data_1KIM # _model_server_result.job_id p80JzIhAzIKj7IrTdUKfYw _model_server_result.datetime_utc '2024-11-23 00:56:23' _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 1kim # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1}' # _entry.id 1KIM # _exptl.entry_id 1KIM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 242.229 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description THYMIDINE _entity.pdbx_number_of_molecules 2 _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 1KIM _cell.length_a 113.4 _cell.length_b 116.6 _cell.length_c 108.2 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KIM _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N # _chem_comp.formula 'C10 H14 N2 O5' _chem_comp.formula_weight 242.229 _chem_comp.id THM _chem_comp.mon_nstd_flag . _chem_comp.name THYMIDINE _chem_comp.type 'dna oh 5 prime terminus' _chem_comp.pdbx_synonyms "DEOXYTHYMIDINE;2'-DEOXYTHYMIDINE" # 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 O5' C5' THM sing 294 n n O5' HO5' THM sing 295 n n C5' C4' THM sing 296 n n C5' "H5'1" THM sing 297 n n C5' "H5'2" THM sing 298 n n C4' O4' THM sing 299 n n C4' C3' THM sing 300 n n C4' H4' THM sing 301 n n O4' C1' THM sing 302 n n C3' O3' THM sing 303 n n C3' C2' THM sing 304 n n C3' H3' THM sing 305 n n O3' HO3' THM sing 306 n n C2' C1' THM sing 307 n n C2' "H2'1" THM sing 308 n n C2' "H2'2" THM sing 309 n n C1' N1 THM sing 310 n n C1' H1' THM sing 311 n n N1 C2 THM sing 312 n n N1 C6 THM sing 313 n n C2 O2 THM doub 314 n n C2 N3 THM sing 315 n n N3 C4 THM sing 316 n n N3 HN3 THM sing 317 n n C4 O4 THM doub 318 n n C4 C5 THM sing 319 n n C5 C5M THM sing 320 n n C5 C6 THM doub 321 n n C5M HM51 THM sing 322 n n C5M HM52 THM sing 323 n n C5M HM53 THM sing 324 n n C6 H6 THM sing 325 n n # _atom_sites.entry_id 1KIM _atom_sites.fract_transf_matrix[1][1] 0.008818 _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] 0.008576 _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] 0.009242 _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 2 SO4 A 1 3 3 SO4 SO4 . D 3 THM A 1 1 1 THM THM . E 2 SO4 B 1 4 4 SO4 SO4 . F 3 THM B 1 2 2 THM THM . G 4 HOH A 1 377 401 HOH HOH . G 4 HOH A 2 378 402 HOH HOH . G 4 HOH A 3 379 403 HOH HOH . G 4 HOH A 4 380 404 HOH HOH . G 4 HOH A 5 381 405 HOH HOH . G 4 HOH A 6 382 406 HOH HOH . G 4 HOH A 7 383 407 HOH HOH . G 4 HOH A 8 384 408 HOH HOH . G 4 HOH A 9 385 409 HOH HOH . G 4 HOH A 10 386 410 HOH HOH . G 4 HOH A 11 387 411 HOH HOH . G 4 HOH A 12 388 412 HOH HOH . G 4 HOH A 13 389 413 HOH HOH . G 4 HOH A 14 390 414 HOH HOH . G 4 HOH A 15 391 415 HOH HOH . G 4 HOH A 16 392 416 HOH HOH . G 4 HOH A 17 393 417 HOH HOH . G 4 HOH A 18 394 418 HOH HOH . G 4 HOH A 19 395 420 HOH HOH . G 4 HOH A 20 396 421 HOH HOH . G 4 HOH A 21 397 422 HOH HOH . G 4 HOH A 22 398 423 HOH HOH . G 4 HOH A 23 399 424 HOH HOH . G 4 HOH A 24 400 425 HOH HOH . G 4 HOH A 25 401 426 HOH HOH . G 4 HOH A 26 402 427 HOH HOH . G 4 HOH A 27 403 428 HOH HOH . G 4 HOH A 28 404 429 HOH HOH . G 4 HOH A 29 405 430 HOH HOH . G 4 HOH A 30 406 431 HOH HOH . G 4 HOH A 31 407 432 HOH HOH . G 4 HOH A 32 408 433 HOH HOH . G 4 HOH A 33 409 434 HOH HOH . G 4 HOH A 34 410 435 HOH HOH . G 4 HOH A 35 411 436 HOH HOH . G 4 HOH A 36 412 437 HOH HOH . G 4 HOH A 37 413 438 HOH HOH . G 4 HOH A 38 414 439 HOH HOH . G 4 HOH A 39 415 440 HOH HOH . G 4 HOH A 40 416 441 HOH HOH . G 4 HOH A 41 417 442 HOH HOH . G 4 HOH A 42 418 443 HOH HOH . G 4 HOH A 43 419 444 HOH HOH . G 4 HOH A 44 420 445 HOH HOH . G 4 HOH A 45 421 446 HOH HOH . G 4 HOH A 46 422 447 HOH HOH . G 4 HOH A 47 423 448 HOH HOH . G 4 HOH A 48 424 449 HOH HOH . G 4 HOH A 49 425 450 HOH HOH . G 4 HOH A 50 426 451 HOH HOH . G 4 HOH A 51 427 452 HOH HOH . G 4 HOH A 52 428 453 HOH HOH . G 4 HOH A 53 429 454 HOH HOH . G 4 HOH A 54 430 455 HOH HOH . G 4 HOH A 55 431 456 HOH HOH . G 4 HOH A 56 432 457 HOH HOH . G 4 HOH A 57 433 458 HOH HOH . G 4 HOH A 58 434 459 HOH HOH . G 4 HOH A 59 435 460 HOH HOH . G 4 HOH A 60 436 461 HOH HOH . G 4 HOH A 61 437 462 HOH HOH . G 4 HOH A 62 438 463 HOH HOH . G 4 HOH A 63 439 464 HOH HOH . G 4 HOH A 64 440 465 HOH HOH . G 4 HOH A 65 441 466 HOH HOH . G 4 HOH A 66 442 467 HOH HOH . G 4 HOH A 67 443 468 HOH HOH . G 4 HOH A 68 444 469 HOH HOH . G 4 HOH A 69 445 470 HOH HOH . G 4 HOH A 70 446 471 HOH HOH . G 4 HOH A 71 447 472 HOH HOH . G 4 HOH A 72 448 473 HOH HOH . G 4 HOH A 73 449 474 HOH HOH . G 4 HOH A 74 450 475 HOH HOH . G 4 HOH A 75 451 601 HOH HOH . G 4 HOH A 76 452 603 HOH HOH . G 4 HOH A 77 453 606 HOH HOH . G 4 HOH A 78 454 607 HOH HOH . G 4 HOH A 79 455 608 HOH HOH . G 4 HOH A 80 456 612 HOH HOH . G 4 HOH A 81 457 614 HOH HOH . G 4 HOH A 82 458 616 HOH HOH . G 4 HOH A 83 459 617 HOH HOH . G 4 HOH A 84 460 618 HOH HOH . G 4 HOH A 85 461 622 HOH HOH . G 4 HOH A 86 462 623 HOH HOH . G 4 HOH A 87 463 625 HOH HOH . G 4 HOH A 88 464 626 HOH HOH . G 4 HOH A 89 465 627 HOH HOH . G 4 HOH A 90 466 628 HOH HOH . G 4 HOH A 91 467 635 HOH HOH . G 4 HOH A 92 468 638 HOH HOH . G 4 HOH A 93 469 639 HOH HOH . G 4 HOH A 94 470 640 HOH HOH . G 4 HOH A 95 471 643 HOH HOH . G 4 HOH A 96 472 644 HOH HOH . G 4 HOH A 97 473 648 HOH HOH . G 4 HOH A 98 474 650 HOH HOH . G 4 HOH A 99 475 654 HOH HOH . G 4 HOH A 100 476 655 HOH HOH . G 4 HOH A 101 477 656 HOH HOH . G 4 HOH A 102 478 657 HOH HOH . G 4 HOH A 103 479 658 HOH HOH . G 4 HOH A 104 480 663 HOH HOH . G 4 HOH A 105 481 665 HOH HOH . G 4 HOH A 106 482 669 HOH HOH . G 4 HOH A 107 483 673 HOH HOH . G 4 HOH A 108 484 674 HOH HOH . G 4 HOH A 109 485 676 HOH HOH . G 4 HOH A 110 486 679 HOH HOH . G 4 HOH A 111 487 680 HOH HOH . G 4 HOH A 112 488 682 HOH HOH . G 4 HOH A 113 489 684 HOH HOH . G 4 HOH A 114 490 686 HOH HOH . G 4 HOH A 115 491 687 HOH HOH . G 4 HOH A 116 492 688 HOH HOH . G 4 HOH A 117 493 689 HOH HOH . G 4 HOH A 118 494 691 HOH HOH . G 4 HOH A 119 495 695 HOH HOH . G 4 HOH A 120 496 699 HOH HOH . G 4 HOH A 121 497 700 HOH HOH . G 4 HOH A 122 498 701 HOH HOH . G 4 HOH A 123 499 703 HOH HOH . G 4 HOH A 124 500 704 HOH HOH . G 4 HOH A 125 501 707 HOH HOH . G 4 HOH A 126 502 709 HOH HOH . G 4 HOH A 127 503 711 HOH HOH . G 4 HOH A 128 504 412 HOH HOH . G 4 HOH A 129 505 419 HOH HOH . G 4 HOH A 130 506 443 HOH HOH . G 4 HOH A 131 507 444 HOH HOH . G 4 HOH A 132 508 672 HOH HOH . H 4 HOH B 1 377 419 HOH HOH . H 4 HOH B 2 378 621 HOH HOH . H 4 HOH B 3 379 401 HOH HOH . H 4 HOH B 4 380 402 HOH HOH . H 4 HOH B 5 381 403 HOH HOH . H 4 HOH B 6 382 404 HOH HOH . H 4 HOH B 7 383 405 HOH HOH . H 4 HOH B 8 384 406 HOH HOH . H 4 HOH B 9 385 407 HOH HOH . H 4 HOH B 10 386 408 HOH HOH . H 4 HOH B 11 387 409 HOH HOH . H 4 HOH B 12 388 410 HOH HOH . H 4 HOH B 13 389 411 HOH HOH . H 4 HOH B 14 390 413 HOH HOH . H 4 HOH B 15 391 414 HOH HOH . H 4 HOH B 16 392 415 HOH HOH . H 4 HOH B 17 393 416 HOH HOH . H 4 HOH B 18 394 417 HOH HOH . H 4 HOH B 19 395 418 HOH HOH . H 4 HOH B 20 396 420 HOH HOH . H 4 HOH B 21 397 421 HOH HOH . H 4 HOH B 22 398 422 HOH HOH . H 4 HOH B 23 399 423 HOH HOH . H 4 HOH B 24 400 424 HOH HOH . H 4 HOH B 25 401 425 HOH HOH . H 4 HOH B 26 402 426 HOH HOH . H 4 HOH B 27 403 427 HOH HOH . H 4 HOH B 28 404 428 HOH HOH . H 4 HOH B 29 405 429 HOH HOH . H 4 HOH B 30 406 430 HOH HOH . H 4 HOH B 31 407 431 HOH HOH . H 4 HOH B 32 408 432 HOH HOH . H 4 HOH B 33 409 433 HOH HOH . H 4 HOH B 34 410 434 HOH HOH . H 4 HOH B 35 411 435 HOH HOH . H 4 HOH B 36 412 436 HOH HOH . H 4 HOH B 37 413 437 HOH HOH . H 4 HOH B 38 414 438 HOH HOH . H 4 HOH B 39 415 439 HOH HOH . H 4 HOH B 40 416 440 HOH HOH . H 4 HOH B 41 417 441 HOH HOH . H 4 HOH B 42 418 442 HOH HOH . H 4 HOH B 43 419 445 HOH HOH . H 4 HOH B 44 420 446 HOH HOH . H 4 HOH B 45 421 447 HOH HOH . H 4 HOH B 46 422 448 HOH HOH . H 4 HOH B 47 423 449 HOH HOH . H 4 HOH B 48 424 450 HOH HOH . H 4 HOH B 49 425 451 HOH HOH . H 4 HOH B 50 426 452 HOH HOH . H 4 HOH B 51 427 453 HOH HOH . H 4 HOH B 52 428 454 HOH HOH . H 4 HOH B 53 429 455 HOH HOH . H 4 HOH B 54 430 456 HOH HOH . H 4 HOH B 55 431 457 HOH HOH . H 4 HOH B 56 432 458 HOH HOH . H 4 HOH B 57 433 459 HOH HOH . H 4 HOH B 58 434 460 HOH HOH . H 4 HOH B 59 435 461 HOH HOH . H 4 HOH B 60 436 462 HOH HOH . H 4 HOH B 61 437 463 HOH HOH . H 4 HOH B 62 438 464 HOH HOH . H 4 HOH B 63 439 465 HOH HOH . H 4 HOH B 64 440 466 HOH HOH . H 4 HOH B 65 441 467 HOH HOH . H 4 HOH B 66 442 468 HOH HOH . H 4 HOH B 67 443 469 HOH HOH . H 4 HOH B 68 444 470 HOH HOH . H 4 HOH B 69 445 471 HOH HOH . H 4 HOH B 70 446 472 HOH HOH . H 4 HOH B 71 447 473 HOH HOH . H 4 HOH B 72 448 474 HOH HOH . H 4 HOH B 73 449 475 HOH HOH . H 4 HOH B 74 450 602 HOH HOH . H 4 HOH B 75 451 604 HOH HOH . H 4 HOH B 76 452 605 HOH HOH . H 4 HOH B 77 453 609 HOH HOH . H 4 HOH B 78 454 610 HOH HOH . H 4 HOH B 79 455 611 HOH HOH . H 4 HOH B 80 456 613 HOH HOH . H 4 HOH B 81 457 615 HOH HOH . H 4 HOH B 82 458 619 HOH HOH . H 4 HOH B 83 459 620 HOH HOH . H 4 HOH B 84 460 624 HOH HOH . H 4 HOH B 85 461 629 HOH HOH . H 4 HOH B 86 462 630 HOH HOH . H 4 HOH B 87 463 631 HOH HOH . H 4 HOH B 88 464 632 HOH HOH . H 4 HOH B 89 465 633 HOH HOH . H 4 HOH B 90 466 634 HOH HOH . H 4 HOH B 91 467 636 HOH HOH . H 4 HOH B 92 468 637 HOH HOH . H 4 HOH B 93 469 641 HOH HOH . H 4 HOH B 94 470 642 HOH HOH . H 4 HOH B 95 471 645 HOH HOH . H 4 HOH B 96 472 646 HOH HOH . H 4 HOH B 97 473 647 HOH HOH . H 4 HOH B 98 474 649 HOH HOH . H 4 HOH B 99 475 651 HOH HOH . H 4 HOH B 100 476 652 HOH HOH . H 4 HOH B 101 477 653 HOH HOH . H 4 HOH B 102 478 659 HOH HOH . H 4 HOH B 103 479 660 HOH HOH . H 4 HOH B 104 480 661 HOH HOH . H 4 HOH B 105 481 662 HOH HOH . H 4 HOH B 106 482 664 HOH HOH . H 4 HOH B 107 483 666 HOH HOH . H 4 HOH B 108 484 667 HOH HOH . H 4 HOH B 109 485 668 HOH HOH . H 4 HOH B 110 486 670 HOH HOH . H 4 HOH B 111 487 671 HOH HOH . H 4 HOH B 112 488 675 HOH HOH . H 4 HOH B 113 489 677 HOH HOH . H 4 HOH B 114 490 678 HOH HOH . H 4 HOH B 115 491 681 HOH HOH . H 4 HOH B 116 492 683 HOH HOH . H 4 HOH B 117 493 685 HOH HOH . H 4 HOH B 118 494 690 HOH HOH . H 4 HOH B 119 495 692 HOH HOH . H 4 HOH B 120 496 693 HOH HOH . H 4 HOH B 121 497 694 HOH HOH . H 4 HOH B 122 498 696 HOH HOH . H 4 HOH B 123 499 697 HOH HOH . H 4 HOH B 124 500 698 HOH HOH . H 4 HOH B 125 501 702 HOH HOH . H 4 HOH B 126 502 705 HOH HOH . H 4 HOH B 127 503 706 HOH HOH . H 4 HOH B 128 504 708 HOH HOH . H 4 HOH B 129 505 710 HOH HOH . H 4 HOH B 130 506 712 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 O O5' THM . . . D 3 49.862 81.489 53.395 1 17.04 ? O5' THM 1 A 1 HETATM 2 C C5' THM . . . D 3 50.653 82.696 53.146 1 14.35 ? C5' THM 1 A 1 HETATM 3 C C4' THM . . . D 3 50.21 83.873 53.978 1 13.94 ? C4' THM 1 A 1 HETATM 4 O O4' THM . . . D 3 48.869 84.315 53.785 1 15.67 ? O4' THM 1 A 1 HETATM 5 C C3' THM . . . D 3 50.097 83.5 55.434 1 14.69 ? C3' THM 1 A 1 HETATM 6 O O3' THM . . . D 3 50.192 84.715 56.106 1 13.02 ? O3' THM 1 A 1 HETATM 7 C C2' THM . . . D 3 48.647 83.062 55.566 1 11.51 ? C2' THM 1 A 1 HETATM 8 C C1' THM . . . D 3 47.884 84.112 54.851 1 12.07 ? C1' THM 1 A 1 HETATM 9 N N1 THM . . . D 3 46.595 83.79 54.213 1 7.67 ? N1 THM 1 A 1 HETATM 10 C C2 THM . . . D 3 45.5 84.482 54.516 1 10.87 ? C2 THM 1 A 1 HETATM 11 O O2 THM . . . D 3 45.419 85.372 55.352 1 9.04 ? O2 THM 1 A 1 HETATM 12 N N3 THM . . . D 3 44.379 84.118 53.78 1 12.33 ? N3 THM 1 A 1 HETATM 13 C C4 THM . . . D 3 44.258 83.099 52.825 1 11.63 ? C4 THM 1 A 1 HETATM 14 O O4 THM . . . D 3 43.151 82.844 52.302 1 13.11 ? O4 THM 1 A 1 HETATM 15 C C5 THM . . . D 3 45.465 82.434 52.615 1 10.19 ? C5 THM 1 A 1 HETATM 16 C C5M THM . . . D 3 45.56 81.277 51.642 1 9.47 ? C5M THM 1 A 1 HETATM 17 C C6 THM . . . D 3 46.556 82.79 53.305 1 9.09 ? C6 THM 1 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 17 #