data_2PXA # _model_server_result.job_id xa8i4NUWslgQbQkAcj8fcw _model_server_result.datetime_utc '2024-11-23 00:22:07' _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 2pxa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 2PXA # _exptl.entry_id 2PXA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 2PXA _cell.length_a 79.423 _cell.length_b 80.28 _cell.length_c 84.814 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PXA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 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 ? 3 D N N ? 3 F N N # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide linking' _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 N CA SAH sing 327 n n N HN1 SAH sing 328 n n N HN2 SAH sing 329 n n CA CB SAH sing 330 n n CA C SAH sing 331 n n CA HA SAH sing 332 n n CB CG SAH sing 333 n n CB HB1 SAH sing 334 n n CB HB2 SAH sing 335 n n CG SD SAH sing 336 n n CG HG1 SAH sing 337 n n CG HG2 SAH sing 338 n n SD C5' SAH sing 339 n n C O SAH doub 340 n n C OXT SAH sing 341 n n OXT HXT SAH sing 342 n n C5' C4' SAH sing 343 n n C5' "H5'1" SAH sing 344 n n C5' "H5'2" SAH sing 345 n n C4' O4' SAH sing 346 n n C4' C3' SAH sing 347 n n C4' H4' SAH sing 348 n n O4' C1' SAH sing 349 n n C3' O3' SAH sing 350 n n C3' C2' SAH sing 351 n n C3' H3' SAH sing 352 n n O3' HO3' SAH sing 353 n n C2' O2' SAH sing 354 n n C2' C1' SAH sing 355 n n C2' H2' SAH sing 356 n n O2' HO2' SAH sing 357 n n C1' N9 SAH sing 358 n n C1' H1' SAH sing 359 n n N9 C8 SAH sing 360 n y N9 C4 SAH sing 361 n y C8 N7 SAH doub 362 n y C8 H8 SAH sing 363 n n N7 C5 SAH sing 364 n y C5 C6 SAH sing 365 n y C5 C4 SAH doub 366 n y C6 N6 SAH sing 367 n n C6 N1 SAH doub 368 n y N6 HN61 SAH sing 369 n n N6 HN62 SAH sing 370 n n N1 C2 SAH sing 371 n y C2 N3 SAH doub 372 n y C2 H2 SAH sing 373 n n N3 C4 SAH sing 374 n y # _atom_sites.entry_id 2PXA _atom_sites.fract_transf_matrix[1][1] 0.012591 _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] 0.012456 _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] 0.011791 _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 GTP A 1 401 401 GTP GT . D 3 SAH A 1 500 501 SAH SAH . E 2 GTP B 1 403 403 GTP GT . F 3 SAH B 1 500 500 SAH SAH . G 4 HOH A 1 404 404 HOH HOH . G 4 HOH A 2 405 405 HOH HOH . G 4 HOH A 3 407 407 HOH HOH . G 4 HOH A 4 408 408 HOH HOH . G 4 HOH A 5 412 412 HOH HOH . G 4 HOH A 6 414 414 HOH HOH . G 4 HOH A 7 418 418 HOH HOH . G 4 HOH A 8 419 419 HOH HOH . G 4 HOH A 9 421 421 HOH HOH . G 4 HOH A 10 425 425 HOH HOH . G 4 HOH A 11 434 434 HOH HOH . G 4 HOH A 12 435 435 HOH HOH . G 4 HOH A 13 437 437 HOH HOH . G 4 HOH A 14 438 438 HOH HOH . G 4 HOH A 15 441 441 HOH HOH . G 4 HOH A 16 443 443 HOH HOH . G 4 HOH A 17 444 444 HOH HOH . G 4 HOH A 18 446 446 HOH HOH . G 4 HOH A 19 447 447 HOH HOH . G 4 HOH A 20 448 448 HOH HOH . G 4 HOH A 21 449 449 HOH HOH . G 4 HOH A 22 450 450 HOH HOH . G 4 HOH A 23 451 451 HOH HOH . G 4 HOH A 24 454 454 HOH HOH . G 4 HOH A 25 456 456 HOH HOH . G 4 HOH A 26 457 457 HOH HOH . G 4 HOH A 27 458 458 HOH HOH . G 4 HOH A 28 464 464 HOH HOH . G 4 HOH A 29 466 466 HOH HOH . G 4 HOH A 30 467 467 HOH HOH . G 4 HOH A 31 470 470 HOH HOH . G 4 HOH A 32 475 475 HOH HOH . G 4 HOH A 33 477 477 HOH HOH . G 4 HOH A 34 479 479 HOH HOH . G 4 HOH A 35 480 480 HOH HOH . G 4 HOH A 36 488 488 HOH HOH . G 4 HOH A 37 492 492 HOH HOH . G 4 HOH A 38 493 493 HOH HOH . G 4 HOH A 39 494 494 HOH HOH . G 4 HOH A 40 495 495 HOH HOH . G 4 HOH A 41 499 499 HOH HOH . G 4 HOH A 42 502 502 HOH HOH . G 4 HOH A 43 503 503 HOH HOH . G 4 HOH A 44 505 505 HOH HOH . G 4 HOH A 45 508 508 HOH HOH . G 4 HOH A 46 515 515 HOH HOH . G 4 HOH A 47 517 517 HOH HOH . G 4 HOH A 48 518 518 HOH HOH . G 4 HOH A 49 519 519 HOH HOH . G 4 HOH A 50 521 521 HOH HOH . G 4 HOH A 51 534 534 HOH HOH . G 4 HOH A 52 535 535 HOH HOH . G 4 HOH A 53 539 539 HOH HOH . G 4 HOH A 54 546 546 HOH HOH . G 4 HOH A 55 550 550 HOH HOH . G 4 HOH A 56 552 552 HOH HOH . G 4 HOH A 57 554 554 HOH HOH . G 4 HOH A 58 555 555 HOH HOH . G 4 HOH A 59 556 556 HOH HOH . G 4 HOH A 60 560 560 HOH HOH . G 4 HOH A 61 562 562 HOH HOH . G 4 HOH A 62 569 569 HOH HOH . G 4 HOH A 63 573 573 HOH HOH . G 4 HOH A 64 574 574 HOH HOH . G 4 HOH A 65 578 578 HOH HOH . G 4 HOH A 66 579 579 HOH HOH . G 4 HOH A 67 582 582 HOH HOH . G 4 HOH A 68 585 585 HOH HOH . G 4 HOH A 69 586 586 HOH HOH . G 4 HOH A 70 588 588 HOH HOH . G 4 HOH A 71 589 589 HOH HOH . G 4 HOH A 72 593 593 HOH HOH . G 4 HOH A 73 594 594 HOH HOH . G 4 HOH A 74 602 602 HOH HOH . G 4 HOH A 75 604 604 HOH HOH . G 4 HOH A 76 607 607 HOH HOH . G 4 HOH A 77 608 608 HOH HOH . G 4 HOH A 78 609 609 HOH HOH . G 4 HOH A 79 619 619 HOH HOH . G 4 HOH A 80 624 624 HOH HOH . G 4 HOH A 81 625 625 HOH HOH . G 4 HOH A 82 626 626 HOH HOH . G 4 HOH A 83 629 629 HOH HOH . G 4 HOH A 84 630 630 HOH HOH . G 4 HOH A 85 631 631 HOH HOH . G 4 HOH A 86 632 632 HOH HOH . G 4 HOH A 87 634 634 HOH HOH . G 4 HOH A 88 637 637 HOH HOH . G 4 HOH A 89 639 639 HOH HOH . G 4 HOH A 90 641 641 HOH HOH . G 4 HOH A 91 644 644 HOH HOH . G 4 HOH A 92 646 646 HOH HOH . G 4 HOH A 93 648 648 HOH HOH . G 4 HOH A 94 649 649 HOH HOH . G 4 HOH A 95 650 650 HOH HOH . G 4 HOH A 96 653 653 HOH HOH . G 4 HOH A 97 656 656 HOH HOH . G 4 HOH A 98 657 657 HOH HOH . G 4 HOH A 99 658 658 HOH HOH . G 4 HOH A 100 659 659 HOH HOH . G 4 HOH A 101 660 660 HOH HOH . G 4 HOH A 102 661 661 HOH HOH . G 4 HOH A 103 670 670 HOH HOH . G 4 HOH A 104 671 671 HOH HOH . G 4 HOH A 105 672 672 HOH HOH . G 4 HOH A 106 673 673 HOH HOH . G 4 HOH A 107 674 674 HOH HOH . G 4 HOH A 108 675 675 HOH HOH . G 4 HOH A 109 678 678 HOH HOH . G 4 HOH A 110 679 679 HOH HOH . H 4 HOH B 1 501 406 HOH HOH . H 4 HOH B 2 502 409 HOH HOH . H 4 HOH B 3 503 410 HOH HOH . H 4 HOH B 4 504 411 HOH HOH . H 4 HOH B 5 505 413 HOH HOH . H 4 HOH B 6 506 415 HOH HOH . H 4 HOH B 7 507 416 HOH HOH . H 4 HOH B 8 508 417 HOH HOH . H 4 HOH B 9 509 420 HOH HOH . H 4 HOH B 10 510 422 HOH HOH . H 4 HOH B 11 511 423 HOH HOH . H 4 HOH B 12 512 424 HOH HOH . H 4 HOH B 13 513 426 HOH HOH . H 4 HOH B 14 514 427 HOH HOH . H 4 HOH B 15 515 429 HOH HOH . H 4 HOH B 16 516 430 HOH HOH . H 4 HOH B 17 517 431 HOH HOH . H 4 HOH B 18 518 432 HOH HOH . H 4 HOH B 19 519 433 HOH HOH . H 4 HOH B 20 520 436 HOH HOH . H 4 HOH B 21 521 439 HOH HOH . H 4 HOH B 22 522 440 HOH HOH . H 4 HOH B 23 523 442 HOH HOH . H 4 HOH B 24 524 445 HOH HOH . H 4 HOH B 25 525 452 HOH HOH . H 4 HOH B 26 526 453 HOH HOH . H 4 HOH B 27 527 455 HOH HOH . H 4 HOH B 28 528 461 HOH HOH . H 4 HOH B 29 529 463 HOH HOH . H 4 HOH B 30 530 465 HOH HOH . H 4 HOH B 31 531 468 HOH HOH . H 4 HOH B 32 532 471 HOH HOH . H 4 HOH B 33 533 472 HOH HOH . H 4 HOH B 34 534 473 HOH HOH . H 4 HOH B 35 535 474 HOH HOH . H 4 HOH B 36 536 476 HOH HOH . H 4 HOH B 37 537 478 HOH HOH . H 4 HOH B 38 538 481 HOH HOH . H 4 HOH B 39 539 482 HOH HOH . H 4 HOH B 40 540 483 HOH HOH . H 4 HOH B 41 541 484 HOH HOH . H 4 HOH B 42 542 485 HOH HOH . H 4 HOH B 43 543 486 HOH HOH . H 4 HOH B 44 544 487 HOH HOH . H 4 HOH B 45 545 489 HOH HOH . H 4 HOH B 46 546 490 HOH HOH . H 4 HOH B 47 547 491 HOH HOH . H 4 HOH B 48 548 496 HOH HOH . H 4 HOH B 49 549 497 HOH HOH . H 4 HOH B 50 550 498 HOH HOH . H 4 HOH B 51 551 500 HOH HOH . H 4 HOH B 52 552 501 HOH HOH . H 4 HOH B 53 553 504 HOH HOH . H 4 HOH B 54 554 506 HOH HOH . H 4 HOH B 55 555 507 HOH HOH . H 4 HOH B 56 556 509 HOH HOH . H 4 HOH B 57 557 510 HOH HOH . H 4 HOH B 58 558 511 HOH HOH . H 4 HOH B 59 559 514 HOH HOH . H 4 HOH B 60 560 516 HOH HOH . H 4 HOH B 61 561 520 HOH HOH . H 4 HOH B 62 562 522 HOH HOH . H 4 HOH B 63 563 523 HOH HOH . H 4 HOH B 64 564 524 HOH HOH . H 4 HOH B 65 565 525 HOH HOH . H 4 HOH B 66 566 526 HOH HOH . H 4 HOH B 67 567 527 HOH HOH . H 4 HOH B 68 568 528 HOH HOH . H 4 HOH B 69 569 529 HOH HOH . H 4 HOH B 70 570 530 HOH HOH . H 4 HOH B 71 571 531 HOH HOH . H 4 HOH B 72 572 532 HOH HOH . H 4 HOH B 73 573 536 HOH HOH . H 4 HOH B 74 574 537 HOH HOH . H 4 HOH B 75 575 538 HOH HOH . H 4 HOH B 76 576 541 HOH HOH . H 4 HOH B 77 577 542 HOH HOH . H 4 HOH B 78 578 543 HOH HOH . H 4 HOH B 79 579 544 HOH HOH . H 4 HOH B 80 580 547 HOH HOH . H 4 HOH B 81 581 548 HOH HOH . H 4 HOH B 82 582 549 HOH HOH . H 4 HOH B 83 583 551 HOH HOH . H 4 HOH B 84 584 553 HOH HOH . H 4 HOH B 85 585 557 HOH HOH . H 4 HOH B 86 586 558 HOH HOH . H 4 HOH B 87 587 559 HOH HOH . H 4 HOH B 88 588 561 HOH HOH . H 4 HOH B 89 589 563 HOH HOH . H 4 HOH B 90 590 564 HOH HOH . H 4 HOH B 91 591 565 HOH HOH . H 4 HOH B 92 592 566 HOH HOH . H 4 HOH B 93 593 567 HOH HOH . H 4 HOH B 94 594 568 HOH HOH . H 4 HOH B 95 595 570 HOH HOH . H 4 HOH B 96 596 571 HOH HOH . H 4 HOH B 97 597 572 HOH HOH . H 4 HOH B 98 598 575 HOH HOH . H 4 HOH B 99 599 576 HOH HOH . H 4 HOH B 100 600 580 HOH HOH . H 4 HOH B 101 601 581 HOH HOH . H 4 HOH B 102 602 583 HOH HOH . H 4 HOH B 103 603 584 HOH HOH . H 4 HOH B 104 604 590 HOH HOH . H 4 HOH B 105 605 592 HOH HOH . H 4 HOH B 106 606 597 HOH HOH . H 4 HOH B 107 607 598 HOH HOH . H 4 HOH B 108 608 599 HOH HOH . H 4 HOH B 109 609 600 HOH HOH . H 4 HOH B 110 610 601 HOH HOH . H 4 HOH B 111 611 605 HOH HOH . H 4 HOH B 112 612 606 HOH HOH . H 4 HOH B 113 613 611 HOH HOH . H 4 HOH B 114 614 612 HOH HOH . H 4 HOH B 115 615 613 HOH HOH . H 4 HOH B 116 616 614 HOH HOH . H 4 HOH B 117 617 615 HOH HOH . H 4 HOH B 118 618 616 HOH HOH . H 4 HOH B 119 619 618 HOH HOH . H 4 HOH B 120 620 620 HOH HOH . H 4 HOH B 121 621 621 HOH HOH . H 4 HOH B 122 622 623 HOH HOH . H 4 HOH B 123 623 628 HOH HOH . H 4 HOH B 124 624 633 HOH HOH . H 4 HOH B 125 625 635 HOH HOH . H 4 HOH B 126 626 636 HOH HOH . H 4 HOH B 127 627 638 HOH HOH . H 4 HOH B 128 628 640 HOH HOH . H 4 HOH B 129 629 643 HOH HOH . H 4 HOH B 130 630 647 HOH HOH . H 4 HOH B 131 631 651 HOH HOH . H 4 HOH B 132 632 654 HOH HOH . H 4 HOH B 133 633 662 HOH HOH . H 4 HOH B 134 634 663 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 N SAH . . . D 3 -5.404 -20.789 25.15 1 28.91 ? N SAH 500 A 1 HETATM 2 C CA SAH . . . D 3 -5.495 -20.588 23.683 1 30.25 ? CA SAH 500 A 1 HETATM 3 C CB SAH . . . D 3 -4.155 -20.125 23.128 1 37.48 ? CB SAH 500 A 1 HETATM 4 C CG SAH . . . D 3 -4.173 -18.634 22.809 1 35.65 ? CG SAH 500 A 1 HETATM 5 S SD SAH . . . D 3 -2.544 -18.225 22.228 1 46.85 ? SD SAH 500 A 1 HETATM 6 C C SAH . . . D 3 -5.913 -21.875 22.999 1 35.94 ? C SAH 500 A 1 HETATM 7 O O SAH . . . D 3 -6.112 -22.886 23.673 1 37.6 ? O SAH 500 A 1 HETATM 8 O OXT SAH . . . D 3 -6.053 -21.919 21.778 1 34.95 ? OXT SAH 500 A 1 HETATM 9 C C5' SAH . . . D 3 -2.475 -16.63 23.072 1 43.92 ? C5' SAH 500 A 1 HETATM 10 C C4' SAH . . . D 3 -3.159 -15.547 22.274 1 26.13 ? C4' SAH 500 A 1 HETATM 11 O O4' SAH . . . D 3 -3.091 -14.351 23.007 1 30.82 ? O4' SAH 500 A 1 HETATM 12 C C3' SAH . . . D 3 -2.531 -15.273 20.899 1 32.79 ? C3' SAH 500 A 1 HETATM 13 O O3' SAH . . . D 3 -3.298 -15.766 19.826 1 27.63 ? O3' SAH 500 A 1 HETATM 14 C C2' SAH . . . D 3 -2.453 -13.763 20.802 1 26.42 ? C2' SAH 500 A 1 HETATM 15 O O2' SAH . . . D 3 -3.078 -13.243 19.648 1 36.15 ? O2' SAH 500 A 1 HETATM 16 C C1' SAH . . . D 3 -3.192 -13.308 22.045 1 29.46 ? C1' SAH 500 A 1 HETATM 17 N N9 SAH . . . D 3 -2.654 -12.031 22.484 1 27.8 ? N9 SAH 500 A 1 HETATM 18 C C8 SAH . . . D 3 -1.342 -11.615 22.537 1 25.5 ? C8 SAH 500 A 1 HETATM 19 N N7 SAH . . . D 3 -1.339 -10.353 23.014 1 20.47 ? N7 SAH 500 A 1 HETATM 20 C C5 SAH . . . D 3 -2.61 -9.951 23.232 1 15.26 ? C5 SAH 500 A 1 HETATM 21 C C6 SAH . . . D 3 -3.166 -8.777 23.71 1 29.76 ? C6 SAH 500 A 1 HETATM 22 N N6 SAH . . . D 3 -2.394 -7.752 24.036 1 32.9 ? N6 SAH 500 A 1 HETATM 23 N N1 SAH . . . D 3 -4.534 -8.684 23.85 1 27.31 ? N1 SAH 500 A 1 HETATM 24 C C2 SAH . . . D 3 -5.345 -9.749 23.528 1 24.23 ? C2 SAH 500 A 1 HETATM 25 N N3 SAH . . . D 3 -4.779 -10.917 23.058 1 26.9 ? N3 SAH 500 A 1 HETATM 26 C C4 SAH . . . D 3 -3.447 -11.011 22.918 1 20.32 ? C4 SAH 500 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #