data_5YNI # _model_server_result.job_id KLOFPzfoP5UYSUXCexFZEg _model_server_result.datetime_utc '2024-11-23 06:32:54' _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 5yni # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5YNI # _exptl.entry_id 5YNI _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 5YNI _cell.length_a 66.954 _cell.length_b 70.064 _cell.length_c 119.762 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YNI _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc2 B SG CYS 77 B CYS 77 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc3 B NE2 HIS 83 B HIS 83 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc4 B SG CYS 90 B CYS 90 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc5 B SG CYS 117 B CYS 117 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc6 B SG CYS 120 B CYS 120 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc7 B SG CYS 128 B CYS 128 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc8 B SG CYS 130 B CYS 130 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? # _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 364 n n N HN1 SAM sing 365 n n N HN2 SAM sing 366 n n CA C SAM sing 367 n n CA CB SAM sing 368 n n CA HA SAM sing 369 n n C O SAM doub 370 n n C OXT SAM sing 371 n n CB CG SAM sing 372 n n CB HB1 SAM sing 373 n n CB HB2 SAM sing 374 n n CG SD SAM sing 375 n n CG HG1 SAM sing 376 n n CG HG2 SAM sing 377 n n SD CE SAM sing 378 n n SD C5' SAM sing 379 n n CE HE1 SAM sing 380 n n CE HE2 SAM sing 381 n n CE HE3 SAM sing 382 n n C5' C4' SAM sing 383 n n C5' "H5'1" SAM sing 384 n n C5' "H5'2" SAM sing 385 n n C4' O4' SAM sing 386 n n C4' C3' SAM sing 387 n n C4' H4' SAM sing 388 n n O4' C1' SAM sing 389 n n C3' O3' SAM sing 390 n n C3' C2' SAM sing 391 n n C3' H3' SAM sing 392 n n O3' HO3' SAM sing 393 n n C2' O2' SAM sing 394 n n C2' C1' SAM sing 395 n n C2' H2' SAM sing 396 n n O2' HO2' SAM sing 397 n n C1' N9 SAM sing 398 n n C1' H1' SAM sing 399 n n N9 C8 SAM sing 400 n y N9 C4 SAM sing 401 n y C8 N7 SAM doub 402 n y C8 H8 SAM sing 403 n n N7 C5 SAM sing 404 n y C5 C6 SAM sing 405 n y C5 C4 SAM doub 406 n y C6 N6 SAM sing 407 n n C6 N1 SAM doub 408 n y N6 HN61 SAM sing 409 n n N6 HN62 SAM sing 410 n n N1 C2 SAM sing 411 n y C2 N3 SAM doub 412 n y C2 H2 SAM sing 413 n n N3 C4 SAM sing 414 n y # _atom_sites.entry_id 5YNI _atom_sites.fract_transf_matrix[1][1] 0.014936 _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] 0.014273 _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] 0.00835 _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 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 83 HOH HOH . G 6 HOH A 2 502 71 HOH HOH . G 6 HOH A 3 503 75 HOH HOH . G 6 HOH A 4 504 124 HOH HOH . G 6 HOH A 5 505 67 HOH HOH . G 6 HOH A 6 506 16 HOH HOH . G 6 HOH A 7 507 35 HOH HOH . G 6 HOH A 8 508 2 HOH HOH . G 6 HOH A 9 509 13 HOH HOH . G 6 HOH A 10 510 80 HOH HOH . G 6 HOH A 11 511 8 HOH HOH . G 6 HOH A 12 512 17 HOH HOH . G 6 HOH A 13 513 47 HOH HOH . G 6 HOH A 14 514 73 HOH HOH . G 6 HOH A 15 515 138 HOH HOH . G 6 HOH A 16 516 6 HOH HOH . G 6 HOH A 17 517 24 HOH HOH . G 6 HOH A 18 518 99 HOH HOH . G 6 HOH A 19 519 86 HOH HOH . G 6 HOH A 20 520 4 HOH HOH . G 6 HOH A 21 521 3 HOH HOH . G 6 HOH A 22 522 112 HOH HOH . G 6 HOH A 23 523 28 HOH HOH . G 6 HOH A 24 524 76 HOH HOH . G 6 HOH A 25 525 131 HOH HOH . G 6 HOH A 26 526 32 HOH HOH . G 6 HOH A 27 527 18 HOH HOH . G 6 HOH A 28 528 70 HOH HOH . G 6 HOH A 29 529 14 HOH HOH . G 6 HOH A 30 530 55 HOH HOH . G 6 HOH A 31 531 23 HOH HOH . G 6 HOH A 32 532 60 HOH HOH . G 6 HOH A 33 533 26 HOH HOH . G 6 HOH A 34 534 144 HOH HOH . G 6 HOH A 35 535 100 HOH HOH . G 6 HOH A 36 536 119 HOH HOH . G 6 HOH A 37 537 27 HOH HOH . G 6 HOH A 38 538 40 HOH HOH . G 6 HOH A 39 539 56 HOH HOH . G 6 HOH A 40 540 45 HOH HOH . G 6 HOH A 41 541 63 HOH HOH . G 6 HOH A 42 542 49 HOH HOH . G 6 HOH A 43 543 21 HOH HOH . G 6 HOH A 44 544 12 HOH HOH . G 6 HOH A 45 545 102 HOH HOH . G 6 HOH A 46 546 156 HOH HOH . G 6 HOH A 47 547 52 HOH HOH . G 6 HOH A 48 548 43 HOH HOH . G 6 HOH A 49 549 20 HOH HOH . G 6 HOH A 50 550 101 HOH HOH . G 6 HOH A 51 551 37 HOH HOH . G 6 HOH A 52 552 5 HOH HOH . G 6 HOH A 53 553 93 HOH HOH . G 6 HOH A 54 554 111 HOH HOH . G 6 HOH A 55 555 7 HOH HOH . G 6 HOH A 56 556 48 HOH HOH . G 6 HOH A 57 557 141 HOH HOH . G 6 HOH A 58 558 19 HOH HOH . G 6 HOH A 59 559 30 HOH HOH . G 6 HOH A 60 560 44 HOH HOH . G 6 HOH A 61 561 113 HOH HOH . G 6 HOH A 62 562 85 HOH HOH . G 6 HOH A 63 563 36 HOH HOH . G 6 HOH A 64 564 74 HOH HOH . G 6 HOH A 65 565 114 HOH HOH . G 6 HOH A 66 566 147 HOH HOH . G 6 HOH A 67 567 108 HOH HOH . G 6 HOH A 68 568 96 HOH HOH . G 6 HOH A 69 569 9 HOH HOH . G 6 HOH A 70 570 92 HOH HOH . G 6 HOH A 71 571 46 HOH HOH . G 6 HOH A 72 572 33 HOH HOH . G 6 HOH A 73 573 62 HOH HOH . G 6 HOH A 74 574 54 HOH HOH . G 6 HOH A 75 575 133 HOH HOH . G 6 HOH A 76 576 39 HOH HOH . G 6 HOH A 77 577 25 HOH HOH . G 6 HOH A 78 578 122 HOH HOH . G 6 HOH A 79 579 98 HOH HOH . G 6 HOH A 80 580 50 HOH HOH . G 6 HOH A 81 581 121 HOH HOH . G 6 HOH A 82 582 150 HOH HOH . G 6 HOH A 83 583 59 HOH HOH . G 6 HOH A 84 584 57 HOH HOH . G 6 HOH A 85 585 41 HOH HOH . G 6 HOH A 86 586 78 HOH HOH . G 6 HOH A 87 587 143 HOH HOH . G 6 HOH A 88 588 10 HOH HOH . G 6 HOH A 89 589 34 HOH HOH . G 6 HOH A 90 590 145 HOH HOH . G 6 HOH A 91 591 87 HOH HOH . G 6 HOH A 92 592 109 HOH HOH . G 6 HOH A 93 593 58 HOH HOH . G 6 HOH A 94 594 106 HOH HOH . G 6 HOH A 95 595 42 HOH HOH . G 6 HOH A 96 596 15 HOH HOH . G 6 HOH A 97 597 89 HOH HOH . G 6 HOH A 98 598 140 HOH HOH . G 6 HOH A 99 599 94 HOH HOH . G 6 HOH A 100 600 61 HOH HOH . G 6 HOH A 101 601 128 HOH HOH . G 6 HOH A 102 602 82 HOH HOH . G 6 HOH A 103 603 65 HOH HOH . G 6 HOH A 104 604 163 HOH HOH . G 6 HOH A 105 605 79 HOH HOH . G 6 HOH A 106 606 90 HOH HOH . G 6 HOH A 107 607 88 HOH HOH . G 6 HOH A 108 608 68 HOH HOH . G 6 HOH A 109 609 164 HOH HOH . G 6 HOH A 110 610 120 HOH HOH . G 6 HOH A 111 611 125 HOH HOH . G 6 HOH A 112 612 154 HOH HOH . G 6 HOH A 113 613 66 HOH HOH . G 6 HOH A 114 614 137 HOH HOH . G 6 HOH A 115 615 155 HOH HOH . G 6 HOH A 116 616 31 HOH HOH . G 6 HOH A 117 617 22 HOH HOH . G 6 HOH A 118 618 169 HOH HOH . G 6 HOH A 119 619 162 HOH HOH . G 6 HOH A 120 620 134 HOH HOH . G 6 HOH A 121 621 160 HOH HOH . G 6 HOH A 122 622 159 HOH HOH . G 6 HOH A 123 623 149 HOH HOH . G 6 HOH A 124 624 173 HOH HOH . G 6 HOH A 125 625 179 HOH HOH . G 6 HOH A 126 626 152 HOH HOH . G 6 HOH A 127 627 161 HOH HOH . G 6 HOH A 128 628 139 HOH HOH . G 6 HOH A 129 629 151 HOH HOH . G 6 HOH A 130 630 117 HOH HOH . G 6 HOH A 131 631 127 HOH HOH . G 6 HOH A 132 632 178 HOH HOH . G 6 HOH A 133 633 157 HOH HOH . G 6 HOH A 134 634 142 HOH HOH . G 6 HOH A 135 635 130 HOH HOH . G 6 HOH A 136 636 95 HOH HOH . G 6 HOH A 137 637 104 HOH HOH . G 6 HOH A 138 638 1 HOH HOH . G 6 HOH A 139 639 171 HOH HOH . G 6 HOH A 140 640 110 HOH HOH . G 6 HOH A 141 641 174 HOH HOH . G 6 HOH A 142 642 29 HOH HOH . G 6 HOH A 143 643 115 HOH HOH . G 6 HOH A 144 644 167 HOH HOH . G 6 HOH A 145 645 165 HOH HOH . G 6 HOH A 146 646 176 HOH HOH . G 6 HOH A 147 647 153 HOH HOH . G 6 HOH A 148 648 11 HOH HOH . G 6 HOH A 149 649 172 HOH HOH . G 6 HOH A 150 650 136 HOH HOH . G 6 HOH A 151 651 105 HOH HOH . G 6 HOH A 152 652 146 HOH HOH . G 6 HOH A 153 653 158 HOH HOH . G 6 HOH A 154 654 177 HOH HOH . G 6 HOH A 155 655 175 HOH HOH . G 6 HOH A 156 656 170 HOH HOH . H 6 HOH B 1 301 81 HOH HOH . H 6 HOH B 2 302 118 HOH HOH . H 6 HOH B 3 303 126 HOH HOH . H 6 HOH B 4 304 77 HOH HOH . H 6 HOH B 5 305 64 HOH HOH . H 6 HOH B 6 306 53 HOH HOH . H 6 HOH B 7 307 72 HOH HOH . H 6 HOH B 8 308 91 HOH HOH . H 6 HOH B 9 309 38 HOH HOH . H 6 HOH B 10 310 69 HOH HOH . H 6 HOH B 11 311 107 HOH HOH . H 6 HOH B 12 312 116 HOH HOH . H 6 HOH B 13 313 103 HOH HOH . H 6 HOH B 14 314 51 HOH HOH . H 6 HOH B 15 315 132 HOH HOH . H 6 HOH B 16 316 135 HOH HOH . H 6 HOH B 17 317 123 HOH HOH . H 6 HOH B 18 318 168 HOH HOH . H 6 HOH B 19 319 84 HOH HOH . H 6 HOH B 20 320 97 HOH HOH . H 6 HOH B 21 321 166 HOH HOH . H 6 HOH B 22 322 129 HOH HOH . H 6 HOH B 23 323 148 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 67.716 85.631 151.624 1 35.01 ? N SAM 401 A 1 HETATM 2 C CA SAM . . . C 3 67.641 84.359 150.896 1 38.13 ? CA SAM 401 A 1 HETATM 3 C C SAM . . . C 3 68.831 83.488 151.307 1 39.98 ? C SAM 401 A 1 HETATM 4 O O SAM . . . C 3 69.225 82.63 150.486 1 40.43 ? O SAM 401 A 1 HETATM 5 O OXT SAM . . . C 3 69.307 83.7 152.446 1 35.61 ? OXT SAM 401 A 1 HETATM 6 C CB SAM . . . C 3 67.616 84.587 149.378 1 38.4 ? CB SAM 401 A 1 HETATM 7 C CG SAM . . . C 3 66.348 85.386 149.057 1 37.62 ? CG SAM 401 A 1 HETATM 8 S SD SAM . . . C 3 66.166 85.664 147.27 1 38.9 ? SD SAM 401 A 1 HETATM 9 C CE SAM . . . C 3 67.643 86.45 146.66 1 42.11 ? CE SAM 401 A 1 HETATM 10 C C5' SAM . . . C 3 64.749 86.785 146.975 1 35.83 ? C5' SAM 401 A 1 HETATM 11 C C4' SAM . . . C 3 63.538 86.344 147.798 1 35.13 ? C4' SAM 401 A 1 HETATM 12 O O4' SAM . . . C 3 62.615 87.47 147.851 1 35.84 ? O4' SAM 401 A 1 HETATM 13 C C3' SAM . . . C 3 62.77 85.221 147.084 1 36.35 ? C3' SAM 401 A 1 HETATM 14 O O3' SAM . . . C 3 62.668 84.099 147.973 1 37.73 ? O3' SAM 401 A 1 HETATM 15 C C2' SAM . . . C 3 61.415 85.898 146.878 1 36.72 ? C2' SAM 401 A 1 HETATM 16 O O2' SAM . . . C 3 60.341 84.94 146.902 1 37.41 ? O2' SAM 401 A 1 HETATM 17 C C1' SAM . . . C 3 61.343 86.858 148.045 1 37.15 ? C1' SAM 401 A 1 HETATM 18 N N9 SAM . . . C 3 60.25 87.877 147.859 1 37.52 ? N9 SAM 401 A 1 HETATM 19 C C8 SAM . . . C 3 60.102 88.652 146.783 1 37.37 ? C8 SAM 401 A 1 HETATM 20 N N7 SAM . . . C 3 59.035 89.433 146.961 1 34.71 ? N7 SAM 401 A 1 HETATM 21 C C5 SAM . . . C 3 58.517 89.15 148.153 1 35.52 ? C5 SAM 401 A 1 HETATM 22 C C6 SAM . . . C 3 57.451 89.643 148.799 1 34.28 ? C6 SAM 401 A 1 HETATM 23 N N6 SAM . . . C 3 56.744 90.595 148.188 1 30.78 ? N6 SAM 401 A 1 HETATM 24 N N1 SAM . . . C 3 57.102 89.2 150.017 1 33.91 ? N1 SAM 401 A 1 HETATM 25 C C2 SAM . . . C 3 57.873 88.198 150.614 1 35.19 ? C2 SAM 401 A 1 HETATM 26 N N3 SAM . . . C 3 58.979 87.7 149.919 1 34.03 ? N3 SAM 401 A 1 HETATM 27 C C4 SAM . . . C 3 59.274 88.188 148.704 1 35.45 ? C4 SAM 401 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #