data_5U4T # _model_server_result.job_id vSsLq9h3qJTB88PwBCwPHA _model_server_result.datetime_utc '2024-11-13 20:43:40' _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 5u4t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":414}' # _entry.id 5U4T # _exptl.entry_id 5U4T _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 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 5U4T _cell.length_a 66.62 _cell.length_b 66.782 _cell.length_c 69.123 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5U4T _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,F,G,H,I,J,K,L,M,N,O,P,Q _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 3 _struct_asym.id O _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 277 n n N HN1 SAH sing 278 n n N HN2 SAH sing 279 n n CA CB SAH sing 280 n n CA C SAH sing 281 n n CA HA SAH sing 282 n n CB CG SAH sing 283 n n CB HB1 SAH sing 284 n n CB HB2 SAH sing 285 n n CG SD SAH sing 286 n n CG HG1 SAH sing 287 n n CG HG2 SAH sing 288 n n SD C5' SAH sing 289 n n C O SAH doub 290 n n C OXT SAH sing 291 n n OXT HXT SAH sing 292 n n C5' C4' SAH sing 293 n n C5' "H5'1" SAH sing 294 n n C5' "H5'2" SAH sing 295 n n C4' O4' SAH sing 296 n n C4' C3' SAH sing 297 n n C4' H4' SAH sing 298 n n O4' C1' SAH sing 299 n n C3' O3' SAH sing 300 n n C3' C2' SAH sing 301 n n C3' H3' SAH sing 302 n n O3' HO3' SAH sing 303 n n C2' O2' SAH sing 304 n n C2' C1' SAH sing 305 n n C2' H2' SAH sing 306 n n O2' HO2' SAH sing 307 n n C1' N9 SAH sing 308 n n C1' H1' SAH sing 309 n n N9 C8 SAH sing 310 n y N9 C4 SAH sing 311 n y C8 N7 SAH doub 312 n y C8 H8 SAH sing 313 n n N7 C5 SAH sing 314 n y C5 C6 SAH sing 315 n y C5 C4 SAH doub 316 n y C6 N6 SAH sing 317 n n C6 N1 SAH doub 318 n y N6 HN61 SAH sing 319 n n N6 HN62 SAH sing 320 n n N1 C2 SAH sing 321 n y C2 N3 SAH doub 322 n y C2 H2 SAH sing 323 n n N3 C4 SAH sing 324 n y # _atom_sites.entry_id 5U4T _atom_sites.fract_transf_matrix[1][1] 0.015011 _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] 0.014974 _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] 0.014467 _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 IOD A 1 401 1 IOD IOD . C 2 IOD A 1 402 2 IOD IOD . D 2 IOD A 1 403 5 IOD IOD . E 2 IOD A 1 404 7 IOD IOD . F 2 IOD A 1 405 22 IOD IOD . G 2 IOD A 1 406 23 IOD IOD . H 2 IOD A 1 407 24 IOD IOD . I 2 IOD A 1 408 25 IOD IOD . J 2 IOD A 1 409 26 IOD IOD . K 2 IOD A 1 410 27 IOD IOD . L 2 IOD A 1 411 29 IOD IOD . M 2 IOD A 1 412 30 IOD IOD . N 2 IOD A 1 413 32 IOD IOD . O 3 SAH A 1 414 1 SAH SAH . P 4 TRS A 1 415 1 TRS TRS . Q 5 HOH A 1 501 151 HOH HOH . Q 5 HOH A 2 502 110 HOH HOH . Q 5 HOH A 3 503 90 HOH HOH . Q 5 HOH A 4 504 111 HOH HOH . Q 5 HOH A 5 505 157 HOH HOH . Q 5 HOH A 6 506 60 HOH HOH . Q 5 HOH A 7 507 172 HOH HOH . Q 5 HOH A 8 508 169 HOH HOH . Q 5 HOH A 9 509 100 HOH HOH . Q 5 HOH A 10 510 89 HOH HOH . Q 5 HOH A 11 511 52 HOH HOH . Q 5 HOH A 12 512 154 HOH HOH . Q 5 HOH A 13 513 70 HOH HOH . Q 5 HOH A 14 514 94 HOH HOH . Q 5 HOH A 15 515 45 HOH HOH . Q 5 HOH A 16 516 97 HOH HOH . Q 5 HOH A 17 517 38 HOH HOH . Q 5 HOH A 18 518 69 HOH HOH . Q 5 HOH A 19 519 55 HOH HOH . Q 5 HOH A 20 520 14 HOH HOH . Q 5 HOH A 21 521 73 HOH HOH . Q 5 HOH A 22 522 36 HOH HOH . Q 5 HOH A 23 523 77 HOH HOH . Q 5 HOH A 24 524 49 HOH HOH . Q 5 HOH A 25 525 59 HOH HOH . Q 5 HOH A 26 526 131 HOH HOH . Q 5 HOH A 27 527 22 HOH HOH . Q 5 HOH A 28 528 71 HOH HOH . Q 5 HOH A 29 529 75 HOH HOH . Q 5 HOH A 30 530 99 HOH HOH . Q 5 HOH A 31 531 3 HOH HOH . Q 5 HOH A 32 532 23 HOH HOH . Q 5 HOH A 33 533 51 HOH HOH . Q 5 HOH A 34 534 76 HOH HOH . Q 5 HOH A 35 535 16 HOH HOH . Q 5 HOH A 36 536 64 HOH HOH . Q 5 HOH A 37 537 13 HOH HOH . Q 5 HOH A 38 538 88 HOH HOH . Q 5 HOH A 39 539 68 HOH HOH . Q 5 HOH A 40 540 11 HOH HOH . Q 5 HOH A 41 541 17 HOH HOH . Q 5 HOH A 42 542 87 HOH HOH . Q 5 HOH A 43 543 57 HOH HOH . Q 5 HOH A 44 544 129 HOH HOH . Q 5 HOH A 45 545 58 HOH HOH . Q 5 HOH A 46 546 12 HOH HOH . Q 5 HOH A 47 547 15 HOH HOH . Q 5 HOH A 48 548 92 HOH HOH . Q 5 HOH A 49 549 127 HOH HOH . Q 5 HOH A 50 550 134 HOH HOH . Q 5 HOH A 51 551 26 HOH HOH . Q 5 HOH A 52 552 120 HOH HOH . Q 5 HOH A 53 553 46 HOH HOH . Q 5 HOH A 54 554 133 HOH HOH . Q 5 HOH A 55 555 91 HOH HOH . Q 5 HOH A 56 556 98 HOH HOH . Q 5 HOH A 57 557 153 HOH HOH . Q 5 HOH A 58 558 50 HOH HOH . Q 5 HOH A 59 559 106 HOH HOH . Q 5 HOH A 60 560 93 HOH HOH . Q 5 HOH A 61 561 147 HOH HOH . Q 5 HOH A 62 562 6 HOH HOH . Q 5 HOH A 63 563 142 HOH HOH . Q 5 HOH A 64 564 28 HOH HOH . Q 5 HOH A 65 565 10 HOH HOH . Q 5 HOH A 66 566 125 HOH HOH . Q 5 HOH A 67 567 79 HOH HOH . Q 5 HOH