGS 340 A 1 HETATM 2 S S1G AGS . . . B 2 40.304 42.409 8.458 1 19.82 ? S1G AGS 340 A 1 HETATM 3 O O2G AGS . . . B 2 37.794 41.44 8.429 1 16.88 ? O2G AGS 340 A 1 HETATM 4 O O3G AGS . . . B 2 38.719 41.971 10.668 1 17.95 ? O3G AGS 340 A 1 HETATM 5 P PB AGS . . . B 2 40.136 38.812 8.563 1 16.16 ? PB AGS 340 A 1 HETATM 6 O O1B AGS . . . B 2 39.927 39.129 7.132 1 14.56 ? O1B AGS 340 A 1 HETATM 7 O O2B AGS . . . B 2 41.577 38.437 8.92 1 16.94 ? O2B AGS 340 A 1 HETATM 8 O O3B AGS . . . B 2 39.584 39.968 9.551 1 16.93 ? O3B AGS 340 A 1 HETATM 9 P PA AGS . . . B 2 38.599 37.023 10.278 1 17.52 ? PA AGS 340 A 1 HETATM 10 O O1A AGS . . . B 2 39.618 36.404 11.167 1 17.48 ? O1A AGS 340 A 1 HETATM 11 O O2A AGS . . . B 2 37.67 38.004 10.95 1 18.49 ? O2A AGS 340 A 1 HETATM 12 O O3A AGS . . . B 2 39.192 37.551 8.871 1 17.55 ? O3A AGS 340 A 1 HETATM 13 O O5' AGS . . . B 2 37.691 35.83 9.646 1 18.35 ? O5' AGS 340 A 1 HETATM 14 C C5' AGS . . . B 2 36.813 36.088 8.571 1 17.4 ? C5' AGS 340 A 1 HETATM 15 C C4' AGS . . . B 2 35.618 35.152 8.628 1 18.07 ? C4' AGS 340 A 1 HETATM 16 O O4' AGS . . . B 2 36.048 33.806 8.624 1 17.28 ? O4' AGS 340 A 1 HETATM 17 C C3' AGS . . . B 2 34.769 35.318 9.884 1 18.84 ? C3' AGS 340 A 1 HETATM 18 O O3' AGS . . . B 2 33.861 36.395 9.789 1 19.59 ? O3' AGS 340 A 1 HETATM 19 C C2' AGS . . . B 2 34.1 33.968 9.933 1 19 ? C2' AGS 340 A 1 HETATM 20 O O2' AGS . . . B 2 33.02 33.9 9.026 1 19.75 ? O2' AGS 340 A 1 HETATM 21 C C1' AGS . . . B 2 35.205 33.041 9.471 1 17.41 ? C1' AGS 340 A 1 HETATM 22 N N9 AGS . . . B 2 35.967 32.552 10.625 1 17.13 ? N9 AGS 340 A 1 HETATM 23 C C8 AGS . . . B 2 37.067 33.142 11.201 1 16.45 ? C8 AGS 340 A 1 HETATM 24 N N7 AGS . . . B 2 37.464 32.377 12.239 1 16.89 ? N7 AGS 340 A 1 HETATM 25 C C5 AGS . . . B 2 36.636 31.312 12.325 1 17.31 ? C5 AGS 340 A 1 HETATM 26 C C6 AGS . . . B 2 36.593 30.22 13.198 1 17.14 ? C6 AGS 340 A 1 HETATM 27 N N6 AGS . . . B 2 37.47 30.086 14.194 1 16.42 ? N6 AGS 340 A 1 HETATM 28 N N1 AGS . . . B 2 35.607 29.275 13.014 1 16.74 ? N1 AGS 340 A 1 HETATM 29 C C2 AGS . . . B 2 34.668 29.39 12.002 1 16.46 ? C2 AGS 340 A 1 HETATM 30 N N3 AGS . . . B 2 34.703 30.47 11.141 1 17.69 ? N3 AGS 340 A 1 HETATM 31 C C4 AGS . . . B 2 35.685 31.415 11.312 1 17.23 ? C4 AGS 340 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #