data_3CBO # _model_server_result.job_id vntuzZKqDNW2ggADYTQFsw _model_server_result.datetime_utc '2025-03-07 00:17:05' _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 3cbo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1}' # _entry.id 3CBO # _exptl.entry_id 3CBO _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 3CBO _cell.length_a 101.707 _cell.length_b 38.87 _cell.length_c 66.338 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CBO _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1 A,B,C,D,E,F,G,H 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 101.707 0 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 covale ? covale1 A SG CYS 9 A CYS 119 1_555 E S2 BME . A BME 396 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.024 ? covale ? covale2 A SG CYS 178 A CYS 288 1_555 F S2 BME . A BME 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? covale ? covale3 B C SER 4 B SER 301 1_555 B N MLZ 5 B MLZ 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale4 B C MLZ 5 B MLZ 302 1_555 B N LYS 6 B LYS 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? # _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 325 n n N HN1 SAH sing 326 n n N HN2 SAH sing 327 n n CA CB SAH sing 328 n n CA C SAH sing 329 n n CA HA SAH sing 330 n n CB CG SAH sing 331 n n CB HB1 SAH sing 332 n n CB HB2 SAH sing 333 n n CG SD SAH sing 334 n n CG HG1 SAH sing 335 n n CG HG2 SAH sing 336 n n SD C5' SAH sing 337 n n C O SAH doub 338 n n C OXT SAH sing 339 n n OXT HXT SAH sing 340 n n C5' C4' SAH sing 341 n n C5' "H5'1" SAH sing 342 n n C5' "H5'2" SAH sing 343 n n C4' O4' SAH sing 344 n n C4' C3' SAH sing 345 n n C4' H4' SAH sing 346 n n O4' C1' SAH sing 347 n n C3' O3' SAH sing 348 n n C3' C2' SAH sing 349 n n C3' H3' SAH sing 350 n n O3' HO3' SAH sing 351 n n C2' O2' SAH sing 352 n n C2' C1' SAH sing 353 n n C2' H2' SAH sing 354 n n O2' HO2' SAH sing 355 n n C1' N9 SAH sing 356 n n C1' H1' SAH sing 357 n n N9 C8 SAH sing 358 n y N9 C4 SAH sing 359 n y C8 N7 SAH doub 360 n y C8 H8 SAH sing 361 n n N7 C5 SAH sing 362 n y C5 C6 SAH sing 363 n y C5 C4 SAH doub 364 n y C6 N6 SAH sing 365 n n C6 N1 SAH doub 366 n y N6 HN61 SAH sing 367 n n N6 HN62 SAH sing 368 n n N1 C2 SAH sing 369 n y C2 N3 SAH doub 370 n y C2 H2 SAH sing 371 n n N3 C4 SAH sing 372 n y # _atom_sites.entry_id 3CBO _atom_sites.fract_transf_matrix[1][1] 0.009832 _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] 0.025727 _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] 0.015074 _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 1 1 SAH SAH . D 4 BME A 1 395 395 BME BME . E 4 BME A 1 396 396 BME BME . F 4 BME A 1 397 397 BME BME . G 5 GOL A 1 398 397 GOL GOL . H 6 HOH A 1 399 1 HOH TIP . H 6 HOH A 2 400 2 HOH TIP . H 6 HOH A 3 401 3 HOH TIP . H 6 