A 68 568 2 HOH HOH . Q 5 HOH A 69 569 112 HOH HOH . Q 5 HOH A 70 570 19 HOH HOH . Q 5 HOH A 71 571 80 HOH HOH . Q 5 HOH A 72 572 81 HOH HOH . Q 5 HOH A 73 573 47 HOH HOH . Q 5 HOH A 74 574 31 HOH HOH . Q 5 HOH A 75 575 84 HOH HOH . Q 5 HOH A 76 576 34 HOH HOH . Q 5 HOH A 77 577 121 HOH HOH . Q 5 HOH A 78 578 5 HOH HOH . Q 5 HOH A 79 579 105 HOH HOH . Q 5 HOH A 80 580 37 HOH HOH . Q 5 HOH A 81 581 20 HOH HOH . Q 5 HOH A 82 582 126 HOH HOH . Q 5 HOH A 83 583 117 HOH HOH . Q 5 HOH A 84 584 33 HOH HOH . Q 5 HOH A 85 585 18 HOH HOH . Q 5 HOH A 86 586 1 HOH HOH . Q 5 HOH A 87 587 48 HOH HOH . Q 5 HOH A 88 588 44 HOH HOH . Q 5 HOH A 89 589 65 HOH HOH . Q 5 HOH A 90 590 21 HOH HOH . Q 5 HOH A 91 591 32 HOH HOH . Q 5 HOH A 92 592 123 HOH HOH . Q 5 HOH A 93 593 39 HOH HOH . Q 5 HOH A 94 594 173 HOH HOH . Q 5 HOH A 95 595 7 HOH HOH . Q 5 HOH A 96 596 109 HOH HOH . Q 5 HOH A 97 597 152 HOH HOH . Q 5 HOH A 98 598 72 HOH HOH . Q 5 HOH A 99 599 27 HOH HOH . Q 5 HOH A 100 600 9 HOH HOH . Q 5 HOH A 101 601 82 HOH HOH . Q 5 HOH A 102 602 149 HOH HOH . Q 5 HOH A 103 603 30 HOH HOH . Q 5 HOH A 104 604 155 HOH HOH . Q 5 HOH A 105 605 163 HOH HOH . Q 5 HOH A 106 606 130 HOH HOH . Q 5 HOH A 107 607 146 HOH HOH . Q 5 HOH A 108 608 78 HOH HOH . Q 5 HOH A 109 609 166 HOH HOH . Q 5 HOH A 110 610 42 HOH HOH . Q 5 HOH A 111 611 54 HOH HOH . Q 5 HOH A 112 612 8 HOH HOH . Q 5 HOH A 113 613 122 HOH HOH . Q 5 HOH A 114 614 24 HOH HOH . Q 5 HOH A 115 615 115 HOH HOH . Q 5 HOH A 116 616 61 HOH HOH . Q 5 HOH A 117 617 95 HOH HOH . Q 5 HOH A 118 618 35 HOH HOH . Q 5 HOH A 119 619 4 HOH HOH . Q 5 HOH A 120 620 53 HOH HOH . Q 5 HOH A 121 621 29 HOH HOH . Q 5 HOH A 122 622 164 HOH HOH . Q 5 HOH A 123 623 62 HOH HOH . Q 5 HOH A 124 624 43 HOH HOH . Q 5 HOH A 125 625 74 HOH HOH . Q 5 HOH A 126 626 143 HOH HOH . Q 5 HOH A 127 627 113 HOH HOH . Q 5 HOH A 128 628 63 HOH HOH . Q 5 HOH A 129 629 40 HOH HOH . Q 5 HOH A 130 630 67 HOH HOH . Q 5 HOH A 131 631 86 HOH HOH . Q 5 HOH A 132 632 165 HOH HOH . Q 5 HOH A 133 633 139 HOH HOH . Q 5 HOH A 134 634 25 HOH HOH . Q 5 HOH A 135 635 104 HOH HOH . Q 5 HOH A 136 636 174 HOH HOH . Q 5 HOH A 137 637 103 HOH HOH . Q 5 HOH A 138 638 162 HOH HOH . Q 5 HOH A 139 639 170 HOH HOH . Q 5 HOH A 140 640 101 HOH HOH . Q 5 HOH A 141 641 108 HOH HOH . Q 5 HOH A 142 642 148 HOH HOH . Q 5 HOH A 143 643 41 HOH HOH . Q 5 HOH A 144 644 135 HOH HOH . Q 5 HOH A 145 645 140 HOH HOH . Q 5 HOH A 146 646 161 HOH HOH . Q 5 HOH A 147 647 156 HOH HOH . Q 5 HOH A 148 648 144 HOH HOH . Q 5 HOH A 149 649 175 HOH HOH . Q 5 HOH A 150 650 168 HOH HOH . Q 5 HOH A 151 651 158 HOH HOH . Q 5 HOH A 152 652 171 HOH HOH . Q 5 HOH A 153 653 118 HOH HOH . Q 5 HOH A 154 654 145 HOH HOH . Q 5 HOH A 155 655 102 HOH HOH . Q 5 HOH A 156 656 159 HOH HOH . Q 5 HOH A 157 657 85 HOH HOH . Q 5 HOH A 158 658 137 HOH HOH . Q 5 HOH A 159 659 114 HOH HOH . Q 5 HOH A 160 660 141 HOH HOH . Q 5 HOH A 161 661 119 HOH HOH . Q 5 HOH A 162 662 167 HOH HOH . Q 5 HOH A 163 663 132 HOH HOH . Q 5 HOH A 164 664 66 HOH HOH . Q 5 HOH A 165 665 138 HOH HOH . Q 5 HOH A 166 666 107 HOH HOH . Q 5 HOH A 167 667 136 HOH HOH . Q 5 HOH A 168 668 128 HOH HOH . Q 5 HOH A 169 669 56 HOH HOH . Q 5 HOH A 170 670 160 HOH HOH . Q 5 HOH A 171 671 150 HOH HOH . Q 5 HOH A 172 672 124 HOH HOH . Q 5 HOH A 173 673 83 HOH HOH . Q 5 HOH A 174 674 96 HOH HOH . Q 5 HOH A 175 675 116 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 . . . O 3 20.586 53.101 39.582 1 15.95 ? N SAH 414 A 1 HETATM 2 C CA SAH . . . O 3 21.518 52.363 38.719 1 14.51 ? CA SAH 414 A 1 HETATM 3 C CB SAH . . . O 3 21.92 53.086 37.419 1 15.86 ? CB SAH 414 A 1 HETATM 4 C CG SAH . . . O 3 22.243 54.573 37.493 1 16.52 ? CG SAH 414 A 1 HETATM 5 S SD SAH . . . O 3 23.163 55.105 36.03 1 16.42 ? SD SAH 414 A 1 HETATM 6 C C SAH . . . O 3 22.783 52.136 39.509 1 19.86 ? C SAH 414 A 1 HETATM 7 O O SAH . . . O 3 23.641 51.322 39.136 1 15.32 ? O SAH 414 A 1 HETATM 8 O OXT SAH . . . O 3 22.943 52.821 40.524 1 20.22 ? OXT SAH 414 A 1 HETATM 9 C C5' SAH . . . O 3 21.958 56.362 35.529 1 11.96 ? C5' SAH 414 A 1 HETATM 10 C C4' SAH . . . O 3 20.644 55.836 34.969 1 13.35 ? C4' SAH 414 A 1 HETATM 11 O O4' SAH . . . O 3 19.818 56.935 34.584 1 19.24 ? O4' SAH 414 A 1 HETATM 12 C C3' SAH . . . O 3 20.838 54.984 33.728 1 15.74 ? C3' SAH 414 A 1 HETATM 13 O O3' SAH . . . O 3 20.217 53.733 33.913 1 14.65 ? O3' SAH 414 A 1 HETATM 14 C C2' SAH . . . O 3 20.146 55.788 32.632 1 10.44 ? C2' SAH 414 A 1 HETATM 15 O O2' SAH . . . O 3 19.602 54.984 31.632 1 14.12 ? O2' SAH 414 A 1 HETATM 16 C C1' SAH . . . O 3 19.116 56.581 33.418 1 12.61 ? C1' SAH 414 A 1 HETATM 17 N N9 SAH . . . O 3 18.593 57.745 32.677 1 14.56 ? N9 SAH 414 A 1 HETATM 18 C C8 SAH . . . O 3 19.221 58.616 31.82 1 14.19 ? C8 SAH 414 A 1 HETATM 19 N N7 SAH . . . O 3 18.312 59.519 31.367 1 11.62 ? N7 SAH 414 A 1 HETATM 20 C C5 SAH . . . O 3 17.119 59.221 31.916 1 15.93 ? C5 SAH 414 A 1 HETATM 21 C C6 SAH . . . O 3 15.853 59.793 31.837 1 20.81 ? C6 SAH 414 A 1 HETATM 22 N N6 SAH . . . O 3 15.582 60.851 31.091 1 17.77 ? N6 SAH 414 A 1 HETATM 23 N N1 SAH . . . O 3 14.844 59.239 32.576 1 15.62 ? N1 SAH 414 A 1 HETATM 24 C C2 SAH . . . O 3 15.065 58.156 33.394 1 18.4 ? C2 SAH 414 A 1 HETATM 25 N N3 SAH . . . O 3 16.309 57.587 33.478 1 13.4 ? N3 SAH 414 A 1 HETATM 26 C C4 SAH . . . O 3 17.304 58.116 32.749 1 14.9 ? C4 SAH 414 A 1 HETATM 27 H H2 SAH . . . O 3 14.243 57.747 33.982 1 22.08 ? H2 SAH 414 A 1 HETATM 28 H HN1 SAH . . . O 3 19.924 53.453 39.16 1 19.14 ? HN1 SAH 414 A 1 HETATM 29 H HN2 SAH . . . O 3 20.548 52.806 40.389 1 19.14 ? HN2 SAH 414 A 1 HETATM 30 H HA SAH . . . O 3 21.135 51.491 38.488 1 17.41 ? HA SAH 414 A 1 HETATM 31 H HB1 SAH . . . O 3 21.111 52.95 36.702 1 19.04 ? HB1 SAH 414 A 1 HETATM 32 H HB2 SAH . . . O 3 22.79 52.571 37.011 1 19.04 ? HB2 SAH 414 A 1 HETATM 33 H HG1 SAH . . . O 3 22.833 54.774 38.387 1 19.82 ? HG1 SAH 414 A 1 HETATM 34 H HG2 SAH . . . O 3 21.316 55.143 37.567 1 19.82 ? HG2 SAH 414 A 1 HETATM 35 H "H5'1" SAH . . . O 3 22.42 57.003 34.778 1 14.35 ? "H5'1" SAH 414 A 1 HETATM 36 H "H5'2" SAH . . . O 3 21.737 56.991 36.391 1 14.35 ? "H5'2" SAH 414 A 1 HETATM 37 H H4' SAH . . . O 3 20.145 55.241 35.734 1 16.02 ? H4' SAH 414 A 1 HETATM 38 H H3' SAH . . . O 3 21.9 54.877 33.506 1 18.89 ? H3' SAH 414 A 1 HETATM 39 H HO3' SAH . . . O 3 19.465 53.646 33.291 1 17.58 ? HO3' SAH 414 A 1 HETATM 40 H H2' SAH . . . O 3 20.866 56.482 32.199 1 12.53 ? H2' SAH 414 A 1 HETATM 41 H HO2' SAH . . . O 3 18.628 55.085 31.625 1 16.95 ? HO2' SAH 414 A 1 HETATM 42 H H1' SAH . . . O 3 18.293 55.914 33.676 1 15.14 ? H1' SAH 414 A 1 HETATM 43 H H8 SAH . . . O 3 20.276 58.587 31.548 1 17.03 ? H8 SAH 414 A 1 HETATM 44 H HN61 SAH . . . O 3 16.316 61.284 30.539 1 21.32 ? HN61 SAH 414 A 1 HETATM 45 H HN62 SAH . . . O 3 14.641 61.231 31.072 1 21.32 ? HN62 SAH 414 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 45 #