data_5U0T # _model_server_result.job_id UPeYGuIYJPEfFkL3uGahiA _model_server_result.datetime_utc '2025-07-05 08:44:16' _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 5u0t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5U0T # _exptl.entry_id 5U0T _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 90 _cell.entry_id 5U0T _cell.length_a 50.815 _cell.length_b 69.886 _cell.length_c 84.7 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5U0T _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OE1 GLU 118 A GLU 98 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc2 A OD2 ASP 226 A ASP 206 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc3 D MG MG . A MG 403 1_555 E O HOH . A HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc4 D MG MG . A MG 403 1_555 E O HOH . A HOH 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc5 D MG MG . A MG 403 1_555 E O HOH . A HOH 573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc6 D MG MG . A MG 403 1_555 E O HOH . A HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? # _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 352 n n N HN1 SAH sing 353 n n N HN2 SAH sing 354 n n CA CB SAH sing 355 n n CA C SAH sing 356 n n CA HA SAH sing 357 n n CB CG SAH sing 358 n n CB HB1 SAH sing 359 n n CB HB2 SAH sing 360 n n CG SD SAH sing 361 n n CG HG1 SAH sing 362 n n CG HG2 SAH sing 363 n n SD C5' SAH sing 364 n n C O SAH doub 365 n n C OXT SAH sing 366 n n OXT HXT SAH sing 367 n n C5' C4' SAH sing 368 n n C5' "H5'1" SAH sing 369 n n C5' "H5'2" SAH sing 370 n n C4' O4' SAH sing 371 n n C4' C3' SAH sing 372 n n C4' H4' SAH sing 373 n n O4' C1' SAH sing 374 n n C3' O3' SAH sing 375 n n C3' C2' SAH sing 376 n n C3' H3' SAH sing 377 n n O3' HO3' SAH sing 378 n n C2' O2' SAH sing 379 n n C2' C1' SAH sing 380 n n C2' H2' SAH sing 381 n n O2' HO2' SAH sing 382 n n C1' N9 SAH sing 383 n n C1' H1' SAH sing 384 n n N9 C8 SAH sing 385 n y N9 C4 SAH sing 386 n y C8 N7 SAH doub 387 n y C8 H8 SAH sing 388 n n N7 C5 SAH sing 389 n y C5 C6 SAH sing 390 n y C5 C4 SAH doub 391 n y C6 N6 SAH sing 392 n n C6 N1 SAH doub 393 n y N6 HN61 SAH sing 394 n n N6 HN62 SAH sing 395 n n N1 C2 SAH sing 396 n y C2 N3 SAH doub 397 n y C2 H2 SAH sing 398 n n N3 C4 SAH sing 399 n y # _atom_sites.entry_id 5U0T _atom_sites.fract_transf_matrix[1][1] 0.019679 _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] 0.014309 _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] 0.011806 _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 3 SAH SAH . C 3 7QM A 1 402 2 7QM LIG . D 4 MG A 1 403 1 MG MG . E 5 HOH A 1 501 183 HOH HOH . E 5 HOH A 2 502 210 HOH HOH . E 5 HOH A 3 503 123 HOH HOH . E 5 HOH A 4 504 196 HOH HOH . E 5 HOH A 5 505 135 HOH HOH . E 5 HOH A 6 506 38 HOH HOH . E 5 HOH A 7 507 129 HOH HOH . E 5 HOH A 8 508 147 HOH HOH . E 5 HOH A 9 509 132 HOH HOH . E 5 HOH A 10 510 151 HOH HOH . E 5 HOH A 11 511 55 HOH HOH . E 5 HOH A 12 512 158 HOH HOH . E 5 HOH A 13 513 4 HOH HOH . E 5 HOH A 14 514 52 HOH HOH . E 5 HOH A 15 515 64 HOH HOH . E 5 HOH A 16 516 84 HOH HOH . E 5 HOH A 17 517 79 HOH HOH . E 5 HOH A 18 518 17 HOH HOH . E 5 HOH A 19 519 105 HOH HOH . E 5 HOH A 20 520 20 HOH HOH . E 5 HOH A 21 521 44 HOH HOH . E 5 HOH A 22 522 59 HOH HOH . E 5 HOH A 23 523 2 HOH HOH . E 5 HOH A 24 524 8 HOH HOH . E 5 HOH A 25 525 13 HOH HOH . E 5 HOH A 26 526 185 HOH HOH . E 5 HOH A 27 527 18 HOH HOH . E 5 HOH A 28 528 62 HOH HOH . E 5 HOH A 29 529 178 HOH HOH . E 5 HOH A 30 530 49 HOH HOH . E 5 HOH A 31 531 65 HOH HOH . E 5 HOH A 32 532 16 HOH HOH . E 5 HOH A 33 533 29 HOH HOH . E 5 HOH A 34 534 54 HOH HOH . E 5 HOH A 35 535 41 HOH HOH . E 5 HOH A 36 536 25 HOH HOH . E 5 HOH A 37 537 208 HOH HOH . E 5 HOH A 38 538 87 HOH HOH . E 5 HOH A 39 539 90 HOH HOH . E 5 HOH A 40 540 89 HOH HOH . E 5 HOH A 41 541 26 HOH HOH . E 5 HOH A 42 542 12 HOH HOH . E 5 HOH A 43 543 126 HOH HOH . E 5 HOH A 44 544 73 HOH HOH . E 5 HOH A 45 545 3 HOH HOH . E 5 HOH A 46 546 15 HOH HOH . E 5 HOH A 47 547 66 HOH HOH . E 5 HOH A 48 548 21 HOH HOH . E 5 HOH A 49 549 133 HOH HOH . E 5 HOH A 50 550 68 HOH HOH . E 5 HOH A 51 551 6 HOH HOH . E 5 HOH A 52 552 61 HOH HOH . E 5 HOH A 53 553 67 HOH HOH . E 5 HOH A 54 554 85 HOH HOH . E 5 HOH A 55 555 53 HOH HOH . E 5 HOH A 56 556 203 HOH HOH . E 5 HOH A 57 557 184 HOH HOH . E 5 HOH A 58 558 9 HOH HOH . E 5 HOH A 59 559 51 HOH HOH . E 5 HOH A 60 560 11 HOH HOH . E 5 HOH A 61 561 134 HOH HOH . E 5 HOH A 62 562 77 HOH HOH . E 5 HOH A 63 563 176 HOH HOH . E 5 HOH A 64 564 10 HOH HOH . E 5 HOH A 65 565 34 HOH HOH . E 5 HOH A 66 566 57 HOH HOH . E 5 HOH A 67 567 60 HOH HOH . E 5 HOH A 68 568 83 HOH HOH . E 5 HOH A 69 569 5 HOH HOH . E 5 HOH A 70 570 50 HOH HOH . E 5 HOH A 71 571 35 HOH HOH . E 5 HOH A 72 572 19 HOH HOH . E 5 HOH A 73 573 159 HOH HOH . E 5 HOH A 74 574 28 HOH HOH . E 5 HOH A 75 575 94 HOH HOH . E 5 HOH A 76 576 197 HOH HOH . E 5 HOH A 77 577 31 HOH HOH . E 5 HOH A 78 578 168 HOH HOH . E 5 HOH A 79 579 86 HOH HOH . E 5 HOH A 80 580 30 HOH HOH . E 5 HOH A 81 581 39 HOH HOH . E 5 HOH A 82 582 43 HOH HOH . E 5 HOH A 83 583 175 HOH HOH . E 5 HOH A 84 584 75 HOH HOH . E 5 HOH A 85 585 22 HOH HOH . E 5 HOH A 86 586 58 HOH HOH . E 5 HOH A 87 587 7 HOH HOH . E 5 HOH A 88 588 88 HOH HOH . E 5 HOH A 89 589 120 HOH HOH . E 5 HOH A 90 590 40 HOH HOH . E 5 HOH A 91 591 37 HOH HOH . E 5 HOH A 92 592 72 HOH HOH . E 5 HOH A 93 593 205 HOH HOH . E 5 HOH A 94 594 63 HOH HOH . E 5 HOH A 95 595 14 HOH HOH . E 5 HOH A 96 596 122 HOH HOH . E 5 HOH A 97 597 117 HOH HOH . E 5 HOH A 98 598 71 HOH HOH . E 5 HOH A 99 599 103 HOH HOH . E 5 HOH A 100 600 24 HOH HOH . E 5 HOH A 101 601 96 HOH HOH . E 5 HOH A 102 602 112 HOH HOH . E 5 HOH A 103 603 95 HOH HOH . E 5 HOH A 104 604 98 HOH HOH . E 5 HOH A 105 605 56 HOH HOH . E 5 HOH A 106 606 190 HOH HOH . E 5 HOH A 107 607 174 HOH HOH . E 5 HOH A 108 608 48 HOH HOH . E 5 HOH A 109 609 156 HOH HOH . E 5 HOH A 110 610 200 HOH HOH . E 5 HOH A 111 611 27 HOH HOH . E 5 HOH A 112 612 115 HOH HOH . E 5 HOH A 113 613 74 HOH HOH . E 5 HOH A 114 614 111 HOH HOH . E 5 HOH A 115 615 106 HOH HOH . E 5 HOH A 116 616 69 HOH HOH . E 5 HOH A 117 617 164 HOH HOH . E 5 HOH A 118 618 121 HOH HOH . E 5 HOH A 119 619 173 HOH HOH . E 5 HOH A 120 620 91 HOH HOH . E 5 HOH A 121 621 139 HOH HOH . E 5 HOH A 122 622 169 HOH HOH . E 5 HOH A 123 623 116 HOH HOH . E 5 HOH A 124 624 157 HOH HOH . E 5 HOH A 125 625 104 HOH HOH . E 5 HOH A 126 626 81 HOH HOH . E 5 HOH A 127 627 33 HOH HOH . E 5 HOH A 128 628 102 HOH HOH . E 5 HOH A 129 629 92 HOH HOH . E 5 HOH A 130 630 36 HOH HOH . E 5 HOH A 131 631 46 HOH HOH . E 5 HOH A 132 632 186 HOH HOH . E 5 HOH A 133 633 170 HOH HOH . E 5 HOH A 134 634 152 HOH HOH . E 5 HOH A 135 635 182 HOH HOH . E 5 HOH A 136 636 149 HOH HOH . E 5 HOH A 137 637 165 HOH HOH . E 5 HOH A 138 638 42 HOH HOH . E 5 HOH A 139 639 150 HOH HOH . E 5 HOH A 140 640 154 HOH HOH . E 5 HOH A 141 641 119 HOH HOH . E 5 HOH A 142 642 1 HOH HOH . E 5 HOH A 143 643 131 HOH HOH . E 5 HOH A 144 644 80 HOH HOH . E 5 HOH A 145 645 32 HOH HOH . E 5 HOH A 146 646 206 HOH HOH . E 5 HOH A 147 647 127 HOH HOH . E 5 HOH A 148 648 130 HOH HOH . E 5 HOH A 149 649 191 HOH HOH . E 5 HOH A 150 650 211 HOH HOH . E 5 HOH A 151 651 70 HOH HOH . E 5 HOH A 152 652 198 HOH HOH . E 5 HOH A 153 653 209 HOH HOH . E 5 HOH A 154 654 194 HOH HOH . E 5 HOH A 155 655 101 HOH HOH . E 5 HOH A 156 656 155 HOH HOH . E 5 HOH A 157 657 76 HOH HOH . E 5 HOH A 158 658 125 HOH HOH . E 5 HOH A 159 659 118 HOH HOH . E 5 HOH A 160 660 207 HOH HOH . E 5 HOH A 161 661 82 HOH HOH . E 5 HOH A 162 662 179 HOH HOH . E 5 HOH A 163 663 212 HOH HOH . E 5 HOH A 164 664 99 HOH HOH . E 5 HOH A 165 665 180 HOH HOH . E 5 HOH A 166 666 142 HOH HOH . E 5 HOH A 167 667 187 HOH HOH . E 5 HOH A 168 668 193 HOH HOH . E 5 HOH A 169 669 166 HOH HOH . E 5 HOH A 170 670 23 HOH HOH . E 5 HOH A 171 671 100 HOH HOH . E 5 HOH A 172 672 144 HOH HOH . E 5 HOH A 173 673 172 HOH HOH . E 5 HOH A 174 674 47 HOH HOH . E 5 HOH A 175 675 201 HOH HOH . E 5 HOH A 176 676 146 HOH HOH . E 5 HOH A 177 677 199 HOH HOH . E 5 HOH A 178 678 107 HOH HOH . E 5 HOH A 179 679 93 HOH HOH . E 5 HOH A 180 680 167 HOH HOH . E 5 HOH A 181 681 181 HOH HOH . E 5 HOH A 182 682 163 HOH HOH . E 5 HOH A 183 683 138 HOH HOH . E 5 HOH A 184 684 171 HOH HOH . E 5 HOH A 185 685 189 HOH HOH . E 5 HOH A 186 686 128 HOH HOH . E 5 HOH A 187 687 145 HOH HOH . E 5 HOH A 188 688 78 HOH HOH . E 5 HOH A 189 689 45 HOH HOH . E 5 HOH A 190 690 177 HOH HOH . E 5 HOH A 191 691 204 HOH HOH . E 5 HOH A 192 692 195 HOH HOH . E 5 HOH A 193 693 188 HOH HOH . E 5 HOH A 194 694 160 HOH HOH . E 5 HOH A 195 695 161 HOH HOH . E 5 HOH A 196 696 213 HOH HOH . E 5 HOH A 197 697 192 HOH HOH . E 5 HOH A 198 698 143 HOH HOH . E 5 HOH A 199 699 162 HOH HOH . E 5 HOH A 200 700 202 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 -12.339 -4.308 9.32 1 14.51 ? N SAH 401 A 1 HETATM 2 C CA SAH . . . B 2 -11.714 -3.08 9.674 1 15.88 ? CA SAH 401 A 1 HETATM 3 C CB SAH . . . B 2 -12.639 -1.901 9.495 1 16.69 ? CB SAH 401 A 1 HETATM 4 C CG SAH . . . B 2 -13.797 -1.923 10.483 1 15.21 ? CG SAH 401 A 1 HETATM 5 S SD SAH . . . B 2 -14.773 -0.432 10.325 1 15.72 ? SD SAH 401 A 1 HETATM 6 C C SAH . . . B 2 -11.256 -3.198 11.121 1 16.05 ? C SAH 401 A 1 HETATM 7 O O SAH . . . B 2 -10.509 -2.307 11.626 1 19.5 ? O SAH 401 A 1 HETATM 8 O OXT SAH . . . B 2 -11.608 -4.209 11.802 1 14.96 ? OXT SAH 401 A 1 HETATM 9 C C5' SAH . . . B 2 -16.3 -0.819 9.537 1 14.3 ? C5' SAH 401 A 1 HETATM 10 C C4' SAH . . . B 2 -16.252 -0.65 8.048 1 13.53 ? C4' SAH 401 A 1 HETATM 11 O O4' SAH . . . B 2 -17.545 -0.966 7.497 1 12.66 ? O4' SAH 401 A 1 HETATM 12 C C3' SAH . . . B 2 -15.976 0.759 7.602 1 13.53 ? C3' SAH 401 A 1 HETATM 13 O O3' SAH . . . B 2 -14.773 0.826 6.828 1 12.54 ? O3' SAH 401 A 1 HETATM 14 C C2' SAH . . . B 2 -17.158 1.124 6.764 1 15.84 ? C2' SAH 401 A 1 HETATM 15 O O2' SAH . . . B 2 -16.827 1.935 5.658 1 13.2 ? O2' SAH 401 A 1 HETATM 16 C C1' SAH . . . B 2 -17.683 -0.205 6.304 1 12.54 ? C1' SAH 401 A 1 HETATM 17 N N9 SAH . . . B 2 -18.995 -0.094 5.792 1 12.32 ? N9 SAH 401 A 1 HETATM 18 C C8 SAH . . . B 2 -19.868 0.773 6.275 1 16.98 ? C8 SAH 401 A 1 HETATM 19 N N7 SAH . . . B 2 -21.034 0.687 5.557 1 15.37 ? N7 SAH 401 A 1 HETATM 20 C C5 SAH . . . B 2 -20.764 -0.332 4.573 1 11.53 ? C5 SAH 401 A 1 HETATM 21 C C6 SAH . . . B 2 -21.389 -1.047 3.45 1 14.15 ? C6 SAH 401 A 1 HETATM 22 N N6 SAH . . . B 2 -22.64 -0.573 2.937 1 13.11 ? N6 SAH 401 A 1 HETATM 23 N N1 SAH . . . B 2 -20.622 -1.927 2.658 1 15.94 ? N1 SAH 401 A 1 HETATM 24 C C2 SAH . . . B 2 -19.294 -2.151 2.83 1 17.63 ? C2 SAH 401 A 1 HETATM 25 N N3 SAH . . . B 2 -18.893 -1.732 3.999 1 13.97 ? N3 SAH 401 A 1 HETATM 26 C C4 SAH . . . B 2 -19.44 -0.822 4.733 1 15.38 ? C4 SAH 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 241 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 26 #