data_5YN6 # _model_server_result.job_id FJZOObFrxhh01QqLcF6zgA _model_server_result.datetime_utc '2024-11-27 16:45:23' _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 5yn6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5YN6 # _exptl.entry_id 5YN6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYLMETHIONINE _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 5YN6 _cell.length_a 66.962 _cell.length_b 70.171 _cell.length_c 119.804 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YN6 _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 metalc ? metalc1 B SG CYS 74 B CYS 74 1_555 D ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc2 B SG CYS 77 B CYS 77 1_555 D ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc3 B NE2 HIS 83 B HIS 83 1_555 D ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc4 B SG CYS 90 B CYS 90 1_555 D ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc5 B SG CYS 117 B CYS 117 1_555 E ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc6 B SG CYS 120 B CYS 120 1_555 E ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc7 B SG CYS 128 B CYS 128 1_555 E ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc8 B SG CYS 130 B CYS 130 1_555 E ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? # _chem_comp.formula 'C15 H22 N6 O5 S' _chem_comp.formula_weight 398.437 _chem_comp.id SAM _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYLMETHIONINE _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 SAM sing 277 n n N HN1 SAM sing 278 n n N HN2 SAM sing 279 n n CA C SAM sing 280 n n CA CB SAM sing 281 n n CA HA SAM sing 282 n n C O SAM doub 283 n n C OXT SAM sing 284 n n CB CG SAM sing 285 n n CB HB1 SAM sing 286 n n CB HB2 SAM sing 287 n n CG SD SAM sing 288 n n CG HG1 SAM sing 289 n n CG HG2 SAM sing 290 n n SD CE SAM sing 291 n n SD C5' SAM sing 292 n n CE HE1 SAM sing 293 n n CE HE2 SAM sing 294 n n CE HE3 SAM sing 295 n n C5' C4' SAM sing 296 n n C5' "H5'1" SAM sing 297 n n C5' "H5'2" SAM sing 298 n n C4' O4' SAM sing 299 n n C4' C3' SAM sing 300 n n C4' H4' SAM sing 301 n n O4' C1' SAM sing 302 n n C3' O3' SAM sing 303 n n C3' C2' SAM sing 304 n n C3' H3' SAM sing 305 n n O3' HO3' SAM sing 306 n n C2' O2' SAM sing 307 n n C2' C1' SAM sing 308 n n C2' H2' SAM sing 309 n n O2' HO2' SAM sing 310 n n C1' N9 SAM sing 311 n n C1' H1' SAM sing 312 n n N9 C8 SAM sing 313 n y N9 C4 SAM sing 314 n y C8 N7 SAM doub 315 n y C8 H8 SAM sing 316 n n N7 C5 SAM sing 317 n y C5 C6 SAM sing 318 n y C5 C4 SAM doub 319 n y C6 N6 SAM sing 320 n n C6 N1 SAM doub 321 n y N6 HN61 SAM sing 322 n n N6 HN62 SAM sing 323 n n N1 C2 SAM sing 324 n y C2 N3 SAM doub 325 n y C2 H2 SAM sing 326 n n N3 C4 SAM sing 327 n y # _atom_sites.entry_id 5YN6 _atom_sites.fract_transf_matrix[1][1] 0.014934 _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] 0.014251 _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] 0.008347 _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 SAM A 1 401 302 SAM SAM . D 4 ZN B 1 201 998 ZN ZN . E 4 ZN B 1 202 999 ZN ZN . F 5 HOH A 1 501 75 HOH HOH . F 5 HOH A 2 502 22 HOH HOH . F 5 HOH A 3 503 55 HOH HOH . F 5 HOH A 4 504 26 HOH HOH . F 5 HOH A 5 505 97 HOH HOH . F 5 HOH A 6 506 47 HOH HOH . F 5 HOH A 7 507 19 HOH HOH . F 5 HOH A 8 508 2 HOH HOH . F 5 HOH A 9 509 59 HOH HOH . F 5 HOH A 10 510 84 HOH HOH . F 5 HOH A 11 511 21 HOH HOH . F 5 HOH A 12 512 43 HOH HOH . F 5 HOH A 13 513 56 HOH HOH . F 5 HOH A 14 514 12 HOH HOH . F 5 HOH A 15 515 32 HOH HOH . F 5 HOH A 16 516 5 HOH HOH . F 5 HOH A 17 517 54 HOH HOH . F 5 HOH A 18 518 35 HOH HOH . F 5 HOH A 19 519 36 HOH HOH . F 5 HOH A 20 520 46 HOH HOH . F 5 HOH A 21 521 92 HOH HOH . F 5 HOH A 22 522 51 HOH HOH . F 5 HOH A 23 523 74 HOH HOH . F 5 HOH A 24 524 80 HOH HOH . F 5 HOH A 25 525 50 HOH HOH . F 5 HOH A 26 526 14 HOH HOH . F 5 HOH A 27 527 17 HOH HOH . F 5 HOH A 28 528 33 HOH HOH . F 5 HOH A 29 529 123 HOH HOH . F 5 HOH A 30 530 82 HOH HOH . F 5 HOH A 31 531 24 HOH HOH . F 5 HOH A 32 532 23 HOH HOH . F 5 HOH A 33 533 7 HOH HOH . F 5 HOH A 34 534 1 HOH HOH . F 5 HOH A 35 535 53 HOH HOH . F 5 HOH A 36 536 115 HOH HOH . F 5 HOH A 37 537 77 HOH HOH . F 5 HOH A 38 538 20 HOH HOH . F 5 HOH A 39 539 62 HOH HOH . F 5 HOH A 40 540 37 HOH HOH . F 5 HOH A 41 541 61 HOH HOH . F 5 HOH A 42 542 25 HOH HOH . F 5 HOH A 43 543 8 HOH HOH . F 5 HOH A 44 544 44 HOH HOH . F 5 HOH A 45 545 15 HOH HOH . F 5 HOH A 46 546 124 HOH HOH . F 5 HOH A 47 547 4 HOH HOH . F 5 HOH A 48 548 28 HOH HOH . F 5 HOH A 49 549 86 HOH HOH . F 5 HOH A 50 550 10 HOH HOH . F 5 HOH A 51 551 71 HOH HOH . F 5 HOH A 52 552 3 HOH HOH . F 5 HOH A 53 553 41 HOH HOH . F 5 HOH A 54 554 68 HOH HOH . F 5 HOH A 55 555 13 HOH HOH . F 5 HOH A 56 556 38 HOH HOH . F 5 HOH A 57 557 93 HOH HOH . F 5 HOH A 58 558 99 HOH HOH . F 5 HOH A 59 559 122 HOH HOH . F 5 HOH A 60 560 85 HOH HOH . F 5 HOH A 61 561 29 HOH HOH . F 5 HOH A 62 562 57 HOH HOH . F 5 HOH A 63 563 94 HOH HOH . F 5 HOH A 64 564 40 HOH HOH . F 5 HOH A 65 565 121 HOH HOH . F 5 HOH A 66 566 66 HOH HOH . F 5 HOH A 67 567 16 HOH HOH . F 5 HOH A 68 568 87 HOH HOH . F 5 HOH A 69 569 34 HOH HOH . F 5 HOH A 70 570 83 HOH HOH . F 5 HOH A 71 571 31 HOH HOH . F 5 HOH A 72 572 39 HOH HOH . F 5 HOH A 73 573 81 HOH HOH . F 5 HOH A 74 574 78 HOH HOH . F 5 HOH A 75 575 96 HOH HOH . F 5 HOH A 76 576 112 HOH HOH . F 5 HOH A 77 577 125 HOH HOH . F 5 HOH A 78 578 30 HOH HOH . F 5 HOH A 79 579 65 HOH HOH . F 5 HOH A 80 580 90 HOH HOH . F 5 HOH A 81 581 60 HOH HOH . F 5 HOH A 82 582 63 HOH HOH . F 5 HOH A 83 583 6 HOH HOH . F 5 HOH A 84 584 72 HOH HOH . F 5 HOH A 85 585 18 HOH HOH . F 5 HOH A 86 586 9 HOH HOH . F 5 HOH A 87 587 67 HOH HOH . F 5 HOH A 88 588 48 HOH HOH . F 5 HOH A 89 589 27 HOH HOH . F 5 HOH A 90 590 117 HOH HOH . F 5 HOH A 91 591 114 HOH HOH . F 5 HOH A 92 592 127 HOH HOH . F 5 HOH A 93 593 126 HOH HOH . F 5 HOH A 94 594 109 HOH HOH . F 5 HOH A 95 595 102 HOH HOH . F 5 HOH A 96 596 105 HOH HOH . F 5 HOH A 97 597 52 HOH HOH . F 5 HOH A 98 598 58 HOH HOH . F 5 HOH A 99 599 108 HOH HOH . F 5 HOH A 100 600 73 HOH HOH . F 5 HOH A 101 601 91 HOH HOH . F 5 HOH A 102 602 116 HOH HOH . F 5 HOH A 103 603 76 HOH HOH . F 5 HOH A 104 604 111 HOH HOH . F 5 HOH A 105 605 103 HOH HOH . F 5 HOH A 106 606 113 HOH HOH . F 5 HOH A 107 607 128 HOH HOH . F 5 HOH A 108 608 88 HOH HOH . F 5 HOH A 109 609 64 HOH HOH . F 5 HOH A 110 610 120 HOH HOH . F 5 HOH A 111 611 95 HOH HOH . F 5 HOH A 112 612 45 HOH HOH . F 5 HOH A 113 613 110 HOH HOH . F 5 HOH A 114 614 118 HOH HOH . F 5 HOH A 115 615 79 HOH HOH . F 5 HOH A 116 616 98 HOH HOH . F 5 HOH A 117 617 70 HOH HOH . F 5 HOH A 118 618 69 HOH HOH . F 5 HOH A 119 619 106 HOH HOH . F 5 HOH A 120 620 89 HOH HOH . F 5 HOH A 121 621 100 HOH HOH . F 5 HOH A 122 622 107 HOH HOH . F 5 HOH A 123 623 101 HOH HOH . G 5 HOH B 1 301 42 HOH HOH . G 5 HOH B 2 302 11 HOH HOH . G 5 HOH B 3 303 49 HOH HOH . G 5 HOH B 4 304 104 HOH HOH . G 5 HOH B 5 305 119 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 SAM . . . C 3 67.436 85.712 151.548 1 44.1 ? N SAM 401 A 1 HETATM 2 C CA SAM . . . C 3 67.406 84.418 150.88 1 48.19 ? CA SAM 401 A 1 HETATM 3 C C SAM . . . C 3 68.582 83.562 151.376 1 49.27 ? C SAM 401 A 1 HETATM 4 O O SAM . . . C 3 69.066 82.787 150.528 1 49.95 ? O SAM 401 A 1 HETATM 5 O OXT SAM . . . C 3 68.912 83.644 152.587 1 47.19 ? OXT SAM 401 A 1 HETATM 6 C CB SAM . . . C 3 67.45 84.601 149.352 1 47.56 ? CB SAM 401 A 1 HETATM 7 C CG SAM . . . C 3 66.294 85.583 149.081 1 46.58 ? CG SAM 401 A 1 HETATM 8 S SD SAM . . . C 3 65.829 85.789 147.31 1 50.93 ? SD SAM 401 A 1 HETATM 9 C CE SAM . . . C 3 67.306 86.39 146.518 1 52.81 ? CE SAM 401 A 1 HETATM 10 C C5' SAM . . . C 3 64.465 87.012 147.16 1 43.14 ? C5' SAM 401 A 1 HETATM 11 C C4' SAM . . . C 3 63.179 86.618 147.918 1 40.96 ? C4' SAM 401 A 1 HETATM 12 O O4' SAM . . . C 3 62.26 87.751 148.007 1 40.77 ? O4' SAM 401 A 1 HETATM 13 C C3' SAM . . . C 3 62.383 85.5 147.088 1 43.9 ? C3' SAM 401 A 1 HETATM 14 O O3' SAM . . . C 3 62.473 84.321 147.857 1 43.74 ? O3' SAM 401 A 1 HETATM 15 C C2' SAM . . . C 3 60.963 86.108 147.028 1 45.56 ? C2' SAM 401 A 1 HETATM 16 O O2' SAM . . . C 3 59.927 85.135 147.238 1 47.01 ? O2' SAM 401 A 1 HETATM 17 C C1' SAM . . . C 3 60.938 87.162 148.18 1 42.91 ? C1' SAM 401 A 1 HETATM 18 N N9 SAM . . . C 3 59.87 88.206 147.951 1 39.89 ? N9 SAM 401 A 1 HETATM 19 C C8 SAM . . . C 3 59.728 89.014 146.878 1 39.85 ? C8 SAM 401 A 1 HETATM 20 N N7 SAM . . . C 3 58.669 89.823 147.054 1 37.94 ? N7 SAM 401 A 1 HETATM 21 C C5 SAM . . . C 3 58.138 89.521 148.247 1 39.09 ? C5 SAM 401 A 1 HETATM 22 C C6 SAM . . . C 3 57.071 89.998 148.925 1 40.26 ? C6 SAM 401 A 1 HETATM 23 N N6 SAM . . . C 3 56.306 90.953 148.38 1 36.44 ? N6 SAM 401 A 1 HETATM 24 N N1 SAM . . . C 3 56.732 89.531 150.117 1 39.23 ? N1 SAM 401 A 1 HETATM 25 C C2 SAM . . . C 3 57.523 88.536 150.696 1 38.91 ? C2 SAM 401 A 1 HETATM 26 N N3 SAM . . . C 3 58.626 88.034 150.012 1 39.41 ? N3 SAM 401 A 1 HETATM 27 C C4 SAM . . . C 3 58.906 88.541 148.798 1 40.2 ? C4 SAM 401 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #