data_8XTF # _model_server_result.job_id oAwWKl2-HB_ASFxRQAi2lQ _model_server_result.datetime_utc '2025-07-31 07:33:23' _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 8xtf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8XTF # _exptl.entry_id 8XTF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 90 _cell.angle_gamma 120 _cell.entry_id 8XTF _cell.length_a 211.754 _cell.length_b 211.754 _cell.length_c 67.424 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XTF _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall 'R 3 2"' _symmetry.space_group_name_H-M 'H 3 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 11_444 x-y-1/3,-y-2/3,-z-2/3 1 0 0 0 -1 0 0 0 -1 0 -122.256229 -44.949333 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 331 n n N HN1 SAH sing 332 n n N HN2 SAH sing 333 n n CA CB SAH sing 334 n n CA C SAH sing 335 n n CA HA SAH sing 336 n n CB CG SAH sing 337 n n CB HB1 SAH sing 338 n n CB HB2 SAH sing 339 n n CG SD SAH sing 340 n n CG HG1 SAH sing 341 n n CG HG2 SAH sing 342 n n SD C5' SAH sing 343 n n C O SAH doub 344 n n C OXT SAH sing 345 n n OXT HXT SAH sing 346 n n C5' C4' SAH sing 347 n n C5' "H5'1" SAH sing 348 n n C5' "H5'2" SAH sing 349 n n C4' O4' SAH sing 350 n n C4' C3' SAH sing 351 n n C4' H4' SAH sing 352 n n O4' C1' SAH sing 353 n n C3' O3' SAH sing 354 n n C3' C2' SAH sing 355 n n C3' H3' SAH sing 356 n n O3' HO3' SAH sing 357 n n C2' O2' SAH sing 358 n n C2' C1' SAH sing 359 n n C2' H2' SAH sing 360 n n O2' HO2' SAH sing 361 n n C1' N9 SAH sing 362 n n C1' H1' SAH sing 363 n n N9 C8 SAH sing 364 n y N9 C4 SAH sing 365 n y C8 N7 SAH doub 366 n y C8 H8 SAH sing 367 n n N7 C5 SAH sing 368 n y C5 C6 SAH sing 369 n y C5 C4 SAH doub 370 n y C6 N6 SAH sing 371 n n C6 N1 SAH doub 372 n y N6 HN61 SAH sing 373 n n N6 HN62 SAH sing 374 n n N1 C2 SAH sing 375 n y C2 N3 SAH doub 376 n y C2 H2 SAH sing 377 n n N3 C4 SAH sing 378 n y # _atom_sites.entry_id 8XTF _atom_sites.fract_transf_matrix[1][1] 0.004722 _atom_sites.fract_transf_matrix[1][2] 0.002727 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005453 _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] 0.014832 _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 B 2 SAH A 1 401 401 SAH SAH . C 3 A1LWC A 1 402 501 A1LWC YCA . D 4 HOH A 1 501 168 HOH HOH . D 4 HOH A 2 502 187 HOH HOH . D 4 HOH A 3 503 141 HOH HOH . D 4 HOH A 4 504 123 HOH HOH . D 4 HOH A 5 505 156 HOH HOH . D 4 HOH A 6 506 2 HOH HOH . D 4 HOH A 7 507 186 HOH HOH . D 4 HOH A 8 508 135 HOH HOH . D 4 HOH A 9 509 70 HOH HOH . D 4 HOH A 10 510 134 HOH HOH . D 4 HOH A 11 511 46 HOH HOH . D 4 HOH A 12 512 89 HOH HOH . D 4 HOH A 13 513 161 HOH HOH . D 4 HOH A 14 514 121 HOH HOH . D 4 HOH A 15 515 113 HOH HOH . D 4 HOH A 16 516 92 HOH HOH . D 4 HOH A 17 517 84 HOH HOH . D 4 HOH A 18 518 79 HOH HOH . D 4 HOH A 19 519 109 HOH HOH . D 4 HOH A 20 520 138 HOH HOH . D 4 HOH A 21 521 106 HOH HOH . D 4 HOH A 22 522 149 HOH HOH . D 4 HOH A 23 523 48 HOH HOH . D 4 HOH A 24 524 53 HOH HOH . D 4 HOH A 25 525 159 HOH HOH . D 4 HOH A 26 526 62 HOH HOH . D 4 HOH A 27 527 103 HOH HOH . D 4 HOH A 28 528 111 HOH HOH . D 4 HOH A 29 529 83 HOH HOH . D 4 HOH A 30 530 88 HOH HOH . D 4 HOH A 31 531 147 HOH HOH . D 4 HOH A 32 532 137 HOH HOH . D 4 HOH A 33 533 118 HOH HOH . D 4 HOH A 34 534 75 HOH HOH . D 4 HOH A 35 535 167 HOH HOH . D 4 HOH A 36 536 114 HOH HOH . D 4 HOH A 37 537 74 HOH HOH . D 4 HOH A 38 538 184 HOH HOH . D 4 HOH A 39 539 173 HOH HOH . D 4 HOH A 40 540 45 HOH HOH . D 4 HOH A 41 541 40 HOH HOH . D 4 HOH A 42 542 80 HOH HOH . D 4 HOH A 43 543 76 HOH HOH . D 4 HOH A 44 544 170 HOH HOH . D 4 HOH A 45 545 7 HOH HOH . D 4 HOH A 46 546 58 HOH HOH . D 4 HOH A 47 547 183 HOH HOH . D 4 HOH A 48 548 128 HOH HOH . D 4 HOH A 49 549 95 HOH HOH . D 4 HOH A 50 550 33 HOH HOH . D 4 HOH A 51 551 31 HOH HOH . D 4 HOH A 52 552 150 HOH HOH . D 4 HOH A 53 553 64 HOH HOH . D 4 HOH A 54 554 132 HOH HOH . D 4 HOH A 55 555 133 HOH HOH . D 4 HOH A 56 556 177 HOH HOH . D 4 HOH A 57 557 97 HOH HOH . D 4 HOH A 58 558 61 HOH HOH . D 4 HOH A 59 559 56 HOH HOH . D 4 HOH A 60 560 115 HOH HOH . D 4 HOH A 61 561 4 HOH HOH . D 4 HOH A 62 562 26 HOH HOH . D 4 HOH A 63 563 12 HOH HOH . D 4 HOH A 64 564 162 HOH HOH . D 4 HOH A 65 565 145 HOH HOH . D 4 HOH A 66 566 139 HOH HOH . D 4 HOH A 67 567 20 HOH HOH . D 4 HOH A 68 568 36 HOH HOH . D 4 HOH A 69 569 107 HOH HOH . D 4 HOH A 70 570 124 HOH HOH . D 4 HOH A 71 571 16 HOH HOH . D 4 HOH A 72 572 188 HOH HOH . D 4 HOH A 73 573 17 HOH HOH . D 4 HOH A 74 574 185 HOH HOH . D 4 HOH A 75 575 104 HOH HOH . D 4 HOH A 76 576 34 HOH HOH . D 4 HOH A 77 577 119 HOH HOH . D 4 HOH A 78 578 51 HOH HOH . D 4 HOH A 79 579 43 HOH HOH . D 4 HOH A 80 580 23 HOH HOH . D 4 HOH A 81 581 120 HOH HOH . D 4 HOH A 82 582 136 HOH HOH . D 4 HOH A 83 583 77 HOH HOH . D 4 HOH A 84 584 39 HOH HOH . D 4 HOH A 85 585 25 HOH HOH . D 4 HOH A 86 586 10 HOH HOH . D 4 HOH A 87 587 94 HOH HOH . D 4 HOH A 88 588 153 HOH HOH . D 4 HOH A 89 589 87 HOH HOH . D 4 HOH A 90 590 144 HOH HOH . D 4 HOH A 91 591 67 HOH HOH . D 4 HOH A 92 592 131 HOH HOH . D 4 HOH A 93 593 160 HOH HOH . D 4 HOH A 94 594 27 HOH HOH . D 4 HOH A 95 595 55 HOH HOH . D 4 HOH A 96 596 117 HOH HOH . D 4 HOH A 97 597 54 HOH HOH . D 4 HOH A 98 598 166 HOH HOH . D 4 HOH A 99 599 11 HOH HOH . D 4 HOH A 100 600 5 HOH HOH . D 4 HOH A 101 601 57 HOH HOH . D 4 HOH A 102 602 155 HOH HOH . D 4 HOH A 103 603 37 HOH HOH . D 4 HOH A 104 604 32 HOH HOH . D 4 HOH A 105 605 60 HOH HOH . D 4 HOH A 106 606 28 HOH HOH . D 4 HOH A 107 607 9 HOH HOH . D 4 HOH A 108 608 105 HOH HOH . D 4 HOH A 109 609 102 HOH HOH . D 4 HOH A 110 610 86 HOH HOH . D 4 HOH A 111 611 110 HOH HOH . D 4 HOH A 112 612 52 HOH HOH . D 4 HOH A 113 613 13 HOH HOH . D 4 HOH A 114 614 171 HOH HOH . D 4 HOH A 115 615 30 HOH HOH . D 4 HOH A 116 616 140 HOH HOH . D 4 HOH A 117 617 98 HOH HOH . D 4 HOH A 118 618 41 HOH HOH . D 4 HOH A 119 619 154 HOH HOH . D 4 HOH A 120 620 68 HOH HOH . D 4 HOH A 121 621 81 HOH HOH . D 4 HOH A 122 622 96 HOH HOH . D 4 HOH A 123 623 143 HOH HOH . D 4 HOH A 124 624 151 HOH HOH . D 4 HOH A 125 625 50 HOH HOH . D 4 HOH A 126 626 18 HOH HOH . D 4 HOH A 127 627 108 HOH HOH . D 4 HOH A 128 628 22 HOH HOH . D 4 HOH A 129 629 148 HOH HOH . D 4 HOH A 130 630 158 HOH HOH . D 4 HOH A 131 631 78 HOH HOH . D 4 HOH A 132 632 91 HOH HOH . D 4 HOH A 133 633 29 HOH HOH . D 4 HOH A 134 634 59 HOH HOH . D 4 HOH A 135 635 24 HOH HOH . D 4 HOH A 136 636 165 HOH HOH . D 4 HOH A 137 637 19 HOH HOH . D 4 HOH A 138 638 35 HOH HOH . D 4 HOH A 139 639 66 HOH HOH . D 4 HOH A 140 640 90 HOH HOH . D 4 HOH A 141 641 112 HOH HOH . D 4 HOH A 142 642 93 HOH HOH . D 4 HOH A 143 643 15 HOH HOH . D 4 HOH A 144 644 38 HOH HOH . D 4 HOH A 145 645 65 HOH HOH . D 4 HOH A 146 646 130 HOH HOH . D 4 HOH A 147 647 44 HOH HOH . D 4 HOH A 148 648 42 HOH HOH . D 4 HOH A 149 649 116 HOH HOH . D 4 HOH A 150 650 142 HOH HOH . D 4 HOH A 151 651 49 HOH HOH . D 4 HOH A 152 652 6 HOH HOH . D 4 HOH A 153 653 82 HOH HOH . D 4 HOH A 154 654 73 HOH HOH . D 4 HOH A 155 655 72 HOH HOH . D 4 HOH A 156 656 1 HOH HOH . D 4 HOH A 157 657 178 HOH HOH . D 4 HOH A 158 658 14 HOH HOH . D 4 HOH A 159 659 175 HOH HOH . D 4 HOH A 160 660 47 HOH HOH . D 4 HOH A 161 661 63 HOH HOH . D 4 HOH A 162 662 129 HOH HOH . D 4 HOH A 163 663 21 HOH HOH . D 4 HOH A 164 664 8 HOH HOH . D 4 HOH A 165 665 101 HOH HOH . D 4 HOH A 166 666 69 HOH HOH . D 4 HOH A 167 667 71 HOH HOH . D 4 HOH A 168 668 3 HOH HOH . D 4 HOH A 169 669 157 HOH HOH . D 4 HOH A 170 670 176 HOH HOH . D 4 HOH A 171 671 169 HOH HOH . D 4 HOH A 172 672 125 HOH HOH . D 4 HOH A 173 673 179 HOH HOH . D 4 HOH A 174 674 99 HOH HOH . D 4 HOH A 175 675 126 HOH HOH . D 4 HOH A 176 676 127 HOH HOH . D 4 HOH A 177 677 163 HOH HOH . D 4 HOH A 178 678 172 HOH HOH . D 4 HOH A 179 679 181 HOH HOH . D 4 HOH A 180 680 152 HOH HOH . D 4 HOH A 181 681 182 HOH HOH . D 4 HOH A 182 682 180 HOH HOH . D 4 HOH A 183 683 122 HOH HOH . D 4 HOH A 184 684 174 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 . . . B 2 3.481 -39.044 -8.03 1 17.84 ? N SAH 401 A 1 HETATM 2 C CA SAH . . . B 2 3.698 -39.349 -9.453 1 20.88 ? CA SAH 401 A 1 HETATM 3 C CB SAH . . . B 2 5.038 -40.062 -9.673 1 19.21 ? CB SAH 401 A 1 HETATM 4 C CG SAH . . . B 2 5.163 -41.391 -8.934 1 18.26 ? CG SAH 401 A 1 HETATM 5 S SD SAH . . . B 2 6.705 -42.262 -9.335 1 19.66 ? SD SAH 401 A 1 HETATM 6 C C SAH . . . B 2 2.586 -40.227 -10.039 1 24.43 ? C SAH 401 A 1 HETATM 7 O O SAH . . . B 2 2.262 -40.127 -11.236 1 23.9 ? O SAH 401 A 1 HETATM 8 O OXT SAH . . . B 2 2.007 -41.069 -9.333 1 23.38 ? OXT SAH 401 A 1 HETATM 9 C C5' SAH . . . B 2 7.627 -41.799 -7.846 1 15.58 ? C5' SAH 401 A 1 HETATM 10 C C4' SAH . . . B 2 8.144 -40.358 -7.827 1 19.14 ? C4' SAH 401 A 1 HETATM 11 O O4' SAH . . . B 2 8.96 -40.17 -6.675 1 22.88 ? O4' SAH 401 A 1 HETATM 12 C C3' SAH . . . B 2 9.013 -39.976 -9.021 1 18.69 ? C3' SAH 401 A 1 HETATM 13 O O3' SAH . . . B 2 8.509 -38.781 -9.562 1 17.1 ? O3' SAH 401 A 1 HETATM 14 C C2' SAH . . . B 2 10.404 -39.765 -8.423 1 19.04 ? C2' SAH 401 A 1 HETATM 15 O O2' SAH . . . B 2 11.202 -38.802 -9.081 1 16.99 ? O2' SAH 401 A 1 HETATM 16 C C1' SAH . . . B 2 10.076 -39.368 -6.993 1 17.08 ? C1' SAH 401 A 1 HETATM 17 N N9 SAH . . . B 2 11.203 -39.576 -6.061 1 19.38 ? N9 SAH 401 A 1 HETATM 18 C C8 SAH . . . B 2 11.907 -40.731 -5.882 1 21.18 ? C8 SAH 401 A 1 HETATM 19 N N7 SAH . . . B 2 12.849 -40.521 -4.938 1 19.82 ? N7 SAH 401 A 1 HETATM 20 C C5 SAH . . . B 2 12.765 -39.237 -4.519 1 19.88 ? C5 SAH 401 A 1 HETATM 21 C C6 SAH . . . B 2 13.497 -38.493 -3.583 1 20.5 ? C6 SAH 401 A 1 HETATM 22 N N6 SAH . . . B 2 14.509 -39.026 -2.888 1 19.59 ? N6 SAH 401 A 1 HETATM 23 N N1 SAH . . . B 2 13.142 -37.178 -3.363 1 19.84 ? N1 SAH 401 A 1 HETATM 24 C C2 SAH . . . B 2 12.105 -36.62 -4.074 1 18.65 ? C2 SAH 401 A 1 HETATM 25 N N3 SAH . . . B 2 11.398 -37.36 -4.988 1 17.89 ? N3 SAH 401 A 1 HETATM 26 C C4 SAH . . . B 2 11.725 -38.646 -5.213 1 17.41 ? C4 SAH 401 A 1 # _model_server_stats.io_time_ms 91 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 521 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #