data_5YNQ # _model_server_result.job_id lRzlGbHZ4zfgM9LMyEhugw _model_server_result.datetime_utc '2024-11-14 19:42:04' _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 5ynq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5YNQ # _exptl.entry_id 5YNQ _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 5YNQ _cell.length_a 66.874 _cell.length_b 70.101 _cell.length_c 118.937 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YNQ _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc2 B SG CYS 77 B CYS 77 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc3 B NE2 HIS 83 B HIS 83 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc4 B SG CYS 90 B CYS 90 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc5 B SG CYS 117 B CYS 117 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc6 B SG CYS 120 B CYS 120 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc7 B SG CYS 128 B CYS 128 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc8 B SG CYS 130 B CYS 130 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? # _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 364 n n N HN1 SAH sing 365 n n N HN2 SAH sing 366 n n CA CB SAH sing 367 n n CA C SAH sing 368 n n CA HA SAH sing 369 n n CB CG SAH sing 370 n n CB HB1 SAH sing 371 n n CB HB2 SAH sing 372 n n CG SD SAH sing 373 n n CG HG1 SAH sing 374 n n CG HG2 SAH sing 375 n n SD C5' SAH sing 376 n n C O SAH doub 377 n n C OXT SAH sing 378 n n OXT HXT SAH sing 379 n n C5' C4' SAH sing 380 n n C5' "H5'1" SAH sing 381 n n C5' "H5'2" SAH sing 382 n n C4' O4' SAH sing 383 n n C4' C3' SAH sing 384 n n C4' H4' SAH sing 385 n n O4' C1' SAH sing 386 n n C3' O3' SAH sing 387 n n C3' C2' SAH sing 388 n n C3' H3' SAH sing 389 n n O3' HO3' SAH sing 390 n n C2' O2' SAH sing 391 n n C2' C1' SAH sing 392 n n C2' H2' SAH sing 393 n n O2' HO2' SAH sing 394 n n C1' N9 SAH sing 395 n n C1' H1' SAH sing 396 n n N9 C8 SAH sing 397 n y N9 C4 SAH sing 398 n y C8 N7 SAH doub 399 n y C8 H8 SAH sing 400 n n N7 C5 SAH sing 401 n y C5 C6 SAH sing 402 n y C5 C4 SAH doub 403 n y C6 N6 SAH sing 404 n n C6 N1 SAH doub 405 n y N6 HN61 SAH sing 406 n n N6 HN62 SAH sing 407 n n N1 C2 SAH sing 408 n y C2 N3 SAH doub 409 n y C2 H2 SAH sing 410 n n N3 C4 SAH sing 411 n y # _atom_sites.entry_id 5YNQ _atom_sites.fract_transf_matrix[1][1] 0.014953 _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] 0.014265 _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] 0.008408 _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 GTG A 1 402 501 GTG GTG . E 5 ZN B 1 201 998 ZN ZN . F 5 ZN B 1 202 999 ZN ZN . G 6 HOH A 1 501 143 HOH HOH . G 6 HOH A 2 502 12 HOH HOH . G 6 HOH A 3 503 26 HOH HOH . G 6 HOH A 4 504 63 HOH HOH . G 6 HOH A 5 505 14 HOH HOH . G 6 HOH A 6 506 116 HOH HOH . G 6 HOH A 7 507 70 HOH HOH . G 6 HOH A 8 508 32 HOH HOH . G 6 HOH A 9 509 5 HOH HOH . G 6 HOH A 10 510 25 HOH HOH . G 6 HOH A 11 511 31 HOH HOH . G 6 HOH A 12 512 69 HOH HOH . G 6 HOH A 13 513 9 HOH HOH . G 6 HOH A 14 514 71 HOH HOH . G 6 HOH A 15 515 3 HOH HOH . G 6 HOH A 16 516 43 HOH HOH . G 6 HOH A 17 517 50 HOH HOH . G 6 HOH A 18 518 38 HOH HOH . G 6 HOH A 19 519 49 HOH HOH . G 6 HOH A 20 520 8 HOH HOH . G 6 HOH A 21 521 35 HOH HOH . G 6 HOH A 22 522 88 HOH HOH . G 6 HOH A 23 523 62 HOH HOH . G 6 HOH A 24 524 40 HOH HOH . G 6 HOH A 25 525 42 HOH HOH . G 6 HOH A 26 526 11 HOH HOH . G 6 HOH A 27 527 37 HOH HOH . G 6 HOH A 28 528 1 HOH HOH . G 6 HOH A 29 529 54 HOH HOH . G 6 HOH A 30 530 60 HOH HOH . G 6 HOH A 31 531 34 HOH HOH . G 6 HOH A 32 532 51 HOH HOH . G 6 HOH A 33 533 21 HOH HOH . G 6 HOH A 34 534 55 HOH HOH . G 6 HOH A 35 535 10 HOH HOH . G 6 HOH A 36 536 147 HOH HOH . G 6 HOH A 37 537 94 HOH HOH . G 6 HOH A 38 538 20 HOH HOH . G 6 HOH A 39 539 150 HOH HOH . G 6 HOH A 40 540 146 HOH HOH . G 6 HOH A 41 541 117 HOH HOH . G 6 HOH A 42 542 13 HOH HOH . G 6 HOH A 43 543 101 HOH HOH . G 6 HOH A 44 544 81 HOH HOH . G 6 HOH A 45 545 98 HOH HOH . G 6 HOH A 46 546 16 HOH HOH . G 6 HOH A 47 547 121 HOH HOH . G 6 HOH A 48 548 73 HOH HOH . G 6 HOH A 49 549 96 HOH HOH . G 6 HOH A 50 550 56 HOH HOH . G 6 HOH A 51 551 111 HOH HOH . G 6 HOH A 52 552 59 HOH HOH . G 6 HOH A 53 553 33 HOH HOH . G 6 HOH A 54 554 2 HOH HOH . G 6 HOH A 55 555 92 HOH HOH . G 6 HOH A 56 556 28 HOH HOH . G 6 HOH A 57 557 138 HOH HOH . G 6 HOH A 58 558 15 HOH HOH . G 6 HOH A 59 559 58 HOH HOH . G 6 HOH A 60 560 145 HOH HOH . G 6 HOH A 61 561 45 HOH HOH . G 6 HOH A 62 562 154 HOH HOH . G 6 HOH A 63 563 102 HOH HOH . G 6 HOH A 64 564 84 HOH HOH . G 6 HOH A 65 565 7 HOH HOH . G 6 HOH A 66 566 93 HOH HOH . G 6 HOH A 67 567 80 HOH HOH . G 6 HOH A 68 568 22 HOH HOH . G 6 HOH A 69 569 100 HOH HOH . G 6 HOH A 70 570 53 HOH HOH . G 6 HOH A 71 571 124 HOH HOH . G 6 HOH A 72 572 41 HOH HOH . G 6 HOH A 73 573 46 HOH HOH . G 6 HOH A 74 574 165 HOH HOH . G 6 HOH A 75 575 65 HOH HOH . G 6 HOH A 76 576 64 HOH HOH . G 6 HOH A 77 577 4 HOH HOH . G 6 HOH A 78 578 139 HOH HOH . G 6 HOH A 79 579 6 HOH HOH . G 6 HOH A 80 580 125 HOH HOH . G 6 HOH A 81 581 106 HOH HOH . G 6 HOH A 82 582 29 HOH HOH . G 6 HOH A 83 583 149 HOH HOH . G 6 HOH A 84 584 17 HOH HOH . G 6 HOH A 85 585 119 HOH HOH . G 6 HOH A 86 586 47 HOH HOH . G 6 HOH A 87 587 19 HOH HOH . G 6 HOH A 88 588 82 HOH HOH . G 6 HOH A 89 589 66 HOH HOH . G 6 HOH A 90 590 39 HOH HOH . G 6 HOH A 91 591 91 HOH HOH . G 6 HOH A 92 592 48 HOH HOH . G 6 HOH A 93 593 75 HOH HOH . G 6 HOH A 94 594 115 HOH HOH . G 6 HOH A 95 595 107 HOH HOH . G 6 HOH A 96 596 123 HOH HOH . G 6 HOH A 97 597 52 HOH HOH . G 6 HOH A 98 598 99 HOH HOH . G 6 HOH A 99 599 30 HOH HOH . G 6 HOH A 100 600 77 HOH HOH . G 6 HOH A 101 601 109 HOH HOH . G 6 HOH A 102 602 27 HOH HOH . G 6 HOH A 103 603 23 HOH HOH . G 6 HOH A 104 604 144 HOH HOH . G 6 HOH A 105 605 163 HOH HOH . G 6 HOH A 106 606 24 HOH HOH . G 6 HOH A 107 607 57 HOH HOH . G 6 HOH A 108 608 126 HOH HOH . G 6 HOH A 109 609 67 HOH HOH . G 6 HOH A 110 610 105 HOH HOH . G 6 HOH A 111 611 108 HOH HOH . G 6 HOH A 112 612 72 HOH HOH . G 6 HOH A 113 613 155 HOH HOH . G 6 HOH A 114 614 112 HOH HOH . G 6 HOH A 115 615 86 HOH HOH . G 6 HOH A 116 616 152 HOH HOH . G 6 HOH A 117 617 44 HOH HOH . G 6 HOH A 118 618 118 HOH HOH . G 6 HOH A 119 619 68 HOH HOH . G 6 HOH A 120 620 113 HOH HOH . G 6 HOH A 121 621 166 HOH HOH . G 6 HOH A 122 622 78 HOH HOH . G 6 HOH A 123 623 130 HOH HOH . G 6 HOH A 124 624 137 HOH HOH . G 6 HOH A 125 625 136 HOH HOH . G 6 HOH A 126 626 160 HOH HOH . G 6 HOH A 127 627 167 HOH HOH . G 6 HOH A 128 628 89 HOH HOH . G 6 HOH A 129 629 114 HOH HOH . G 6 HOH A 130 630 140 HOH HOH . G 6 HOH A 131 631 131 HOH HOH . G 6 HOH A 132 632 133 HOH HOH . G 6 HOH A 133 633 103 HOH HOH . G 6 HOH A 134 634 134 HOH HOH . G 6 HOH A 135 635 161 HOH HOH . G 6 HOH A 136 636 95 HOH HOH . G 6 HOH A 137 637 156 HOH HOH . G 6 HOH A 138 638 36 HOH HOH . G 6 HOH A 139 639 128 HOH HOH . G 6 HOH A 140 640 148 HOH HOH . G 6 HOH A 141 641 153 HOH HOH . G 6 HOH A 142 642 164 HOH HOH . G 6 HOH A 143 643 129 HOH HOH . G 6 HOH A 144 644 132 HOH HOH . G 6 HOH A 145 645 142 HOH HOH . G 6 HOH A 146 646 79 HOH HOH . G 6 HOH A 147 647 157 HOH HOH . G 6 HOH A 148 648 162 HOH HOH . G 6 HOH A 149 649 158 HOH HOH . G 6 HOH A 150 650 159 HOH HOH . H 6 HOH B 1 301 83 HOH HOH . H 6 HOH B 2 302 74 HOH HOH . H 6 HOH B 3 303 87 HOH HOH . H 6 HOH B 4 304 18 HOH HOH . H 6 HOH B 5 305 85 HOH HOH . H 6 HOH B 6 306 90 HOH HOH . H 6 HOH B 7 307 61 HOH HOH . H 6 HOH B 8 308 97 HOH HOH . H 6 HOH B 9 309 104 HOH HOH . H 6 HOH B 10 310 76 HOH HOH . H 6 HOH B 11 311 110 HOH HOH . H 6 HOH B 12 312 122 HOH HOH . H 6 HOH B 13 313 141 HOH HOH . H 6 HOH B 14 314 135 HOH HOH . H 6 HOH B 15 315 127 HOH HOH . H 6 HOH B 16 316 120 HOH HOH . H 6 HOH B 17 317 151 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 67.682 85.66 149.924 1 42.63 ? N SAH 401 A 1 HETATM 2 C CA SAH . . . C 3 67.455 84.422 149.163 1 48.17 ? CA SAH 401 A 1 HETATM 3 C CB SAH . . . C 3 67.426 84.686 147.651 1 43.87 ? CB SAH 401 A 1 HETATM 4 C CG SAH . . . C 3 66.195 85.525 147.29 1 44.92 ? CG SAH 401 A 1 HETATM 5 S SD SAH . . . C 3 66.029 85.828 145.492 1 49.32 ? SD SAH 401 A 1 HETATM 6 C C SAH . . . C 3 68.556 83.408 149.5 1 56.03 ? C SAH 401 A 1 HETATM 7 O O SAH . . . C 3 68.803 82.541 148.634 1 55.19 ? O SAH 401 A 1 HETATM 8 O OXT SAH . . . C 3 69.121 83.52 150.614 1 52.91 ? OXT SAH 401 A 1 HETATM 9 C C5' SAH . . . C 3 64.74 87.129 145.472 1 44.05 ? C5' SAH 401 A 1 HETATM 10 C C4' SAH . . . C 3 63.461 86.747 146.224 1 43.18 ? C4' SAH 401 A 1 HETATM 11 O O4' SAH . . . C 3 62.546 87.873 146.214 1 43.25 ? O4' SAH 401 A 1 HETATM 12 C C3' SAH . . . C 3 62.699 85.609 145.508 1 45.29 ? C3' SAH 401 A 1 HETATM 13 O O3' SAH . . . C 3 62.606 84.487 146.396 1 44.84 ? O3' SAH 401 A 1 HETATM 14 C C2' SAH . . . C 3 61.335 86.256 145.329 1 45 ? C2' SAH 401 A 1 HETATM 15 O O2' SAH . . . C 3 60.295 85.275 145.435 1 45.1 ? O2' SAH 401 A 1 HETATM 16 C C1' SAH . . . C 3 61.297 87.243 146.485 1 43 ? C1' SAH 401 A 1 HETATM 17 N N9 SAH . . . C 3 60.173 88.23 146.364 1 35.11 ? N9 SAH 401 A 1 HETATM 18 C C8 SAH . . . C 3 59.999 89.056 145.333 1 35.34 ? C8 SAH 401 A 1 HETATM 19 N N7 SAH . . . C 3 58.911 89.791 145.558 1 34.07 ? N7 SAH 401 A 1 HETATM 20 C C5 SAH . . . C 3 58.4 89.423 146.729 1 34.42 ? C5 SAH 401 A 1 HETATM 21 C C6 SAH . . . C 3 57.324 89.851 147.396 1 37.66 ? C6 SAH 401 A 1 HETATM 22 N N6 SAH . . . C 3 56.603 90.821 146.828 1 39.35 ? N6 SAH 401 A 1 HETATM 23 N N1 SAH . . . C 3 56.983 89.342 148.584 1 37.55 ? N1 SAH 401 A 1 HETATM 24 C C2 SAH . . . C 3 57.778 88.332 149.131 1 39.07 ? C2 SAH 401 A 1 HETATM 25 N N3 SAH . . . C 3 58.902 87.901 148.416 1 37.2 ? N3 SAH 401 A 1 HETATM 26 C C4 SAH . . . C 3 59.185 88.459 147.23 1 35.37 ? C4 SAH 401 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #