data_5AYF # _model_server_result.job_id Uu1nftBCYxGR9iIflEQ8Qw _model_server_result.datetime_utc '2024-10-12 12:22:27' _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 5ayf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5AYF # _exptl.entry_id 5AYF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 2 _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 5AYF _cell.length_a 102.463 _cell.length_b 39.366 _cell.length_c 67.275 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5AYF _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 2 _struct_asym.id B _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 covale ? covale1 A C UNK 236 A UNK 339 1_555 A N UNK 237 A UNK 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A C UNK 237 A UNK 340 1_555 A N UNK 238 A UNK 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale3 A C UNK 238 A UNK 341 1_555 A N UNK 239 A UNK 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale4 A C UNK 239 A UNK 342 1_555 A N UNK 240 A UNK 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 A C UNK 240 A UNK 343 1_555 A N UNK 241 A UNK 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? # _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 323 n n N HN1 SAM sing 324 n n N HN2 SAM sing 325 n n CA C SAM sing 326 n n CA CB SAM sing 327 n n CA HA SAM sing 328 n n C O SAM doub 329 n n C OXT SAM sing 330 n n CB CG SAM sing 331 n n CB HB1 SAM sing 332 n n CB HB2 SAM sing 333 n n CG SD SAM sing 334 n n CG HG1 SAM sing 335 n n CG HG2 SAM sing 336 n n SD CE SAM sing 337 n n SD C5' SAM sing 338 n n CE HE1 SAM sing 339 n n CE HE2 SAM sing 340 n n CE HE3 SAM sing 341 n n C5' C4' SAM sing 342 n n C5' "H5'1" SAM sing 343 n n C5' "H5'2" SAM sing 344 n n C4' O4' SAM sing 345 n n C4' C3' SAM sing 346 n n C4' H4' SAM sing 347 n n O4' C1' SAM sing 348 n n C3' O3' SAM sing 349 n n C3' C2' SAM sing 350 n n C3' H3' SAM sing 351 n n O3' HO3' SAM sing 352 n n C2' O2' SAM sing 353 n n C2' C1' SAM sing 354 n n C2' H2' SAM sing 355 n n O2' HO2' SAM sing 356 n n C1' N9 SAM sing 357 n n C1' H1' SAM sing 358 n n N9 C8 SAM sing 359 n y N9 C4 SAM sing 360 n y C8 N7 SAM doub 361 n y C8 H8 SAM sing 362 n n N7 C5 SAM sing 363 n y C5 C6 SAM sing 364 n y C5 C4 SAM doub 365 n y C6 N6 SAM sing 366 n n C6 N1 SAM doub 367 n y N6 HN61 SAM sing 368 n n N6 HN62 SAM sing 369 n n N1 C2 SAM sing 370 n y C2 N3 SAM doub 371 n y C2 H2 SAM sing 372 n n N3 C4 SAM sing 373 n y # _atom_sites.entry_id 5AYF _atom_sites.fract_transf_matrix[1][1] 0.00976 _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] 0.025403 _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] 0.014864 _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 SAM A 1 401 401 SAM SAM . C 3 C7H A 1 402 501 C7H C7D . D 4 TRS A 1 403 601 TRS TRS . E 5 HOH A 1 501 61 HOH HOH . E 5 HOH A 2 502 82 HOH HOH . E 5 HOH A 3 503 59 HOH HOH . E 5 HOH A 4 504 3 HOH HOH . E 5 HOH A 5 505 22 HOH HOH . E 5 HOH A 6 506 169 HOH HOH . E 5 HOH A 7 507 160 HOH HOH . E 5 HOH A 8 508 20 HOH HOH . E 5 HOH A 9 509 1 HOH HOH . E 5 HOH A 10 510 26 HOH HOH . E 5 HOH A 11 511 18 HOH HOH . E 5 HOH A 12 512 36 HOH HOH . E 5 HOH A 13 513 113 HOH HOH . E 5 HOH A 14 514 29 HOH HOH . E 5 HOH A 15 515 77 HOH HOH . E 5 HOH A 16 516 71 HOH HOH . E 5 HOH A 17 517 118 HOH HOH . E 5 HOH A 18 518 138 HOH HOH . E 5 HOH A 19 519 49 HOH HOH . E 5 HOH A 20 520 35 HOH HOH . E 5 HOH A 21 521 6 HOH HOH . E 5 HOH A 22 522 152 HOH HOH . E 5 HOH A 23 523 155 HOH HOH . E 5 HOH A 24 524 179 HOH HOH . E 5 HOH A 25 525 37 HOH HOH . E 5 HOH A 26 526 98 HOH HOH . E 5 HOH A 27 527 21 HOH HOH . E 5 HOH A 28 528 39 HOH HOH . E 5 HOH A 29 529 46 HOH HOH . E 5 HOH A 30 530 7 HOH HOH . E 5 HOH A 31 531 9 HOH HOH . E 5 HOH A 32 532 140 HOH HOH . E 5 HOH A 33 533 63 HOH HOH . E 5 HOH A 34 534 143 HOH HOH . E 5 HOH A 35 535 10 HOH HOH . E 5 HOH A 36 536 4 HOH HOH . E 5 HOH A 37 537 84 HOH HOH . E 5 HOH A 38 538 135 HOH HOH . E 5 HOH A 39 539 66 HOH HOH . E 5 HOH A 40 540 5 HOH HOH . E 5 HOH A 41 541 47 HOH HOH . E 5 HOH A 42 542 172 HOH HOH . E 5 HOH A 43 543 11 HOH HOH . E 5 HOH A 44 544 103 HOH HOH . E 5 HOH A 45 545 12 HOH HOH . E 5 HOH A 46 546 117 HOH HOH . E 5 HOH A 47 547 51 HOH HOH . E 5 HOH A 48 548 64 HOH HOH . E 5 HOH A 49 549 161 HOH HOH . E 5 HOH A 50 550 41 HOH HOH . E 5 HOH A 51 551 48 HOH HOH . E 5 HOH A 52 552 62 HOH HOH . E 5 HOH A 53 553 19 HOH HOH . E 5 HOH A 54 554 24 HOH HOH . E 5 HOH A 55 555 177 HOH HOH . E 5 HOH A 56 556 8 HOH HOH . E 5 HOH A 57 557 28 HOH HOH . E 5 HOH A 58 558 17 HOH HOH . E 5 HOH A 59 559 153 HOH HOH . E 5 HOH A 60 560 125 HOH HOH . E 5 HOH A 61 561 94 HOH HOH . E 5 HOH A 62 562 54 HOH HOH . E 5 HOH A 63 563 75 HOH HOH . E 5 HOH A 64 564 148 HOH HOH . E 5 HOH A 65 565 120 HOH HOH . E 5 HOH A 66 566 126 HOH HOH . E 5 HOH A 67 567 68 HOH HOH . E 5 HOH A 68 568 134 HOH HOH . E 5 HOH A 69 569 85 HOH HOH . E 5 HOH A 70 570 102 HOH HOH . E 5 HOH A 71 571 173 HOH HOH . E 5 HOH A 72 572 69 HOH HOH . E 5 HOH A 73 573 33 HOH HOH . E 5 HOH A 74 574 13 HOH HOH . E 5 HOH A 75 575 73 HOH HOH . E 5 HOH A 76 576 30 HOH HOH . E 5 HOH A 77 577 25 HOH HOH . E 5 HOH A 78 578 90 HOH HOH . E 5 HOH A 79 579 79 HOH HOH . E 5 HOH A 80 580 14 HOH HOH . E 5 HOH A 81 581 87 HOH HOH . E 5 HOH A 82 582 81 HOH HOH . E 5 HOH A 83 583 78 HOH HOH . E 5 HOH A 84 584 115 HOH HOH . E 5 HOH A 85 585 104 HOH HOH . E 5 HOH A 86 586 109 HOH HOH . E 5 HOH A 87 587 168 HOH HOH . E 5 HOH A 88 588 57 HOH HOH . E 5 HOH A 89 589 65 HOH HOH . E 5 HOH A 90 590 43 HOH HOH . E 5 HOH A 91 591 42 HOH HOH . E 5 HOH A 92 592 34 HOH HOH . E 5 HOH A 93 593 15 HOH HOH . E 5 HOH A 94 594 86 HOH HOH . E 5 HOH A 95 595 50 HOH HOH . E 5 HOH A 96 596 60 HOH HOH . E 5 HOH A 97 597 40 HOH HOH . E 5 HOH A 98 598 38 HOH HOH . E 5 HOH A 99 599 96 HOH HOH . E 5 HOH A 100 600 74 HOH HOH . E 5 HOH A 101 601 158 HOH HOH . E 5 HOH A 102 602 174 HOH HOH . E 5 HOH A 103 603 16 HOH HOH . E 5 HOH A 104 604 2 HOH HOH . E 5 HOH A 105 605 32 HOH HOH . E 5 HOH A 106 606 93 HOH HOH . E 5 HOH A 107 607 149 HOH HOH . E 5 HOH A 108 608 141 HOH HOH . E 5 HOH A 109 609 127 HOH HOH . E 5 HOH A 110 610 70 HOH HOH . E 5 HOH A 111 611 55 HOH HOH . E 5 HOH A 112 612 128 HOH HOH . E 5 HOH A 113 613 76 HOH HOH . E 5 HOH A 114 614 133 HOH HOH . E 5 HOH A 115 615 67 HOH HOH . E 5 HOH A 116 616 123 HOH HOH . E 5 HOH A 117 617 72 HOH HOH . E 5 HOH A 118 618 80 HOH HOH . E 5 HOH A 119 619 122 HOH HOH . E 5 HOH A 120 620 31 HOH HOH . E 5 HOH A 121 621 116 HOH HOH . E 5 HOH A 122 622 89 HOH HOH . E 5 HOH A 123 623 27 HOH HOH . E 5 HOH A 124 624 111 HOH HOH . E 5 HOH A 125 625 110 HOH HOH . E 5 HOH A 126 626 157 HOH HOH . E 5 HOH A 127 627 95 HOH HOH . E 5 HOH A 128 628 106 HOH HOH . E 5 HOH A 129 629 139 HOH HOH . E 5 HOH A 130 630 53 HOH HOH . E 5 HOH A 131 631 100 HOH HOH . E 5 HOH A 132 632 175 HOH HOH . E 5 HOH A 133 633 91 HOH HOH . E 5 HOH A 134 634 156 HOH HOH . E 5 HOH A 135 635 107 HOH HOH . E 5 HOH A 136 636 92 HOH HOH . E 5 HOH A 137 637 52 HOH HOH . E 5 HOH A 138 638 146 HOH HOH . E 5 HOH A 139 639 145 HOH HOH . E 5 HOH A 140 640 119 HOH HOH . E 5 HOH A 141 641 170 HOH HOH . E 5 HOH A 142 642 164 HOH HOH . E 5 HOH A 143 643 108 HOH HOH . E 5 HOH A 144 644 99 HOH HOH . E 5 HOH A 145 645 97 HOH HOH . E 5 HOH A 146 646 124 HOH HOH . E 5 HOH A 147 647 132 HOH HOH . E 5 HOH A 148 648 144 HOH HOH . E 5 HOH A 149 649 56 HOH HOH . E 5 HOH A 150 650 114 HOH HOH . E 5 HOH A 151 651 167 HOH HOH . E 5 HOH A 152 652 142 HOH HOH . E 5 HOH A 153 653 151 HOH HOH . E 5 HOH A 154 654 44 HOH HOH . E 5 HOH A 155 655 121 HOH HOH . E 5 HOH A 156 656 178 HOH HOH . E 5 HOH A 157 657 147 HOH HOH . E 5 HOH A 158 658 101 HOH HOH . E 5 HOH A 159 659 136 HOH HOH . E 5 HOH A 160 660 171 HOH HOH . E 5 HOH A 161 661 88 HOH HOH . E 5 HOH A 162 662 130 HOH HOH . E 5 HOH A 163 663 176 HOH HOH . E 5 HOH A 164 664 162 HOH HOH . E 5 HOH A 165 665 105 HOH HOH . E 5 HOH A 166 666 137 HOH HOH . E 5 HOH A 167 667 154 HOH HOH . E 5 HOH A 168 668 23 HOH HOH . E 5 HOH A 169 669 150 HOH HOH . E 5 HOH A 170 670 112 HOH HOH . E 5 HOH A 171 671 163 HOH HOH . E 5 HOH A 172 672 45 HOH HOH . E 5 HOH A 173 673 58 HOH HOH . E 5 HOH A 174 674 131 HOH HOH . E 5 HOH A 175 675 166 HOH HOH . E 5 HOH A 176 676 83 HOH HOH . E 5 HOH A 177 677 129 HOH HOH . E 5 HOH A 178 678 165 HOH HOH . E 5 HOH A 179 679 159 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 . . . B 2 38.764 2.578 22.509 1 26.25 ? N SAM 401 A 1 HETATM 2 C CA SAM . . . B 2 38.137 3.12 21.308 1 31.39 ? CA SAM 401 A 1 HETATM 3 C C SAM . . . B 2 38.312 4.627 21.278 1 33.16 ? C SAM 401 A 1 HETATM 4 O O SAM . . . B 2 38.911 5.182 22.2 1 34.11 ? O SAM 401 A 1 HETATM 5 O OXT SAM . . . B 2 37.865 5.313 20.351 1 33.39 ? OXT SAM 401 A 1 HETATM 6 C CB SAM . . . B 2 36.654 2.75 21.236 1 22.85 ? CB SAM 401 A 1 HETATM 7 C CG SAM . . . B 2 36.398 1.357 20.694 1 29.69 ? CG SAM 401 A 1 HETATM 8 S SD SAM . . . B 2 36.882 1.266 18.952 1 31.58 ? SD SAM 401 A 1 HETATM 9 C CE SAM . . . B 2 35.48 0.383 18.192 1 26.99 ? CE SAM 401 A 1 HETATM 10 C C5' SAM . . . B 2 37.979 -0.177 18.996 1 36.62 ? C5' SAM 401 A 1 HETATM 11 C C4' SAM . . . B 2 39.401 0.144 19.435 1 35.41 ? C4' SAM 401 A 1 HETATM 12 O O4' SAM . . . B 2 39.457 0.28 20.843 1 35.53 ? O4' SAM 401 A 1 HETATM 13 C C3' SAM . . . B 2 40.348 -0.99 19.064 1 40.04 ? C3' SAM 401 A 1 HETATM 14 O O3' SAM . . . B 2 40.948 -0.761 17.807 1 43.59 ? O3' SAM 401 A 1 HETATM 15 C C2' SAM . . . B 2 41.361 -0.945 20.179 1 38.12 ? C2' SAM 401 A 1 HETATM 16 O O2' SAM . . . B 2 42.307 0.041 19.86 1 41.38 ? O2' SAM 401 A 1 HETATM 17 C C1' SAM . . . B 2 40.574 -0.417 21.359 1 35.34 ? C1' SAM 401 A 1 HETATM 18 N N9 SAM . . . B 2 40.085 -1.532 22.187 1 40.46 ? N9 SAM 401 A 1 HETATM 19 C C8 SAM . . . B 2 38.835 -2.098 22.132 1 35.79 ? C8 SAM 401 A 1 HETATM 20 N N7 SAM . . . B 2 38.774 -3.09 23.045 1 36.8 ? N7 SAM 401 A 1 HETATM 21 C C5 SAM . . . B 2 39.969 -3.18 23.676 1 40.87 ? C5 SAM 401 A 1 HETATM 22 C C6 SAM . . . B 2 40.447 -4.011 24.687 1 39.73 ? C6 SAM 401 A 1 HETATM 23 N N6 SAM . . . B 2 39.677 -4.953 25.214 1 37.06 ? N6 SAM 401 A 1 HETATM 24 N N1 SAM . . . B 2 41.738 -3.861 25.143 1 42.5 ? N1 SAM 401 A 1 HETATM 25 C C2 SAM . . . B 2 42.545 -2.889 24.598 1 40.47 ? C2 SAM 401 A 1 HETATM 26 N N3 SAM . . . B 2 42.072 -2.062 23.601 1 42.71 ? N3 SAM 401 A 1 HETATM 27 C C4 SAM . . . B 2 40.802 -2.205 23.145 1 40.97 ? C4 SAM 401 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #