data_5YNO # _model_server_result.job_id yfX64hTAivHINVV_wPO2CQ _model_server_result.datetime_utc '2024-11-12 21:06:27' _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 5yno # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5YNO # _exptl.entry_id 5YNO _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 5YNO _cell.length_a 67.193 _cell.length_b 70.186 _cell.length_c 119.353 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YNO _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,H _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 metalc ? metalc1 B SG CYS 74 B CYS 74 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc2 B SG CYS 77 B CYS 77 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc3 B NE2 HIS 83 B HIS 83 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc4 B SG CYS 90 B CYS 90 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc5 B SG CYS 117 B CYS 117 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc6 B SG CYS 120 B CYS 120 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc7 B SG CYS 128 B CYS 128 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc8 B SG CYS 130 B CYS 130 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? # _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 363 n n N HN1 SAH sing 364 n n N HN2 SAH sing 365 n n CA CB SAH sing 366 n n CA C SAH sing 367 n n CA HA SAH sing 368 n n CB CG SAH sing 369 n n CB HB1 SAH sing 370 n n CB HB2 SAH sing 371 n n CG SD SAH sing 372 n n CG HG1 SAH sing 373 n n CG HG2 SAH sing 374 n n SD C5' SAH sing 375 n n C O SAH doub 376 n n C OXT SAH sing 377 n n OXT HXT SAH sing 378 n n C5' C4' SAH sing 379 n n C5' "H5'1" SAH sing 380 n n C5' "H5'2" SAH sing 381 n n C4' O4' SAH sing 382 n n C4' C3' SAH sing 383 n n C4' H4' SAH sing 384 n n O4' C1' SAH sing 385 n n C3' O3' SAH sing 386 n n C3' C2' SAH sing 387 n n C3' H3' SAH sing 388 n n O3' HO3' SAH sing 389 n n C2' O2' SAH sing 390 n n C2' C1' SAH sing 391 n n C2' H2' SAH sing 392 n n O2' HO2' SAH sing 393 n n C1' N9 SAH sing 394 n n C1' H1' SAH sing 395 n n N9 C8 SAH sing 396 n y N9 C4 SAH sing 397 n y C8 N7 SAH doub 398 n y C8 H8 SAH sing 399 n n N7 C5 SAH sing 400 n y C5 C6 SAH sing 401 n y C5 C4 SAH doub 402 n y C6 N6 SAH sing 403 n n C6 N1 SAH doub 404 n y N6 HN61 SAH sing 405 n n N6 HN62 SAH sing 406 n n N1 C2 SAH sing 407 n y C2 N3 SAH doub 408 n y C2 H2 SAH sing 409 n n N3 C4 SAH sing 410 n y # _atom_sites.entry_id 5YNO _atom_sites.fract_transf_matrix[1][1] 0.014883 _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] 0.014248 _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] 0.008379 _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 GTA A 1 402 451 GTA GTA . E 5 ZN B 1 201 998 ZN ZN . F 5 ZN B 1 202 999 ZN ZN . G 6 HOH A 1 501 120 HOH HOH . G 6 HOH A 2 502 57 HOH HOH . G 6 HOH A 3 503 29 HOH HOH . G 6 HOH A 4 504 17 HOH HOH . G 6 HOH A 5 505 15 HOH HOH . G 6 HOH A 6 506 71 HOH HOH . G 6 HOH A 7 507 61 HOH HOH . G 6 HOH A 8 508 4 HOH HOH . G 6 HOH A 9 509 21 HOH HOH . G 6 HOH A 10 510 31 HOH HOH . G 6 HOH A 11 511 41 HOH HOH . G 6 HOH A 12 512 24 HOH HOH . G 6 HOH A 13 513 112 HOH HOH . G 6 HOH A 14 514 5 HOH HOH . G 6 HOH A 15 515 2 HOH HOH . G 6 HOH A 16 516 6 HOH HOH . G 6 HOH A 17 517 145 HOH HOH . G 6 HOH A 18 518 105 HOH HOH . G 6 HOH A 19 519 108 HOH HOH . G 6 HOH A 20 520 42 HOH HOH . G 6 HOH A 21 521 167 HOH HOH . G 6 HOH A 22 522 174 HOH HOH . G 6 HOH A 23 523 53 HOH HOH . G 6 HOH A 24 524 40 HOH HOH . G 6 HOH A 25 525 161 HOH HOH . G 6 HOH A 26 526 44 HOH HOH . G 6 HOH A 27 527 70 HOH HOH . G 6 HOH A 28 528 16 HOH HOH . G 6 HOH A 29 529 64 HOH HOH . G 6 HOH A 30 530 94 HOH HOH . G 6 HOH A 31 531 58 HOH HOH . G 6 HOH A 32 532 87 HOH HOH . G 6 HOH A 33 533 122 HOH HOH . G 6 HOH A 34 534 13 HOH HOH . G 6 HOH A 35 535 3 HOH HOH . G 6 HOH A 36 536 59 HOH HOH . G 6 HOH A 37 537 12 HOH HOH . G 6 HOH A 38 538 62 HOH HOH . G 6 HOH A 39 539 118 HOH HOH . G 6 HOH A 40 540 95 HOH HOH . G 6 HOH A 41 541 27 HOH HOH . G 6 HOH A 42 542 139 HOH HOH . G 6 HOH A 43 543 77 HOH HOH . G 6 HOH A 44 544 28 HOH HOH . G 6 HOH A 45 545 9 HOH HOH . G 6 HOH A 46 546 46 HOH HOH . G 6 HOH A 47 547 88 HOH HOH . G 6 HOH A 48 548 33 HOH HOH . G 6 HOH A 49 549 68 HOH HOH . G 6 HOH A 50 550 85 HOH HOH . G 6 HOH A 51 551 10 HOH HOH . G 6 HOH A 52 552 123 HOH HOH . G 6 HOH A 53 553 101 HOH HOH . G 6 HOH A 54 554 141 HOH HOH . G 6 HOH A 55 555 133 HOH HOH . G 6 HOH A 56 556 20 HOH HOH . G 6 HOH A 57 557 37 HOH HOH . G 6 HOH A 58 558 11 HOH HOH . G 6 HOH A 59 559 138 HOH HOH . G 6 HOH A 60 560 81 HOH HOH . G 6 HOH A 61 561 26 HOH HOH . G 6 HOH A 62 562 22 HOH HOH . G 6 HOH A 63 563 140 HOH HOH . G 6 HOH A 64 564 69 HOH HOH . G 6 HOH A 65 565 25 HOH HOH . G 6 HOH A 66 566 67 HOH HOH . G 6 HOH A 67 567 72 HOH HOH . G 6 HOH A 68 568 1 HOH HOH . G 6 HOH A 69 569 8 HOH HOH . G 6 HOH A 70 570 14 HOH HOH . G 6 HOH A 71 571 137 HOH HOH . G 6 HOH A 72 572 179 HOH HOH . G 6 HOH A 73 573 92 HOH HOH . G 6 HOH A 74 574 56 HOH HOH . G 6 HOH A 75 575 75 HOH HOH . G 6 HOH A 76 576 30 HOH HOH . G 6 HOH A 77 577 35 HOH HOH . G 6 HOH A 78 578 116 HOH HOH . G 6 HOH A 79 579 134 HOH HOH . G 6 HOH A 80 580 130 HOH HOH . G 6 HOH A 81 581 79 HOH HOH . G 6 HOH A 82 582 78 HOH HOH . G 6 HOH A 83 583 51 HOH HOH . G 6 HOH A 84 584 48 HOH HOH . G 6 HOH A 85 585 178 HOH HOH . G 6 HOH A 86 586 109 HOH HOH . G 6 HOH A 87 587 34 HOH HOH . G 6 HOH A 88 588 39 HOH HOH . G 6 HOH A 89 589 38 HOH HOH . G 6 HOH A 90 590 73 HOH HOH . G 6 HOH A 91 591 50 HOH HOH . G 6 HOH A 92 592 111 HOH HOH . G 6 HOH A 93 593 147 HOH HOH . G 6 HOH A 94 594 149 HOH HOH . G 6 HOH A 95 595 55 HOH HOH . G 6 HOH A 96 596 169 HOH HOH . G 6 HOH A 97 597 86 HOH HOH . G 6 HOH A 98 598 18 HOH HOH . G 6 HOH A 99 599 113 HOH HOH . G 6 HOH A 100 600 124 HOH HOH . G 6 HOH A 101 601 23 HOH HOH . G 6 HOH A 102 602 52 HOH HOH . G 6 HOH A 103 603 135 HOH HOH . G 6 HOH A 104 604 146 HOH HOH . G 6 HOH A 105 605 89 HOH HOH . G 6 HOH A 106 606 60 HOH HOH . G 6 HOH A 107 607 114 HOH HOH . G 6 HOH A 108 608 170 HOH HOH . G 6 HOH A 109 609 98 HOH HOH . G 6 HOH A 110 610 7 HOH HOH . G 6 HOH A 111 611 127 HOH HOH . G 6 HOH A 112 612 65 HOH HOH . G 6 HOH A 113 613 158 HOH HOH . G 6 HOH A 114 614 121 HOH HOH . G 6 HOH A 115 615 49 HOH HOH . G 6 HOH A 116 616 132 HOH HOH . G 6 HOH A 117 617 177 HOH HOH . G 6 HOH A 118 618 100 HOH HOH . G 6 HOH A 119 619 168 HOH HOH . G 6 HOH A 120 620 63 HOH HOH . G 6 HOH A 121 621 107 HOH HOH . G 6 HOH A 122 622 184 HOH HOH . G 6 HOH A 123 623 171 HOH HOH . G 6 HOH A 124 624 157 HOH HOH . G 6 HOH A 125 625 45 HOH HOH . G 6 HOH A 126 626 162 HOH HOH . G 6 HOH A 127 627 106 HOH HOH . G 6 HOH A 128 628 128 HOH HOH . G 6 HOH A 129 629 54 HOH HOH . G 6 HOH A 130 630 32 HOH HOH . G 6 HOH A 131 631 165 HOH HOH . G 6 HOH A 132 632 110 HOH HOH . G 6 HOH A 133 633 129 HOH HOH . G 6 HOH A 134 634 142 HOH HOH . G 6 HOH A 135 635 166 HOH HOH . G 6 HOH A 136 636 136 HOH HOH . G 6 HOH A 137 637 154 HOH HOH . G 6 HOH A 138 638 76 HOH HOH . G 6 HOH A 139 639 151 HOH HOH . G 6 HOH A 140 640 156 HOH HOH . G 6 HOH A 141 641 160 HOH HOH . G 6 HOH A 142 642 182 HOH HOH . G 6 HOH A 143 643 80 HOH HOH . G 6 HOH A 144 644 90 HOH HOH . G 6 HOH A 145 645 43 HOH HOH . G 6 HOH A 146 646 152 HOH HOH . G 6 HOH A 147 647 150 HOH HOH . G 6 HOH A 148 648 183 HOH HOH . G 6 HOH A 149 649 180 HOH HOH . G 6 HOH A 150 650 148 HOH HOH . G 6 HOH A 151 651 119 HOH HOH . G 6 HOH A 152 652 175 HOH HOH . G 6 HOH A 153 653 82 HOH HOH . G 6 HOH A 154 654 155 HOH HOH . G 6 HOH A 155 655 125 HOH HOH . G 6 HOH A 156 656 185 HOH HOH . G 6 HOH A 157 657 181 HOH HOH . G 6 HOH A 158 658 153 HOH HOH . G 6 HOH A 159 659 176 HOH HOH . G 6 HOH A 160 660 159 HOH HOH . H 6 HOH B 1 301 102 HOH HOH . H 6 HOH B 2 302 93 HOH HOH . H 6 HOH B 3 303 83 HOH HOH . H 6 HOH B 4 304 66 HOH HOH . H 6 HOH B 5 305 19 HOH HOH . H 6 HOH B 6 306 144 HOH HOH . H 6 HOH B 7 307 96 HOH HOH . H 6 HOH B 8 308 143 HOH HOH . H 6 HOH B 9 309 117 HOH HOH . H 6 HOH B 10 310 84 HOH HOH . H 6 HOH B 11 311 74 HOH HOH . H 6 HOH B 12 312 36 HOH HOH . H 6 HOH B 13 313 91 HOH HOH . H 6 HOH B 14 314 104 HOH HOH . H 6 HOH B 15 315 47 HOH HOH . H 6 HOH B 16 316 126 HOH HOH . H 6 HOH B 17 317 97 HOH HOH . H 6 HOH B 18 318 173 HOH HOH . H 6 HOH B 19 319 99 HOH HOH . H 6 HOH B 20 320 163 HOH HOH . H 6 HOH B 21 321 115 HOH HOH . H 6 HOH B 22 322 164 HOH HOH . H 6 HOH B 23 323 172 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 67.961 85.805 150.639 1 42.67 ? N SAH 401 A 1 HETATM 2 C CA SAH . . . C 3 67.791 84.61 149.818 1 44.11 ? CA SAH 401 A 1 HETATM 3 C CB SAH . . . C 3 67.743 84.922 148.315 1 43.08 ? CB SAH 401 A 1 HETATM 4 C CG SAH . . . C 3 66.463 85.689 147.955 1 42.8 ? CG SAH 401 A 1 HETATM 5 S SD SAH . . . C 3 66.412 86.07 146.178 1 42.92 ? SD SAH 401 A 1 HETATM 6 C C SAH . . . C 3 68.95 83.651 150.086 1 46.82 ? C SAH 401 A 1 HETATM 7 O O SAH . . . C 3 69.171 82.824 149.169 1 48.25 ? O SAH 401 A 1 HETATM 8 O OXT SAH . . . C 3 69.57 83.769 151.177 1 45.01 ? OXT SAH 401 A 1 HETATM 9 C C5' SAH . . . C 3 65.126 87.357 146.173 1 40.43 ? C5' SAH 401 A 1 HETATM 10 C C4' SAH . . . C 3 63.837 86.905 146.862 1 40.23 ? C4' SAH 401 A 1 HETATM 11 O O4' SAH . . . C 3 62.923 88.029 146.895 1 40.03 ? O4' SAH 401 A 1 HETATM 12 C C3' SAH . . . C 3 63.113 85.823 146.035 1 41.76 ? C3' SAH 401 A 1 HETATM 13 O O3' SAH . . . C 3 63.1 84.642 146.808 1 42.2 ? O3' SAH 401 A 1 HETATM 14 C C2' SAH . . . C 3 61.715 86.433 145.946 1 42.33 ? C2' SAH 401 A 1 HETATM 15 O O2' SAH . . . C 3 60.702 85.445 146.057 1 40.84 ? O2' SAH 401 A 1 HETATM 16 C C1' SAH . . . C 3 61.676 87.398 147.129 1 41.26 ? C1' SAH 401 A 1 HETATM 17 N N9 SAH . . . C 3 60.568 88.4 146.992 1 39.31 ? N9 SAH 401 A 1 HETATM 18 C C8 SAH . . . C 3 60.412 89.22 145.948 1 39.31 ? C8 SAH 401 A 1 HETATM 19 N N7 SAH . . . C 3 59.33 89.973 146.153 1 38.08 ? N7 SAH 401 A 1 HETATM 20 C C5 SAH . . . C 3 58.809 89.628 147.338 1 38.47 ? C5 SAH 401 A 1 HETATM 21 C C6 SAH . . . C 3 57.723 90.071 148.009 1 37.88 ? C6 SAH 401 A 1 HETATM 22 N N6 SAH . . . C 3 56.994 91.041 147.44 1 36.5 ? N6 SAH 401 A 1 HETATM 23 N N1 SAH . . . C 3 57.373 89.571 149.209 1 35.71 ? N1 SAH 401 A 1 HETATM 24 C C2 SAH . . . C 3 58.17 88.549 149.756 1 35.44 ? C2 SAH 401 A 1 HETATM 25 N N3 SAH . . . C 3 59.295 88.096 149.041 1 34.89 ? N3 SAH 401 A 1 HETATM 26 C C4 SAH . . . C 3 59.582 88.65 147.853 1 37.98 ? C4 SAH 401 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 26 #