data_2YY8 # _model_server_result.job_id MUD9Fayk21NI7mzFVMfGjw _model_server_result.datetime_utc '2024-11-04 22:39:26' _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 2yy8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 2YY8 # _exptl.entry_id 2YY8 _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 120 _cell.entry_id 2YY8 _cell.length_a 56.151 _cell.length_b 56.151 _cell.length_c 121.844 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YY8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32' # _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 _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 D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 301 n n N HN1 SAM sing 302 n n N HN2 SAM sing 303 n n CA C SAM sing 304 n n CA CB SAM sing 305 n n CA HA SAM sing 306 n n C O SAM doub 307 n n C OXT SAM sing 308 n n CB CG SAM sing 309 n n CB HB1 SAM sing 310 n n CB HB2 SAM sing 311 n n CG SD SAM sing 312 n n CG HG1 SAM sing 313 n n CG HG2 SAM sing 314 n n SD CE SAM sing 315 n n SD C5' SAM sing 316 n n CE HE1 SAM sing 317 n n CE HE2 SAM sing 318 n n CE HE3 SAM sing 319 n n C5' C4' SAM sing 320 n n C5' "H5'1" SAM sing 321 n n C5' "H5'2" SAM sing 322 n n C4' O4' SAM sing 323 n n C4' C3' SAM sing 324 n n C4' H4' SAM sing 325 n n O4' C1' SAM sing 326 n n C3' O3' SAM sing 327 n n C3' C2' SAM sing 328 n n C3' H3' SAM sing 329 n n O3' HO3' SAM sing 330 n n C2' O2' SAM sing 331 n n C2' C1' SAM sing 332 n n C2' H2' SAM sing 333 n n O2' HO2' SAM sing 334 n n C1' N9 SAM sing 335 n n C1' H1' SAM sing 336 n n N9 C8 SAM sing 337 n y N9 C4 SAM sing 338 n y C8 N7 SAM doub 339 n y C8 H8 SAM sing 340 n n N7 C5 SAM sing 341 n y C5 C6 SAM sing 342 n y C5 C4 SAM doub 343 n y C6 N6 SAM sing 344 n n C6 N1 SAM doub 345 n y N6 HN61 SAM sing 346 n n N6 HN62 SAM sing 347 n n N1 C2 SAM sing 348 n y C2 N3 SAM doub 349 n y C2 H2 SAM sing 350 n n N3 C4 SAM sing 351 n y # _atom_sites.entry_id 2YY8 _atom_sites.fract_transf_matrix[1][1] 0.017809 _atom_sites.fract_transf_matrix[1][2] 0.010282 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020564 _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] 0.008207 _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 2 MTA A 1 400 400 MTA MTA . D 3 SAM B 1 500 500 SAM SAM . E 4 HOH A 1 401 1 HOH TIP . E 4 HOH A 2 402 2 HOH TIP . E 4 HOH A 3 403 4 HOH TIP . E 4 HOH A 4 404 6 HOH TIP . E 4 HOH A 5 405 9 HOH TIP . E 4 HOH A 6 406 10 HOH TIP . E 4 HOH A 7 407 11 HOH TIP . E 4 HOH A 8 408 12 HOH TIP . E 4 HOH A 9 409 13 HOH TIP . E 4 HOH A 10 410 19 HOH TIP . E 4 HOH A 11 411 23 HOH TIP . E 4 HOH A 12 412 24 HOH TIP . E 4 HOH A 13 413 25 HOH TIP . E 4 HOH A 14 414 29 HOH TIP . E 4 HOH A 15 415 31 HOH TIP . E 4 HOH A 16 416 32 HOH TIP . E 4 HOH A 17 417 33 HOH TIP . E 4 HOH A 18 418 36 HOH TIP . E 4 HOH A 19 419 39 HOH TIP . E 4 HOH A 20 420 42 HOH TIP . E 4 HOH A 21 421 43 HOH TIP . E 4 HOH A 22 422 45 HOH TIP . E 4 HOH A 23 423 46 HOH TIP . E 4 HOH A 24 424 47 HOH TIP . E 4 HOH A 25 425 48 HOH TIP . E 4 HOH A 26 426 50 HOH TIP . E 4 HOH A 27 427 52 HOH TIP . E 4 HOH A 28 428 53 HOH TIP . E 4 HOH A 29 429 55 HOH TIP . E 4 HOH A 30 430 57 HOH TIP . E 4 HOH A 31 431 58 HOH TIP . E 4 HOH A 32 432 59 HOH TIP . E 4 HOH A 33 433 60 HOH TIP . E 4 HOH A 34 434 63 HOH TIP . E 4 HOH A 35 435 64 HOH TIP . E 4 HOH A 36 436 65 HOH TIP . E 4 HOH A 37 437 66 HOH TIP . E 4 HOH A 38 438 74 HOH TIP . E 4 HOH A 39 439 75 HOH TIP . E 4 HOH A 40 440 76 HOH TIP . E 4 HOH A 41 441 79 HOH TIP . E 4 HOH A 42 442 85 HOH TIP . E 4 HOH A 43 443 86 HOH TIP . E 4 HOH A 44 444 87 HOH TIP . E 4 HOH A 45 445 90 HOH TIP . E 4 HOH A 46 446 91 HOH TIP . E 4 HOH A 47 447 93 HOH TIP . E 4 HOH A 48 448 95 HOH TIP . E 4 HOH A 49 449 96 HOH TIP . E 4 HOH A 50 450 99 HOH TIP . E 4 HOH A 51 451 100 HOH TIP . F 4 HOH B 1 501 3 HOH TIP . F 4 HOH B 2 502 5 HOH TIP . F 4 HOH B 3 503 7 HOH TIP . F 4 HOH B 4 504 8 HOH TIP . F 4 HOH B 5 505 14 HOH TIP . F 4 HOH B 6 506 15 HOH TIP . F 4 HOH B 7 507 16 HOH TIP . F 4 HOH B 8 508 17 HOH TIP . F 4 HOH B 9 509 18 HOH TIP . F 4 HOH B 10 510 20 HOH TIP . F 4 HOH B 11 511 21 HOH TIP . F 4 HOH B 12 512 22 HOH TIP . F 4 HOH B 13 513 26 HOH TIP . F 4 HOH B 14 514 27 HOH TIP . F 4 HOH B 15 515 28 HOH TIP . F 4 HOH B 16 516 30 HOH TIP . F 4 HOH B 17 517 34 HOH TIP . F 4 HOH B 18 518 35 HOH TIP . F 4 HOH B 19 519 37 HOH TIP . F 4 HOH B 20 520 38 HOH TIP . F 4 HOH B 21 521 40 HOH TIP . F 4 HOH B 22 522 41 HOH TIP . F 4 HOH B 23 523 44 HOH TIP . F 4 HOH B 24 524 49 HOH TIP . F 4 HOH B 25 525 51 HOH TIP . F 4 HOH B 26 526 54 HOH TIP . F 4 HOH B 27 527 56 HOH TIP . F 4 HOH B 28 528 61 HOH TIP . F 4 HOH B 29 529 62 HOH TIP . F 4 HOH B 30 530 67 HOH TIP . F 4 HOH B 31 531 68 HOH TIP . F 4 HOH B 32 532 69 HOH TIP . F 4 HOH B 33 533 70 HOH TIP . F 4 HOH B 34 534 71 HOH TIP . F 4 HOH B 35 535 72 HOH TIP . F 4 HOH B 36 536 73 HOH TIP . F 4 HOH B 37 537 77 HOH TIP . F 4 HOH B 38 538 78 HOH TIP . F 4 HOH B 39 539 80 HOH TIP . F 4 HOH B 40 540 81 HOH TIP . F 4 HOH B 41 541 82 HOH TIP . F 4 HOH B 42 542 83 HOH TIP . F 4 HOH B 43 543 84 HOH TIP . F 4 HOH B 44 544 88 HOH TIP . F 4 HOH B 45 545 89 HOH TIP . F 4 HOH B 46 546 92 HOH TIP . F 4 HOH B 47 547 94 HOH TIP . F 4 HOH B 48 548 97 HOH TIP . F 4 HOH B 49 549 98 HOH TIP . F 4 HOH B 50 550 101 HOH TIP . # 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 . . . D 3 18.676 21.276 -7.638 1 60.62 ? N SAM 500 B 1 HETATM 2 C CA SAM . . . D 3 17.232 21.463 -7.843 1 60.82 ? CA SAM 500 B 1 HETATM 3 C C SAM . . . D 3 16.802 22.861 -7.407 1 62.06 ? C SAM 500 B 1 HETATM 4 O O SAM . . . D 3 17.31 23.27 -6.339 1 62.95 ? O SAM 500 B 1 HETATM 5 O OXT SAM . . . D 3 15.97 23.456 -8.128 1 62.92 ? OXT SAM 500 B 1 HETATM 6 C CB SAM . . . D 3 16.507 20.425 -6.985 1 58.56 ? CB SAM 500 B 1 HETATM 7 C CG SAM . . . D 3 17.121 19.091 -7.439 1 57.42 ? CG SAM 500 B 1 HETATM 8 S SD SAM . . . D 3 16.512 17.738 -6.374 1 54.38 ? SD SAM 500 B 1 HETATM 9 C CE SAM . . . D 3 16.454 16.079 -7.029 1 53.74 ? CE SAM 500 B 1 HETATM 10 C C5' SAM . . . D 3 15.073 18.095 -5.306 1 50.41 ? C5' SAM 500 B 1 HETATM 11 C C4' SAM . . . D 3 13.656 18.461 -5.746 1 45.33 ? C4' SAM 500 B 1 HETATM 12 O O4' SAM . . . D 3 13.127 17.623 -4.689 1 43.9 ? O4' SAM 500 B 1 HETATM 13 C C3' SAM . . . D 3 13.091 19.859 -5.644 1 43.04 ? C3' SAM 500 B 1 HETATM 14 O O3' SAM . . . D 3 12.443 20.124 -6.9 1 44.05 ? O3' SAM 500 B 1 HETATM 15 C C2' SAM . . . D 3 12.194 19.637 -4.415 1 43.21 ? C2' SAM 500 B 1 HETATM 16 O O2' SAM . . . D 3 10.868 19.323 -4.849 1 41.7 ? O2' SAM 500 B 1 HETATM 17 C C1' SAM . . . D 3 12.872 18.481 -3.66 1 42.5 ? C1' SAM 500 B 1 HETATM 18 N N9 SAM . . . D 3 13.61 18.64 -2.556 1 40.38 ? N9 SAM 500 B 1 HETATM 19 C C8 SAM . . . D 3 14.894 18.373 -2.315 1 41.73 ? C8 SAM 500 B 1 HETATM 20 N N7 SAM . . . D 3 15.351 18.905 -1.181 1 39.95 ? N7 SAM 500 B 1 HETATM 21 C C5 SAM . . . D 3 14.297 19.514 -0.641 1 41.15 ? C5 SAM 500 B 1 HETATM 22 C C6 SAM . . . D 3 14.058 20.092 0.606 1 40.73 ? C6 SAM 500 B 1 HETATM 23 N N6 SAM . . . D 3 15.038 20.289 1.489 1 39.27 ? N6 SAM 500 B 1 HETATM 24 N N1 SAM . . . D 3 12.806 20.466 0.912 1 41.34 ? N1 SAM 500 B 1 HETATM 25 C C2 SAM . . . D 3 11.8 20.307 0.061 1 42.63 ? C2 SAM 500 B 1 HETATM 26 N N3 SAM . . . D 3 11.988 19.765 -1.132 1 39.72 ? N3 SAM 500 B 1 HETATM 27 C C4 SAM . . . D 3 13.212 19.358 -1.509 1 40.35 ? C4 SAM 500 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #