data_5YN8 # _model_server_result.job_id FWWKVIo1hIiQZmOKkHnCrg _model_server_result.datetime_utc '2024-11-15 00:00:08' _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 5yn8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5YN8 # _exptl.entry_id 5YN8 _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 5YN8 _cell.length_a 66.399 _cell.length_b 70.233 _cell.length_c 119.203 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YN8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 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 _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 C _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 disulf ? disulf1 B SG CYS 117 B CYS 117 1_555 B SG CYS 128 B CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.894 ? metalc ? metalc1 B SG CYS 74 B CYS 74 1_555 D ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc2 B SG CYS 77 B CYS 77 1_555 D ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc3 B NE2 HIS 83 B HIS 83 1_555 D ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.848 ? metalc ? metalc4 B SG CYS 90 B CYS 90 1_555 D ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc5 B SG CYS 117 B CYS 117 1_555 E ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc6 B SG CYS 120 B CYS 120 1_555 E ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc7 B SG CYS 128 B CYS 128 1_555 E ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type non-polymer _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 5YN8 _atom_sites.fract_transf_matrix[1][1] 0.01506 _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] 0.014238 _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] 0.008389 _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 3 SAH A 1 401 401 SAH SAH . D 4 ZN B 1 201 998 ZN ZN . E 4 ZN B 1 202 999 ZN ZN . F 5 HOH A 1 501 59 HOH HOH . F 5 HOH A 2 502 83 HOH HOH . F 5 HOH A 3 503 150 HOH HOH . F 5 HOH A 4 504 27 HOH HOH . F 5 HOH A 5 505 108 HOH HOH . F 5 HOH A 6 506 84 HOH HOH . F 5 HOH A 7 507 58 HOH HOH . F 5 HOH A 8 508 12 HOH HOH . F 5 HOH A 9 509 32 HOH HOH . F 5 HOH A 10 510 149 HOH HOH . F 5 HOH A 11 511 52 HOH HOH . F 5 HOH A 12 512 49 HOH HOH . F 5 HOH A 13 513 69 HOH HOH . F 5 HOH A 14 514 8 HOH HOH . F 5 HOH A 15 515 42 HOH HOH . F 5 HOH A 16 516 82 HOH HOH . F 5 HOH A 17 517 40 HOH HOH . F 5 HOH A 18 518 92 HOH HOH . F 5 HOH A 19 519 53 HOH HOH . F 5 HOH A 20 520 118 HOH HOH . F 5 HOH A 21 521 61 HOH HOH . F 5 HOH A 22 522 117 HOH HOH . F 5 HOH A 23 523 45 HOH HOH . F 5 HOH A 24 524 5 HOH HOH . F 5 HOH A 25 525 11 HOH HOH . F 5 HOH A 26 526 37 HOH HOH . F 5 HOH A 27 527 10 HOH HOH . F 5 HOH A 28 528 39 HOH HOH . F 5 HOH A 29 529 20 HOH HOH . F 5 HOH A 30 530 19 HOH HOH . F 5 HOH A 31 531 147 HOH HOH . F 5 HOH A 32 532 1 HOH HOH . F 5 HOH A 33 533 50 HOH HOH . F 5 HOH A 34 534 25 HOH HOH . F 5 HOH A 35 535 110 HOH HOH . F 5 HOH A 36 536 138 HOH HOH . F 5 HOH A 37 537 65 HOH HOH . F 5 HOH A 38 538 33 HOH HOH . F 5 HOH A 39 539 70 HOH HOH . F 5 HOH A 40 540 86 HOH HOH . F 5 HOH A 41 541 85 HOH HOH . F 5 HOH A 42 542 15 HOH HOH . F 5 HOH A 43 543 133 HOH HOH . F 5 HOH A 44 544 2 HOH HOH . F 5 HOH A 45 545 135 HOH HOH . F 5 HOH A 46 546 14 HOH HOH . F 5 HOH A 47 547 79 HOH HOH . F 5 HOH A 48 548 111 HOH HOH . F 5 HOH A 49 549 141 HOH HOH . F 5 HOH A 50 550 120 HOH HOH . F 5 HOH A 51 551 72 HOH HOH . F 5 HOH A 52 552 99 HOH HOH . F 5 HOH A 53 553 34 HOH HOH . F 5 HOH A 54 554 87 HOH HOH . F 5 HOH A 55 555 125 HOH HOH . F 5 HOH A 56 556 48 HOH HOH . F 5 HOH A 57 557 6 HOH HOH . F 5 HOH A 58 558 24 HOH HOH . F 5 HOH A 59 559 13 HOH HOH . F 5 HOH A 60 560 139 HOH HOH . F 5 HOH A 61 561 105 HOH HOH . F 5 HOH A 62 562 18 HOH HOH . F 5 HOH A 63 563 71 HOH HOH . F 5 HOH A 64 564 22 HOH HOH . F 5 HOH A 65 565 104 HOH HOH . F 5 HOH A 66 566 140 HOH HOH . F 5 HOH A 67 567 153 HOH HOH . F 5 HOH A 68 568 137 HOH HOH . F 5 HOH A 69 569 3 HOH HOH . F 5 HOH A 70 570 106 HOH HOH . F 5 HOH A 71 571 96 HOH HOH . F 5 HOH A 72 572 35 HOH HOH . F 5 HOH A 73 573 4 HOH HOH . F 5 HOH A 74 574 68 HOH HOH . F 5 HOH A 75 575 29 HOH HOH . F 5 HOH A 76 576 41 HOH HOH . F 5 HOH A 77 577 9 HOH HOH . F 5 HOH A 78 578 62 HOH HOH . F 5 HOH A 79 579 28 HOH HOH . F 5 HOH A 80 580 26 HOH HOH . F 5 HOH A 81 581 21 HOH HOH . F 5 HOH A 82 582 129 HOH HOH . F 5 HOH A 83 583 36 HOH HOH . F 5 HOH A 84 584 101 HOH HOH . F 5 HOH A 85 585 46 HOH HOH . F 5 HOH A 86 586 43 HOH HOH . F 5 HOH A 87 587 89 HOH HOH . F 5 HOH A 88 588 161 HOH HOH . F 5 HOH A 89 589 60 HOH HOH . F 5 HOH A 90 590 78 HOH HOH . F 5 HOH A 91 591 131 HOH HOH . F 5 HOH A 92 592 17 HOH HOH . F 5 HOH A 93 593 102 HOH HOH . F 5 HOH A 94 594 63 HOH HOH . F 5 HOH A 95 595 155 HOH HOH . F 5 HOH A 96 596 38 HOH HOH . F 5 HOH A 97 597 7 HOH HOH . F 5 HOH A 98 598 152 HOH HOH . F 5 HOH A 99 599 75 HOH HOH . F 5 HOH A 100 600 123 HOH HOH . F 5 HOH A 101 601 172 HOH HOH . F 5 HOH A 102 602 23 HOH HOH . F 5 HOH A 103 603 134 HOH HOH . F 5 HOH A 104 604 30 HOH HOH . F 5 HOH A 105 605 95 HOH HOH . F 5 HOH A 106 606 55 HOH HOH . F 5 HOH A 107 607 64 HOH HOH . F 5 HOH A 108 608 88 HOH HOH . F 5 HOH A 109 609 130 HOH HOH . F 5 HOH A 110 610 112 HOH HOH . F 5 HOH A 111 611 166 HOH HOH . F 5 HOH A 112 612 97 HOH HOH . F 5 HOH A 113 613 157 HOH HOH . F 5 HOH A 114 614 167 HOH HOH . F 5 HOH A 115 615 91 HOH HOH . F 5 HOH A 116 616 56 HOH HOH . F 5 HOH A 117 617 81 HOH HOH . F 5 HOH A 118 618 115 HOH HOH . F 5 HOH A 119 619 109 HOH HOH . F 5 HOH A 120 620 169 HOH HOH . F 5 HOH A 121 621 51 HOH HOH . F 5 HOH A 122 622 128 HOH HOH . F 5 HOH A 123 623 31 HOH HOH . F 5 HOH A 124 624 175 HOH HOH . F 5 HOH A 125 625 156 HOH HOH . F 5 HOH A 126 626 173 HOH HOH . F 5 HOH A 127 627 98 HOH HOH . F 5 HOH A 128 628 160 HOH HOH . F 5 HOH A 129 629 114 HOH HOH . F 5 HOH A 130 630 103 HOH HOH . F 5 HOH A 131 631 132 HOH HOH . F 5 HOH A 132 632 170 HOH HOH . F 5 HOH A 133 633 74 HOH HOH . F 5 HOH A 134 634 159 HOH HOH . F 5 HOH A 135 635 126 HOH HOH . F 5 HOH A 136 636 113 HOH HOH . F 5 HOH A 137 637 148 HOH HOH . F 5 HOH A 138 638 162 HOH HOH . F 5 HOH A 139 639 163 HOH HOH . F 5 HOH A 140 640 174 HOH HOH . F 5 HOH A 141 641 171 HOH HOH . F 5 HOH A 142 642 66 HOH HOH . F 5 HOH A 143 643 94 HOH HOH . F 5 HOH A 144 644 54 HOH HOH . F 5 HOH A 145 645 164 HOH HOH . F 5 HOH A 146 646 93 HOH HOH . F 5 HOH A 147 647 151 HOH HOH . F 5 HOH A 148 648 122 HOH HOH . F 5 HOH A 149 649 107 HOH HOH . F 5 HOH A 150 650 121 HOH HOH . F 5 HOH A 151 651 90 HOH HOH . F 5 HOH A 152 652 47 HOH HOH . F 5 HOH A 153 653 44 HOH HOH . F 5 HOH A 154 654 116 HOH HOH . F 5 HOH A 155 655 154 HOH HOH . F 5 HOH A 156 656 158 HOH HOH . F 5 HOH A 157 657 124 HOH HOH . F 5 HOH A 158 658 165 HOH HOH . G 5 HOH B 1 301 73 HOH HOH . G 5 HOH B 2 302 67 HOH HOH . G 5 HOH B 3 303 100 HOH HOH . G 5 HOH B 4 304 77 HOH HOH . G 5 HOH B 5 305 80 HOH HOH . G 5 HOH B 6 306 119 HOH HOH . G 5 HOH B 7 307 142 HOH HOH . G 5 HOH B 8 308 57 HOH HOH . G 5 HOH B 9 309 76 HOH HOH . G 5 HOH B 10 310 168 HOH HOH . G 5 HOH B 11 311 16 HOH HOH . G 5 HOH B 12 312 143 HOH HOH . G 5 HOH B 13 313 146 HOH HOH . G 5 HOH B 14 314 144 HOH HOH . G 5 HOH B 15 315 145 HOH HOH . G 5 HOH B 16 316 136 HOH HOH . G 5 HOH B 17 317 127 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 . . . C 3 66.877 85.708 150.408 1 38.88 ? N SAH 401 A 1 HETATM 2 C CA SAH . . . C 3 66.824 84.421 149.7 1 41.37 ? CA SAH 401 A 1 HETATM 3 C CB SAH . . . C 3 66.784 84.634 148.177 1 38.26 ? CB SAH 401 A 1 HETATM 4 C CG SAH . . . C 3 65.559 85.508 147.837 1 39.9 ? CG SAH 401 A 1 HETATM 5 S SD SAH . . . C 3 65.296 85.736 146.036 1 39.56 ? SD SAH 401 A 1 HETATM 6 C C SAH . . . C 3 68.042 83.579 150.128 1 45.99 ? C SAH 401 A 1 HETATM 7 O O SAH . . . C 3 68.554 82.849 149.252 1 46.91 ? O SAH 401 A 1 HETATM 8 O OXT SAH . . . C 3 68.416 83.667 151.326 1 44.9 ? OXT SAH 401 A 1 HETATM 9 C C5' SAH . . . C 3 64.089 87.109 145.976 1 36.26 ? C5' SAH 401 A 1 HETATM 10 C C4' SAH . . . C 3 62.786 86.748 146.672 1 38.92 ? C4' SAH 401 A 1 HETATM 11 O O4' SAH . . . C 3 61.886 87.893 146.69 1 37.03 ? O4' SAH 401 A 1 HETATM 12 C C3' SAH . . . C 3 62.039 85.658 145.859 1 40.48 ? C3' SAH 401 A 1 HETATM 13 O O3' SAH . . . C 3 62.048 84.432 146.626 1 39.3 ? O3' SAH 401 A 1 HETATM 14 C C2' SAH . . . C 3 60.645 86.309 145.783 1 38.84 ? C2' SAH 401 A 1 HETATM 15 O O2' SAH . . . C 3 59.599 85.353 145.908 1 41.95 ? O2' SAH 401 A 1 HETATM 16 C C1' SAH . . . C 3 60.635 87.309 146.947 1 36.89 ? C1' SAH 401 A 1 HETATM 17 N N9 SAH . . . C 3 59.541 88.323 146.746 1 38.07 ? N9 SAH 401 A 1 HETATM 18 C C8 SAH . . . C 3 59.324 89.127 145.697 1 38.83 ? C8 SAH 401 A 1 HETATM 19 N N7 SAH . . . C 3 58.228 89.871 145.933 1 36.13 ? N7 SAH 401 A 1 HETATM 20 C C5 SAH . . . C 3 57.751 89.519 147.132 1 38.22 ? C5 SAH 401 A 1 HETATM 21 C C6 SAH . . . C 3 56.685 89.921 147.844 1 37.19 ? C6 SAH 401 A 1 HETATM 22 N N6 SAH . . . C 3 55.89 90.868 147.331 1 32.95 ? N6 SAH 401 A 1 HETATM 23 N N1 SAH . . . C 3 56.408 89.405 149.042 1 32.95 ? N1 SAH 401 A 1 HETATM 24 C C2 SAH . . . C 3 57.259 88.409 149.566 1 35.86 ? C2 SAH 401 A 1 HETATM 25 N N3 SAH . . . C 3 58.352 87.992 148.815 1 35.74 ? N3 SAH 401 A 1 HETATM 26 C C4 SAH . . . C 3 58.565 88.557 147.616 1 38.88 ? C4 SAH 401 A 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 26 #