data_6QMM # _model_server_result.job_id Udt8eFiTfXCoatxASk40wg _model_server_result.datetime_utc '2024-11-26 16:46:24' _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 6qmm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":302}' # _entry.id 6QMM # _exptl.entry_id 6QMM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 297.334 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-DEOXY-5'-METHYLTHIOADENOSINE" _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 92.72 _cell.angle_gamma 90 _cell.entry_id 6QMM _cell.length_a 57.64 _cell.length_b 63.82 _cell.length_c 73.5 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QMM _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 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 _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 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C11 H15 N5 O3 S' _chem_comp.formula_weight 297.334 _chem_comp.id MTA _chem_comp.mon_nstd_flag . _chem_comp.name "5'-DEOXY-5'-METHYLTHIOADENOSINE" _chem_comp.type non-polymer _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 CS S5' MTA sing 237 n n CS HCS1 MTA sing 238 n n CS HCS2 MTA sing 239 n n CS HCS3 MTA sing 240 n n S5' C5' MTA sing 241 n n C5' C4' MTA sing 242 n n C5' "H5'1" MTA sing 243 n n C5' "H5'2" MTA sing 244 n n C4' O4' MTA sing 245 n n C4' C3' MTA sing 246 n n C4' H4' MTA sing 247 n n O4' C1' MTA sing 248 n n C2' O2' MTA sing 249 n n C2' C3' MTA sing 250 n n C2' C1' MTA sing 251 n n C2' H2' MTA sing 252 n n O2' HO2' MTA sing 253 n n C3' O3' MTA sing 254 n n C3' H3' MTA sing 255 n n O3' H3T MTA sing 256 n n C1' N9 MTA sing 257 n n C1' H1' MTA sing 258 n n N9 C8 MTA sing 259 n y N9 C4 MTA sing 260 n y C8 N7 MTA doub 261 n y C8 H8 MTA sing 262 n n N7 C5 MTA sing 263 n y C5 C6 MTA sing 264 n y C5 C4 MTA doub 265 n y C6 N6 MTA sing 266 n n C6 N1 MTA doub 267 n y N6 H61 MTA sing 268 n n N6 H62 MTA sing 269 n n N1 C2 MTA sing 270 n y C2 N3 MTA doub 271 n y C2 H2 MTA sing 272 n n N3 C4 MTA sing 273 n y # _atom_sites.entry_id 6QMM _atom_sites.fract_transf_matrix[1][1] 0.017349 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000825 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015669 _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] 0.013621 _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 C 3 PUT A 1 301 295 PUT PUT . D 4 SPD B 1 301 295 SPD SPD . E 5 MTA B 1 302 296 MTA MTA . F 6 PXN B 1 303 297 PXN PXN . G 7 HOH A 1 401 342 HOH HOH . G 7 HOH A 2 402 402 HOH HOH . G 7 HOH A 3 403 353 HOH HOH . G 7 HOH A 4 404 357 HOH HOH . G 7 HOH A 5 405 387 HOH HOH . G 7 HOH A 6 406 368 HOH HOH . G 7 HOH A 7 407 314 HOH HOH . G 7 HOH A 8 408 369 HOH HOH . G 7 HOH A 9 409 423 HOH HOH . G 7 HOH A 10 410 325 HOH HOH . G 7 HOH A 11 411 394 HOH HOH . G 7 HOH A 12 412 323 HOH HOH . G 7 HOH A 13 413 334 HOH HOH . G 7 HOH A 14 414 377 HOH HOH . G 7 HOH A 15 415 401 HOH HOH . G 7 HOH A 16 416 336 HOH HOH . G 7 HOH A 17 417 303 HOH HOH . G 7 HOH A 18 418 375 HOH HOH . G 7 HOH A 19 419 319 HOH HOH . G 7 HOH A 20 420 341 HOH HOH . G 7 HOH A 21 421 328 HOH HOH . G 7 HOH A 22 422 421 HOH HOH . G 7 HOH A 23 423 306 HOH HOH . G 7 HOH A 24 424 346 HOH HOH . G 7 HOH A 25 425 393 HOH HOH . G 7 HOH A 26 426 345 HOH HOH . G 7 HOH A 27 427 329 HOH HOH . G 7 HOH A 28 428 374 HOH HOH . G 7 HOH A 29 429 383 HOH HOH . G 7 HOH A 30 430 394 HOH HOH . G 7 HOH A 31 431 306 HOH HOH . G 7 HOH A 32 432 357 HOH HOH . G 7 HOH A 33 433 316 HOH HOH . G 7 HOH A 34 434 410 HOH HOH . G 7 HOH A 35 435 300 HOH HOH . G 7 HOH A 36 436 379 HOH HOH . G 7 HOH A 37 437 309 HOH HOH . G 7 HOH A 38 438 307 HOH HOH . G 7 HOH A 39 439 419 HOH HOH . G 7 HOH A 40 440 363 HOH HOH . G 7 HOH A 41 441 389 HOH HOH . G 7 HOH A 42 442 397 HOH HOH . G 7 HOH A 43 443 318 HOH HOH . G 7 HOH A 44 444 348 HOH HOH . G 7 HOH A 45 445 339 HOH HOH . G 7 HOH A 46 446 418 HOH HOH . G 7 HOH A 47 447 376 HOH HOH . G 7 HOH A 48 448 350 HOH HOH . G 7 HOH A 49 449 313 HOH HOH . G 7 HOH A 50 450 338 HOH HOH . G 7 HOH A 51 451 347 HOH HOH . G 7 HOH A 52 452 309 HOH HOH . G 7 HOH A 53 453 349 HOH HOH . G 7 HOH A 54 454 380 HOH HOH . G 7 HOH A 55 455 386 HOH HOH . G 7 HOH A 56 456 358 HOH HOH . G 7 HOH A 57 457 304 HOH HOH . G 7 HOH A 58 458 383 HOH HOH . G 7 HOH A 59 459 356 HOH HOH . G 7 HOH A 60 460 400 HOH HOH . G 7 HOH A 61 461 416 HOH HOH . G 7 HOH A 62 462 382 HOH HOH . G 7 HOH A 63 463 315 HOH HOH . G 7 HOH A 64 464 337 HOH HOH . G 7 HOH A 65 465 344 HOH HOH . G 7 HOH A 66 466 301 HOH HOH . G 7 HOH A 67 467 402 HOH HOH . G 7 HOH A 68 468 407 HOH HOH . G 7 HOH A 69 469 372 HOH HOH . G 7 HOH A 70 470 314 HOH HOH . G 7 HOH A 71 471 352 HOH HOH . G 7 HOH A 72 472 353 HOH HOH . G 7 HOH A 73 473 359 HOH HOH . G 7 HOH A 74 474 403 HOH HOH . G 7 HOH A 75 475 414 HOH HOH . G 7 HOH A 76 476 420 HOH HOH . G 7 HOH A 77 477 310 HOH HOH . G 7 HOH A 78 478 312 HOH HOH . G 7 HOH A 79 479 399 HOH HOH . G 7 HOH A 80 480 360 HOH HOH . G 7 HOH A 81 481 326 HOH HOH . G 7 HOH A 82 482 355 HOH HOH . G 7 HOH A 83 483 320 HOH HOH . G 7 HOH A 84 484 384 HOH HOH . G 7 HOH A 85 485 327 HOH HOH . G 7 HOH A 86 486 361 HOH HOH . G 7 HOH A 87 487 333 HOH HOH . G 7 HOH A 88 488 378 HOH HOH . G 7 HOH A 89 489 364 HOH HOH . G 7 HOH A 90 490 421 HOH HOH . G 7 HOH A 91 491 415 HOH HOH . G 7 HOH A 92 492 317 HOH HOH . G 7 HOH A 93 493 395 HOH HOH . G 7 HOH A 94 494 385 HOH HOH . G 7 HOH A 95 495 398 HOH HOH . G 7 HOH A 96 496 384 HOH HOH . G 7 HOH A 97 497 330 HOH HOH . G 7 HOH A 98 498 373 HOH HOH . G 7 HOH A 99 499 321 HOH HOH . G 7 HOH A 100 500 324 HOH HOH . G 7 HOH A 101 501 408 HOH HOH . G 7 HOH A 102 502 340 HOH HOH . G 7 HOH A 103 503 405 HOH HOH . G 7 HOH A 104 504 308 HOH HOH . G 7 HOH A 105 505 371 HOH HOH . G 7 HOH A 106 506 381 HOH HOH . G 7 HOH A 107 507 343 HOH HOH . G 7 HOH A 108 508 413 HOH HOH . G 7 HOH A 109 509 387 HOH HOH . G 7 HOH A 110 510 422 HOH HOH . G 7 HOH A 111 511 332 HOH HOH . G 7 HOH A 112 512 302 HOH HOH . G 7 HOH A 113 513 335 HOH HOH . G 7 HOH A 114 514 367 HOH HOH . G 7 HOH A 115 515 396 HOH HOH . G 7 HOH A 116 516 370 HOH HOH . G 7 HOH A 117 517 322 HOH HOH . G 7 HOH A 118 518 404 HOH HOH . G 7 HOH A 119 519 398 HOH HOH . G 7 HOH A 120 520 417 HOH HOH . G 7 HOH A 121 521 392 HOH HOH . G 7 HOH A 122 522 409 HOH HOH . G 7 HOH A 123 523 362 HOH HOH . G 7 HOH A 124 524 388 HOH HOH . G 7 HOH A 125 525 382 HOH HOH . H 7 HOH B 1 401 335 HOH HOH . H 7 HOH B 2 402 329 HOH HOH . H 7 HOH B 3 403 395 HOH HOH . H 7 HOH B 4 404 359 HOH HOH . H 7 HOH B 5 405 379 HOH HOH . H 7 HOH B 6 406 372 HOH HOH . H 7 HOH B 7 407 351 HOH HOH . H 7 HOH B 8 408 305 HOH HOH . H 7 HOH B 9 409 415 HOH HOH . H 7 HOH B 10 410 310 HOH HOH . H 7 HOH B 11 411 420 HOH HOH . H 7 HOH B 12 412 337 HOH HOH . H 7 HOH B 13 413 429 HOH HOH . H 7 HOH B 14 414 354 HOH HOH . H 7 HOH B 15 415 354 HOH HOH . H 7 HOH B 16 416 397 HOH HOH . H 7 HOH B 17 417 341 HOH HOH . H 7 HOH B 18 418 425 HOH HOH . H 7 HOH B 19 419 430 HOH HOH . H 7 HOH B 20 420 403 HOH HOH . H 7 HOH B 21 421 406 HOH HOH . H 7 HOH B 22 422 361 HOH HOH . H 7 HOH B 23 423 412 HOH HOH . H 7 HOH B 24 424 348 HOH HOH . H 7 HOH B 25 425 411 HOH HOH . H 7 HOH B 26 426 360 HOH HOH . H 7 HOH B 27 427 308 HOH HOH . H 7 HOH B 28 428 305 HOH HOH . H 7 HOH B 29 429 316 HOH HOH . H 7 HOH B 30 430 363 HOH HOH . H 7 HOH B 31 431 347 HOH HOH . H 7 HOH B 32 432 405 HOH HOH . H 7 HOH B 33 433 311 HOH HOH . H 7 HOH B 34 434 331 HOH HOH . H 7 HOH B 35 435 417 HOH HOH . H 7 HOH B 36 436 317 HOH HOH . H 7 HOH B 37 437 331 HOH HOH . H 7 HOH B 38 438 378 HOH HOH . H 7 HOH B 39 439 311 HOH HOH . H 7 HOH B 40 440 325 HOH HOH . H 7 HOH B 41 441 408 HOH HOH . H 7 HOH B 42 442 391 HOH HOH . H 7 HOH B 43 443 412 HOH HOH . H 7 HOH B 44 444 336 HOH HOH . H 7 HOH B 45 445 416 HOH HOH . H 7 HOH B 46 446 367 HOH HOH . H 7 HOH B 47 447 321 HOH HOH . H 7 HOH B 48 448 424 HOH HOH . H 7 HOH B 49 449 328 HOH HOH . H 7 HOH B 50 450 339 HOH HOH . H 7 HOH B 51 451 346 HOH HOH . H 7 HOH B 52 452 409 HOH HOH . H 7 HOH B 53 453 356 HOH HOH . H 7 HOH B 54 454 390 HOH HOH . H 7 HOH B 55 455 313 HOH HOH . H 7 HOH B 56 456 334 HOH HOH . H 7 HOH B 57 457 330 HOH HOH . H 7 HOH B 58 458 389 HOH HOH . H 7 HOH B 59 459 365 HOH HOH . H 7 HOH B 60 460 373 HOH HOH . H 7 HOH B 61 461 301 HOH HOH . H 7 HOH B 62 462 327 HOH HOH . H 7 HOH B 63 463 358 HOH HOH . H 7 HOH B 64 464 368 HOH HOH . H 7 HOH B 65 465 380 HOH HOH . H 7 HOH B 66 466 386 HOH HOH . H 7 HOH B 67 467 393 HOH HOH . H 7 HOH B 68 468 427 HOH HOH . H 7 HOH B 69 469 342 HOH HOH . H 7 HOH B 70 470 410 HOH HOH . H 7 HOH B 71 471 315 HOH HOH . H 7 HOH B 72 472 370 HOH HOH . H 7 HOH B 73 473 400 HOH HOH . H 7 HOH B 74 474 376 HOH HOH . H 7 HOH B 75 475 320 HOH HOH . H 7 HOH B 76 476 431 HOH HOH . H 7 HOH B 77 477 419 HOH HOH . H 7 HOH B 78 478 390 HOH HOH . H 7 HOH B 79 479 343 HOH HOH . H 7 HOH B 80 480 340 HOH HOH . H 7 HOH B 81 481 364 HOH HOH . H 7 HOH B 82 482 324 HOH HOH . H 7 HOH B 83 483 407 HOH HOH . H 7 HOH B 84 484 369 HOH HOH . H 7 HOH B 85 485 392 HOH HOH . H 7 HOH B 86 486 401 HOH HOH . H 7 HOH B 87 487 349 HOH HOH . H 7 HOH B 88 488 381 HOH HOH . H 7 HOH B 89 489 366 HOH HOH . H 7 HOH B 90 490 396 HOH HOH . H 7 HOH B 91 491 318 HOH HOH . H 7 HOH B 92 492 391 HOH HOH . H 7 HOH B 93 493 345 HOH HOH . H 7 HOH B 94 494 303 HOH HOH . H 7 HOH B 95 495 304 HOH HOH . H 7 HOH B 96 496 326 HOH HOH . H 7 HOH B 97 497 375 HOH HOH . H 7 HOH B 98 498 319 HOH HOH . H 7 HOH B 99 499 426 HOH HOH . H 7 HOH B 100 500 411 HOH HOH . H 7 HOH B 101 501 366 HOH HOH . H 7 HOH B 102 502 423 HOH HOH . H 7 HOH B 103 503 388 HOH HOH . H 7 HOH B 104 504 371 HOH HOH . H 7 HOH B 105 505 355 HOH HOH . H 7 HOH B 106 506 344 HOH HOH . H 7 HOH B 107 507 333 HOH HOH . H 7 HOH B 108 508 307 HOH HOH . H 7 HOH B 109 509 300 HOH HOH . H 7 HOH B 110 510 322 HOH HOH . H 7 HOH B 111 511 338 HOH HOH . H 7 HOH B 112 512 374 HOH HOH . H 7 HOH B 113 513 404 HOH HOH . H 7 HOH B 114 514 312 HOH HOH . H 7 HOH B 115 515 414 HOH HOH . H 7 HOH B 116 516 350 HOH HOH . H 7 HOH B 117 517 377 HOH HOH . H 7 HOH B 118 518 362 HOH HOH . H 7 HOH B 119 519 351 HOH HOH . H 7 HOH B 120 520 422 HOH HOH . H 7 HOH B 121 521 413 HOH HOH . H 7 HOH B 122 522 428 HOH HOH . H 7 HOH B 123 523 352 HOH HOH . H 7 HOH B 124 524 406 HOH HOH . H 7 HOH B 125 525 385 HOH HOH . H 7 HOH B 126 526 332 HOH HOH . H 7 HOH B 127 527 323 HOH HOH . H 7 HOH B 128 528 399 HOH HOH . H 7 HOH B 129 529 302 HOH HOH . H 7 HOH B 130 530 418 HOH HOH . H 7 HOH B 131 531 365 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 C CS MTA . . . E 5 10.452 -0.822 65.162 1 57.7 ? CS MTA 302 B 1 HETATM 2 S S5' MTA . . . E 5 10.926 -1.863 63.814 1 59.08 ? S5' MTA 302 B 1 HETATM 3 C C5' MTA . . . E 5 9.804 -3.442 63.723 1 46.11 ? C5' MTA 302 B 1 HETATM 4 C C4' MTA . . . E 5 9.839 -3.857 62.215 1 39.32 ? C4' MTA 302 B 1 HETATM 5 O O4' MTA . . . E 5 9.385 -5.127 61.611 1 39.41 ? O4' MTA 302 B 1 HETATM 6 C C2' MTA . . . E 5 8.174 -3.453 60.331 1 38.15 ? C2' MTA 302 B 1 HETATM 7 O O2' MTA . . . E 5 7.68 -2.722 59.131 1 31.99 ? O2' MTA 302 B 1 HETATM 8 C C3' MTA . . . E 5 9.163 -2.745 61.368 1 35.4 ? C3' MTA 302 B 1 HETATM 9 O O3' MTA . . . E 5 10.38 -2.025 60.956 1 32.85 ? O3' MTA 302 B 1 HETATM 10 C C1' MTA . . . E 5 9.02 -4.79 60.135 1 38.87 ? C1' MTA 302 B 1 HETATM 11 N N9 MTA . . . E 5 8.445 -5.925 59.262 1 38.96 ? N9 MTA 302 B 1 HETATM 12 C C8 MTA . . . E 5 7.253 -6.566 59.551 1 43.01 ? C8 MTA 302 B 1 HETATM 13 N N7 MTA . . . E 5 6.972 -7.602 58.651 1 41.01 ? N7 MTA 302 B 1 HETATM 14 C C5 MTA . . . E 5 8.008 -7.692 57.761 1 37.14 ? C5 MTA 302 B 1 HETATM 15 C C6 MTA . . . E 5 8.26 -8.574 56.577 1 35.62 ? C6 MTA 302 B 1 HETATM 16 N N6 MTA . . . E 5 7.331 -9.56 56.214 1 36.14 ? N6 MTA 302 B 1 HETATM 17 N N1 MTA . . . E 5 9.369 -8.289 55.857 1 33.46 ? N1 MTA 302 B 1 HETATM 18 C C2 MTA . . . E 5 10.222 -7.289 56.255 1 36.51 ? C2 MTA 302 B 1 HETATM 19 N N3 MTA . . . E 5 9.998 -6.444 57.346 1 31.06 ? N3 MTA 302 B 1 HETATM 20 C C4 MTA . . . E 5 8.954 -6.577 58.143 1 35.5 ? C4 MTA 302 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #