data_3KT3 # _model_server_result.job_id sQA2iiEfiXHpVK9uXr7M4w _model_server_result.datetime_utc '2024-11-23 00:37:24' _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 3kt3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":500}' # _entry.id 3KT3 # _exptl.entry_id 3KT3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 533.431 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "TRYPTOPHANYL-5'AMP" _entity.pdbx_number_of_molecules 4 _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 3KT3 _cell.length_a 251.759 _cell.length_b 251.759 _cell.length_c 111.102 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KT3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J,K,L,M,V,W 1 1 C,D,N,O,P,Q,R,S,T,U,X,Y 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 J N N ? 2 N N N ? 2 R N N # _chem_comp.formula 'C21 H24 N7 O8 P' _chem_comp.formula_weight 533.431 _chem_comp.id TYM _chem_comp.mon_nstd_flag . _chem_comp.name "TRYPTOPHANYL-5'AMP" _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 P O1P TYM sing 338 n n P O2P TYM doub 339 n n P O5' TYM sing 340 n n P OPP TYM sing 341 n n O1P H1PO TYM sing 342 n n O5' C5' TYM sing 343 n n C5' C4' TYM sing 344 n n C5' "H5'1" TYM sing 345 n n C5' "H5'2" TYM sing 346 n n C4' O4' TYM sing 347 n n C4' C3' TYM sing 348 n n C4' "H4'C" TYM sing 349 n n O4' C1' TYM sing 350 n n C1' N9 TYM sing 351 n n C1' C2' TYM sing 352 n n C1' "H1'C" TYM sing 353 n n N9 C4 TYM sing 354 n y N9 C8 TYM sing 355 n y C4 N3 TYM doub 356 n y C4 C5 TYM sing 357 n y N3 C2 TYM sing 358 n y C2 N1 TYM doub 359 n y C2 HC2 TYM sing 360 n n N1 C6 TYM sing 361 n y C6 N6 TYM sing 362 n n C6 C5 TYM doub 363 n y N6 HN61 TYM sing 364 n n N6 HN62 TYM sing 365 n n C5 N7 TYM sing 366 n y N7 C8 TYM doub 367 n y C8 HC8 TYM sing 368 n n C2' O2' TYM sing 369 n n C2' C3' TYM sing 370 n n C2' "H2'C" TYM sing 371 n n O2' "H2'O" TYM sing 372 n n C3' O3' TYM sing 373 n n C3' "H3'C" TYM sing 374 n n O3' "H3'O" TYM sing 375 n n NH3 CA TYM sing 376 n n NH3 HH31 TYM sing 377 n n NH3 HH32 TYM sing 378 n n CA CB TYM sing 379 n n CA C TYM sing 380 n n CA HCA TYM sing 381 n n CB CG TYM sing 382 n n CB HCB1 TYM sing 383 n n CB HCB2 TYM sing 384 n n CG CD2 TYM sing 385 n y CG CD1 TYM doub 386 n y CD2 CE2 TYM doub 387 n y CD2 CE3 TYM sing 388 n y CE2 NE1 TYM sing 389 n y CE2 CZ2 TYM sing 390 n y CE3 CZ3 TYM doub 391 n y CE3 HE3C TYM sing 392 n n CD1 NE1 TYM sing 393 n y CD1 HD1C TYM sing 394 n n NE1 HE1N TYM sing 395 n n CZ2 CH2 TYM doub 396 n y CZ2 HZ2C TYM sing 397 n n CZ3 CH2 TYM sing 398 n y CZ3 HZ3C TYM sing 399 n n CH2 HH2C TYM sing 400 n n C O TYM doub 401 n n C OPP TYM sing 402 n n # _atom_sites.entry_id 3KT3 _atom_sites.fract_transf_matrix[1][1] 0.003972 _atom_sites.fract_transf_matrix[1][2] 0.002293 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004587 _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] 0.009001 _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 E 2 TYM A 1 500 500 TYM TYM . F 3 SO4 A 1 439 439 SO4 SO4 . G 3 SO4 A 1 440 440 SO4 SO4 . H 3 SO4 A 1 441 441 SO4 SO4 . I 3 SO4 A 1 442 442 SO4 SO4 . J 2 TYM B 1 700 700 TYM TYM . K 3 SO4 B 1 439 439 SO4 SO4 . L 3 SO4 B 1 440 440 SO4 SO4 . M 3 SO4 B 1 441 441 SO4 SO4 . N 2 TYM C 1 600 600 TYM TYM . O 3 SO4 C 1 439 439 SO4 SO4 . P 3 SO4 C 1 440 440 SO4 SO4 . Q 3 SO4 C 1 441 441 SO4 SO4 . R 2 TYM D 1 800 800 TYM TYM . S 3 SO4 D 1 439 439 SO4 SO4 . T 3 SO4 D 1 440 440 SO4 SO4 . U 3 SO4 D 1 441 441 SO4 SO4 . V 4 HOH A 1 443 443 HOH HOH . V 4 HOH A 2 444 444 HOH HOH . V 4 HOH A 3 445 445 HOH HOH . V 4 HOH A 4 446 446 HOH HOH . V 4 HOH A 5 447 447 HOH HOH . V 4 HOH A 6 448 448 HOH HOH . V 4 HOH A 7 449 449 HOH HOH . V 4 HOH A 8 450 450 HOH HOH . V 4 HOH A 9 451 451 HOH HOH . V 4 HOH A 10 452 452 HOH HOH . V 4 HOH A 11 453 453 HOH HOH . V 4 HOH A 12 454 454 HOH HOH . V 4 HOH A 13 455 455 HOH HOH . V 4 HOH A 14 456 456 HOH HOH . V 4 HOH A 15 457 457 HOH HOH . V 4 HOH A 16 458 458 HOH HOH . V 4 HOH A 17 459 459 HOH HOH . V 4 HOH A 18 460 460 HOH HOH . V 4 HOH A 19 461 461 HOH HOH . V 4 HOH A 20 462 462 HOH HOH . V 4 HOH A 21 463 463 HOH HOH . V 4 HOH A 22 464 464 HOH HOH . V 4 HOH A 23 465 465 HOH HOH . V 4 HOH A 24 466 466 HOH HOH . V 4 HOH A 25 467 467 HOH HOH . V 4 HOH A 26 468 468 HOH HOH . V 4 HOH A 27 469 469 HOH HOH . V 4 HOH A 28 470 470 HOH HOH . V 4 HOH A 29 471 471 HOH HOH . V 4 HOH A 30 472 472 HOH HOH . V 4 HOH A 31 473 473 HOH HOH . V 4 HOH A 32 474 474 HOH HOH . V 4 HOH A 33 475 475 HOH HOH . V 4 HOH A 34 476 476 HOH HOH . V 4 HOH A 35 477 477 HOH HOH . V 4 HOH A 36 478 478 HOH HOH . V 4 HOH A 37 479 479 HOH HOH . V 4 HOH A 38 480 480 HOH HOH . V 4 HOH A 39 481 481 HOH HOH . V 4 HOH A 40 482 482 HOH HOH . V 4 HOH A 41 483 483 HOH HOH . V 4 HOH A 42 484 484 HOH HOH . V 4 HOH A 43 485 485 HOH HOH . V 4 HOH A 44 486 486 HOH HOH . V 4 HOH A 45 487 487 HOH HOH . V 4 HOH A 46 488 488 HOH HOH . V 4 HOH A 47 489 489 HOH HOH . V 4 HOH A 48 490 490 HOH HOH . V 4 HOH A 49 491 491 HOH HOH . V 4 HOH A 50 492 492 HOH HOH . V 4 HOH A 51 493 493 HOH HOH . V 4 HOH A 52 494 494 HOH HOH . V 4 HOH A 53 495 495 HOH HOH . V 4 HOH A 54 496 496 HOH HOH . V 4 HOH A 55 497 497 HOH HOH . V 4 HOH A 56 498 498 HOH HOH . V 4 HOH A 57 499 499 HOH HOH . V 4 HOH A 58 501 501 HOH HOH . V 4 HOH A 59 502 502 HOH HOH . V 4 HOH A 60 503 503 HOH HOH . V 4 HOH A 61 504 504 HOH HOH . V 4 HOH A 62 505 505 HOH HOH . V 4 HOH A 63 506 506 HOH HOH . W 4 HOH B 1 442 442 HOH HOH . W 4 HOH B 2 443 443 HOH HOH . W 4 HOH B 3 444 444 HOH HOH . W 4 HOH B 4 445 445 HOH HOH . W 4 HOH B 5 446 446 HOH HOH . W 4 HOH B 6 447 447 HOH HOH . W 4 HOH B 7 448 448 HOH HOH . W 4 HOH B 8 449 449 HOH HOH . W 4 HOH B 9 450 450 HOH HOH . W 4 HOH B 10 451 451 HOH HOH . W 4 HOH B 11 452 452 HOH HOH . W 4 HOH B 12 453 453 HOH HOH . W 4 HOH B 13 454 454 HOH HOH . W 4 HOH B 14 455 455 HOH HOH . W 4 HOH B 15 456 456 HOH HOH . W 4 HOH B 16 457 457 HOH HOH . W 4 HOH B 17 458 458 HOH HOH . W 4 HOH B 18 459 459 HOH HOH . W 4 HOH B 19 460 460 HOH HOH . W 4 HOH B 20 461 461 HOH HOH . W 4 HOH B 21 462 462 HOH HOH . W 4 HOH B 22 463 463 HOH HOH . W 4 HOH B 23 464 464 HOH HOH . W 4 HOH B 24 465 465 HOH HOH . W 4 HOH B 25 466 466 HOH HOH . W 4 HOH B 26 467 467 HOH HOH . W 4 HOH B 27 468 468 HOH HOH . W 4 HOH B 28 469 469 HOH HOH . W 4 HOH B 29 470 470 HOH HOH . W 4 HOH B 30 471 471 HOH HOH . W 4 HOH B 31 472 472 HOH HOH . W 4 HOH B 32 473 473 HOH HOH . W 4 HOH B 33 474 474 HOH HOH . W 4 HOH B 34 475 475 HOH HOH . W 4 HOH B 35 476 476 HOH HOH . W 4 HOH B 36 477 477 HOH HOH . X 4 HOH C 1 442 442 HOH HOH . X 4 HOH C 2 443 443 HOH HOH . X 4 HOH C 3 444 444 HOH HOH . X 4 HOH C 4 445 445 HOH HOH . X 4 HOH C 5 446 446 HOH HOH . X 4 HOH C 6 447 447 HOH HOH . X 4 HOH C 7 448 448 HOH HOH . X 4 HOH C 8 449 449 HOH HOH . X 4 HOH C 9 450 450 HOH HOH . X 4 HOH C 10 451 451 HOH HOH . X 4 HOH C 11 452 452 HOH HOH . X 4 HOH C 12 453 453 HOH HOH . X 4 HOH C 13 454 454 HOH HOH . X 4 HOH C 14 455 455 HOH HOH . X 4 HOH C 15 456 456 HOH HOH . X 4 HOH C 16 457 457 HOH HOH . X 4 HOH C 17 458 458 HOH HOH . X 4 HOH C 18 459 459 HOH HOH . X 4 HOH C 19 460 460 HOH HOH . X 4 HOH C 20 461 461 HOH HOH . X 4 HOH C 21 462 462 HOH HOH . X 4 HOH C 22 463 463 HOH HOH . X 4 HOH C 23 464 464 HOH HOH . X 4 HOH C 24 465 465 HOH HOH . X 4 HOH C 25 466 466 HOH HOH . X 4 HOH C 26 467 467 HOH HOH . X 4 HOH C 27 468 468 HOH HOH . X 4 HOH C 28 469 469 HOH HOH . X 4 HOH C 29 470 470 HOH HOH . X 4 HOH C 30 471 471 HOH HOH . X 4 HOH C 31 472 472 HOH HOH . X 4 HOH C 32 473 473 HOH HOH . X 4 HOH C 33 474 474 HOH HOH . X 4 HOH C 34 475 475 HOH HOH . X 4 HOH C 35 476 476 HOH HOH . X 4 HOH C 36 477 477 HOH HOH . X 4 HOH C 37 478 478 HOH HOH . X 4 HOH C 38 479 479 HOH HOH . X 4 HOH C 39 480 480 HOH HOH . X 4 HOH C 40 481 481 HOH HOH . X 4 HOH C 41 482 482 HOH HOH . X 4 HOH C 42 483 483 HOH HOH . X 4 HOH C 43 484 484 HOH HOH . X 4 HOH C 44 485 485 HOH HOH . X 4 HOH C 45 486 486 HOH HOH . X 4 HOH C 46 487 487 HOH HOH . X 4 HOH C 47 488 488 HOH HOH . X 4 HOH C 48 489 489 HOH HOH . X 4 HOH C 49 490 490 HOH HOH . X 4 HOH C 50 491 491 HOH HOH . X 4 HOH C 51 492 492 HOH HOH . X 4 HOH C 52 493 493 HOH HOH . X 4 HOH C 53 494 494 HOH HOH . X 4 HOH C 54 495 495 HOH HOH . Y 4 HOH D 1 442 442 HOH HOH . Y 4 HOH D 2 443 443 HOH HOH . Y 4 HOH D 3 444 444 HOH HOH . Y 4 HOH D 4 445 445 HOH HOH . Y 4 HOH D 5 446 446 HOH HOH . Y 4 HOH D 6 447 447 HOH HOH . Y 4 HOH D 7 448 448 HOH HOH . Y 4 HOH D 8 449 449 HOH HOH . Y 4 HOH D 9 450 450 HOH HOH . Y 4 HOH D 10 451 451 HOH HOH . Y 4 HOH D 11 452 452 HOH HOH . Y 4 HOH D 12 453 453 HOH HOH . Y 4 HOH D 13 454 454 HOH HOH . Y 4 HOH D 14 455 455 HOH HOH . Y 4 HOH D 15 456 456 HOH HOH . Y 4 HOH D 16 457 457 HOH HOH . Y 4 HOH D 17 458 458 HOH HOH . Y 4 HOH D 18 459 459 HOH HOH . Y 4 HOH D 19 460 460 HOH HOH . Y 4 HOH D 20 461 461 HOH HOH . Y 4 HOH D 21 462 462 HOH HOH . Y 4 HOH D 22 463 463 HOH HOH . Y 4 HOH D 23 464 464 HOH HOH . Y 4 HOH D 24 465 465 HOH HOH . Y 4 HOH D 25 466 466 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 P TYM . . . E 2 -151.515 26.279 -27.514 1 28.85 ? P TYM 500 A 1 HETATM 2 O O1P TYM . . . E 2 -150.09 26.252 -27.109 1 28.05 ? O1P TYM 500 A 1 HETATM 3 O O2P TYM . . . E 2 -151.87 26.396 -28.947 1 28.34 ? O2P TYM 500 A 1 HETATM 4 O O5' TYM . . . E 2 -152.245 27.472 -26.704 1 28.07 ? O5' TYM 500 A 1 HETATM 5 C C5' TYM . . . E 2 -152.058 27.608 -25.288 1 28.31 ? C5' TYM 500 A 1 HETATM 6 C C4' TYM . . . E 2 -153.252 28.337 -24.645 1 28.31 ? C4' TYM 500 A 1 HETATM 7 O O4' TYM . . . E 2 -153.459 29.633 -25.274 1 28.81 ? O4' TYM 500 A 1 HETATM 8 C C1' TYM . . . E 2 -154.825 29.677 -25.769 1 28.6 ? C1' TYM 500 A 1 HETATM 9 N N9 TYM . . . E 2 -154.74 30.574 -26.923 1 29.28 ? N9 TYM 500 A 1 HETATM 10 C C4 TYM . . . E 2 -155.348 31.751 -27.005 1 29.14 ? C4 TYM 500 A 1 HETATM 11 N N3 TYM . . . E 2 -156.169 32.418 -26.176 1 30.05 ? N3 TYM 500 A 1 HETATM 12 C C2 TYM . . . E 2 -156.652 33.606 -26.525 1 28.94 ? C2 TYM 500 A 1 HETATM 13 N N1 TYM . . . E 2 -156.345 34.165 -27.692 1 29.27 ? N1 TYM 500 A 1 HETATM 14 C C6 TYM . . . E 2 -155.528 33.549 -28.565 1 29.35 ? C6 TYM 500 A 1 HETATM 15 N N6 TYM . . . E 2 -155.231 34.131 -29.729 1 29.01 ? N6 TYM 500 A 1 HETATM 16 C C5 TYM . . . E 2 -155.003 32.301 -28.231 1 29.32 ? C5 TYM 500 A 1 HETATM 17 N N7 TYM . . . E 2 -154.189 31.437 -28.842 1 29.34 ? N7 TYM 500 A 1 HETATM 18 C C8 TYM . . . E 2 -154.024 30.384 -28.039 1 29.7 ? C8 TYM 500 A 1 HETATM 19 C C2' TYM . . . E 2 -155.146 28.23 -26.093 1 27.88 ? C2' TYM 500 A 1 HETATM 20 O O2' TYM . . . E 2 -156.554 28.035 -26.127 1 27.58 ? O2' TYM 500 A 1 HETATM 21 C C3' TYM . . . E 2 -154.556 27.56 -24.858 1 27.83 ? C3' TYM 500 A 1 HETATM 22 O O3' TYM . . . E 2 -155.396 27.789 -23.72 1 28.49 ? O3' TYM 500 A 1 HETATM 23 N NH3 TYM . . . E 2 -152.415 21.363 -27.105 1 29.93 ? NH3 TYM 500 A 1 HETATM 24 C CA TYM . . . E 2 -152.501 22.646 -26.393 1 29.87 ? CA TYM 500 A 1 HETATM 25 C CB TYM . . . E 2 -151.734 22.557 -25.075 1 29.81 ? CB TYM 500 A 1 HETATM 26 C CG TYM . . . E 2 -152.603 22.059 -23.913 1 30.4 ? CG TYM 500 A 1 HETATM 27 C CD2 TYM . . . E 2 -153.66 22.721 -23.295 1 30.64 ? CD2 TYM 500 A 1 HETATM 28 C CE2 TYM . . . E 2 -154.118 21.874 -22.288 1 30.78 ? CE2 TYM 500 A 1 HETATM 29 C CE3 TYM . . . E 2 -154.268 23.962 -23.496 1 30.6 ? CE3 TYM 500 A 1 HETATM 30 C CD1 TYM . . . E 2 -152.458 20.89 -23.29 1 30.84 ? CD1 TYM 500 A 1 HETATM 31 N NE1 TYM . . . E 2 -153.366 20.776 -22.318 1 31.02 ? NE1 TYM 500 A 1 HETATM 32 C CZ2 TYM . . . E 2 -155.185 22.257 -21.479 1 30.83 ? CZ2 TYM 500 A 1 HETATM 33 C CZ3 TYM . . . E 2 -155.338 24.345 -22.689 1 30.86 ? CZ3 TYM 500 A 1 HETATM 34 C CH2 TYM . . . E 2 -155.796 23.495 -21.682 1 30.33 ? CH2 TYM 500 A 1 HETATM 35 C C TYM . . . E 2 -151.892 23.767 -27.245 1 29.63 ? C TYM 500 A 1 HETATM 36 O O TYM . . . E 2 -151.099 23.518 -28.154 1 29.75 ? O TYM 500 A 1 HETATM 37 O OPP TYM . . . E 2 -152.321 25.016 -26.885 1 29.49 ? OPP TYM 500 A 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 37 #