data_6QMM # _model_server_result.job_id kTaD0e3bYXqxSpX3A1VwYg _model_server_result.datetime_utc '2024-11-30 01:59:53' _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":"D","auth_seq_id":301}' # _entry.id 6QMM # _exptl.entry_id 6QMM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 145.246 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMIDINE _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C7 H19 N3' _chem_comp.formula_weight 145.246 _chem_comp.id SPD _chem_comp.mon_nstd_flag . _chem_comp.name SPERMIDINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE;PA(34) # 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 N1 C2 SPD sing 404 n n N1 HN11 SPD sing 405 n n N1 HN12 SPD sing 406 n n C2 C3 SPD sing 407 n n C2 H21 SPD sing 408 n n C2 H22 SPD sing 409 n n C3 C4 SPD sing 410 n n C3 H31 SPD sing 411 n n C3 H32 SPD sing 412 n n C4 C5 SPD sing 413 n n C4 H41 SPD sing 414 n n C4 H42 SPD sing 415 n n C5 N6 SPD sing 416 n n C5 H51 SPD sing 417 n n C5 H52 SPD sing 418 n n N6 C7 SPD sing 419 n n N6 HN6 SPD sing 420 n n C7 C8 SPD sing 421 n n C7 H71 SPD sing 422 n n C7 H72 SPD sing 423 n n C8 C9 SPD sing 424 n n C8 H81 SPD sing 425 n n C8 H82 SPD sing 426 n n C9 N10 SPD sing 427 n n C9 H91 SPD sing 428 n n C9 H92 SPD sing 429 n n N10 H101 SPD sing 430 n n N10 H102 SPD sing 431 n n # _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 N N1 SPD . . . D 4 4.624 -5.542 70.653 1 23.54 ? N1 SPD 301 B 1 HETATM 2 C C2 SPD . . . D 4 5.995 -5.286 70.129 1 24.18 ? C2 SPD 301 B 1 HETATM 3 C C3 SPD . . . D 4 6.942 -6.435 69.826 1 27.52 ? C3 SPD 301 B 1 HETATM 4 C C4 SPD . . . D 4 7.679 -6.457 68.474 1 31.49 ? C4 SPD 301 B 1 HETATM 5 C C5 SPD . . . D 4 9.036 -5.744 68.374 1 32.07 ? C5 SPD 301 B 1 HETATM 6 N N6 SPD . . . D 4 9.398 -5.25 67.012 1 31.06 ? N6 SPD 301 B 1 HETATM 7 C C7 SPD . . . D 4 10.191 -3.998 66.86 1 29.48 ? C7 SPD 301 B 1 HETATM 8 C C8 SPD . . . D 4 11.478 -4.062 67.458 1 26.59 ? C8 SPD 301 B 1 HETATM 9 C C9 SPD . . . D 4 12.321 -2.803 67.596 1 23.79 ? C9 SPD 301 B 1 HETATM 10 N N10 SPD . . . D 4 13.621 -2.963 66.892 1 22.98 ? N10 SPD 301 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 10 #