HOH A 4 402 4 HOH TIP . H 6 HOH A 5 403 5 HOH TIP . H 6 HOH A 6 404 6 HOH TIP . H 6 HOH A 7 405 7 HOH TIP . H 6 HOH A 8 406 8 HOH TIP . H 6 HOH A 9 407 9 HOH TIP . H 6 HOH A 10 408 10 HOH TIP . H 6 HOH A 11 409 11 HOH TIP . H 6 HOH A 12 410 12 HOH TIP . H 6 HOH A 13 411 13 HOH TIP . H 6 HOH A 14 412 14 HOH TIP . H 6 HOH A 15 413 15 HOH TIP . H 6 HOH A 16 414 16 HOH TIP . H 6 HOH A 17 415 17 HOH TIP . H 6 HOH A 18 416 18 HOH TIP . H 6 HOH A 19 417 19 HOH TIP . H 6 HOH A 20 418 20 HOH TIP . H 6 HOH A 21 419 21 HOH TIP . H 6 HOH A 22 420 22 HOH TIP . H 6 HOH A 23 421 23 HOH TIP . H 6 HOH A 24 422 24 HOH TIP . H 6 HOH A 25 423 25 HOH TIP . H 6 HOH A 26 424 26 HOH TIP . H 6 HOH A 27 425 27 HOH TIP . H 6 HOH A 28 426 28 HOH TIP . H 6 HOH A 29 427 29 HOH TIP . H 6 HOH A 30 428 30 HOH TIP . H 6 HOH A 31 429 31 HOH TIP . H 6 HOH A 32 430 32 HOH TIP . H 6 HOH A 33 431 33 HOH TIP . H 6 HOH A 34 432 34 HOH TIP . H 6 HOH A 35 433 35 HOH TIP . H 6 HOH A 36 434 36 HOH TIP . H 6 HOH A 37 435 37 HOH TIP . H 6 HOH A 38 436 38 HOH TIP . H 6 HOH A 39 437 39 HOH TIP . H 6 HOH A 40 438 40 HOH TIP . H 6 HOH A 41 439 41 HOH TIP . H 6 HOH A 42 440 42 HOH TIP . H 6 HOH A 43 441 43 HOH TIP . H 6 HOH A 44 442 44 HOH TIP . H 6 HOH A 45 443 45 HOH TIP . H 6 HOH A 46 444 46 HOH TIP . H 6 HOH A 47 445 47 HOH TIP . H 6 HOH A 48 446 48 HOH TIP . H 6 HOH A 49 447 49 HOH TIP . H 6 HOH A 50 448 50 HOH TIP . H 6 HOH A 51 449 51 HOH TIP . H 6 HOH A 52 450 54 HOH TIP . H 6 HOH A 53 451 57 HOH TIP . H 6 HOH A 54 452 58 HOH TIP . H 6 HOH A 55 453 59 HOH TIP . H 6 HOH A 56 454 60 HOH TIP . H 6 HOH A 57 455 61 HOH TIP . H 6 HOH A 58 456 62 HOH TIP . H 6 HOH A 59 457 63 HOH TIP . H 6 HOH A 60 458 64 HOH TIP . H 6 HOH A 61 459 65 HOH TIP . H 6 HOH A 62 460 66 HOH TIP . H 6 HOH A 63 461 67 HOH TIP . H 6 HOH A 64 462 68 HOH TIP . H 6 HOH A 65 463 69 HOH TIP . H 6 HOH A 66 464 70 HOH TIP . H 6 HOH A 67 465 71 HOH TIP . H 6 HOH A 68 466 73 HOH TIP . H 6 HOH A 69 467 74 HOH TIP . H 6 HOH A 70 468 75 HOH TIP . H 6 HOH A 71 469 76 HOH TIP . H 6 HOH A 72 470 77 HOH TIP . H 6 HOH A 73 471 78 HOH TIP . H 6 HOH A 74 472 79 HOH TIP . H 6 HOH A 75 473 81 HOH TIP . H 6 HOH A 76 474 82 HOH TIP . H 6 HOH A 77 475 83 HOH TIP . H 6 HOH A 78 476 84 HOH TIP . H 6 HOH A 79 477 85 HOH TIP . H 6 HOH A 80 478 86 HOH TIP . H 6 HOH A 81 479 87 HOH TIP . H 6 HOH A 82 480 88 HOH TIP . H 6 HOH A 83 481 89 HOH TIP . H 6 HOH A 84 482 90 HOH TIP . H 6 HOH A 85 483 92 HOH TIP . H 6 HOH A 86 484 93 HOH TIP . H 6 HOH A 87 485 94 HOH TIP . H 6 HOH A 88 486 95 HOH TIP . H 6 HOH A 89 487 96 HOH TIP . H 6 HOH A 90 488 98 HOH TIP . H 6 HOH A 91 489 99 HOH TIP . H 6 HOH A 92 490 100 HOH TIP . H 6 HOH A 93 491 101 HOH TIP . H 6 HOH A 94 492 102 HOH TIP . H 6 HOH A 95 493 103 HOH TIP . H 6 HOH A 96 494 104 HOH TIP . H 6 HOH A 97 495 105 HOH TIP . H 6 HOH A 98 496 106 HOH TIP . H 6 HOH A 99 497 107 HOH TIP . H 6 HOH A 100 498 108 HOH TIP . H 6 HOH A 101 499 109 HOH TIP . H 6 HOH A 102 500 110 HOH TIP . H 6 HOH A 103 501 113 HOH TIP . H 6 HOH A 104 502 114 HOH TIP . H 6 HOH A 105 503 115 HOH TIP . H 6 HOH A 106 504 116 HOH TIP . H 6 HOH A 107 505 117 HOH TIP . H 6 HOH A 108 506 118 HOH TIP . H 6 HOH A 109 507 119 HOH TIP . H 6 HOH A 110 508 120 HOH TIP . H 6 HOH A 111 509 121 HOH TIP . H 6 HOH A 112 510 124 HOH TIP . H 6 HOH A 113 511 126 HOH TIP . H 6 HOH A 114 512 127 HOH TIP . H 6 HOH A 115 513 128 HOH TIP . H 6 HOH A 116 514 129 HOH TIP . H 6 HOH A 117 515 130 HOH TIP . H 6 HOH A 118 516 132 HOH TIP . H 6 HOH A 119 517 134 HOH TIP . H 6 HOH A 120 518 135 HOH TIP . H 6 HOH A 121 519 136 HOH TIP . H 6 HOH A 122 520 139 HOH TIP . H 6 HOH A 123 521 141 HOH TIP . H 6 HOH A 124 522 142 HOH TIP . H 6 HOH A 125 523 143 HOH TIP . H 6 HOH A 126 524 144 HOH TIP . H 6 HOH A 127 525 148 HOH TIP . H 6 HOH A 128 526 149 HOH TIP . H 6 HOH A 129 527 154 HOH TIP . H 6 HOH A 130 528 155 HOH TIP . H 6 HOH A 131 529 156 HOH TIP . H 6 HOH A 132 530 157 HOH TIP . H 6 HOH A 133 531 159 HOH TIP . H 6 HOH A 134 532 160 HOH TIP . H 6 HOH A 135 533 161 HOH TIP . H 6 HOH A 136 534 162 HOH TIP . H 6 HOH A 137 535 163 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 SAH . . . C 3 11.965 3.12 10.212 1 19.58 ? N SAH 1 A 1 HETATM 2 C CA SAH . . . C 3 12.556 3.776 11.462 1 22.43 ? CA SAH 1 A 1 HETATM 3 C CB SAH . . . C 3 13.953 3.424 11.862 1 24.8 ? CB SAH 1 A 1 HETATM 4 C CG SAH . . . C 3 14.264 1.997 12.237 1 23.94 ? CG SAH 1 A 1 HETATM 5 S SD SAH . . . C 3 13.683 2.013 13.984 1 22.02 ? SD SAH 1 A 1 HETATM 6 C C SAH . . . C 3 12.414 5.333 11.27 1 21.83 ? C SAH 1 A 1 HETATM 7 O O SAH . . . C 3 11.874 5.806 10.254 1 26.82 ? O SAH 1 A 1 HETATM 8 O OXT SAH . . . C 3 12.879 6.028 12.25 1 24.53 ? OXT SAH 1 A 1 HETATM 9 C C5' SAH . . . C 3 12.642 0.616 14.088 1 21.29 ? C5' SAH 1 A 1 HETATM 10 C C4' SAH . . . C 3 11.181 0.928 13.573 1 22.8 ? C4' SAH 1 A 1 HETATM 11 O O4' SAH . . . C 3 11.172 0.937 12.146 1 22.65 ? O4' SAH 1 A 1 HETATM 12 C C3' SAH . . . C 3 10.145 -0.065 13.966 1 25.8 ? C3' SAH 1 A 1 HETATM 13 O O3' SAH . . . C 3 9.53 0.353 15.179 1 28.26 ? O3' SAH 1 A 1 HETATM 14 C C2' SAH . . . C 3 9.197 -0.098 12.707 1 28.54 ? C2' SAH 1 A 1 HETATM 15 O O2' SAH . . . C 3 8.186 0.901 12.803 1 26.73 ? O2' SAH 1 A 1 HETATM 16 C C1' SAH . . . C 3 10.129 0.117 11.5 1 25.36 ? C1' SAH 1 A 1 HETATM 17 N N9 SAH . . . C 3 10.666 -0.966 10.923 1 21.7 ? N9 SAH 1 A 1 HETATM 18 C C8 SAH . . . C 3 11.913 -1.569 10.956 1 21.64 ? C8 SAH 1 A 1 HETATM 19 N N7 SAH . . . C 3 12.05 -2.629 10.222 1 22.43 ? N7 SAH 1 A 1 HETATM 20 C C5 SAH . . . C 3 10.773 -2.783 9.617 1 23.42 ? C5 SAH 1 A 1 HETATM 21 C C6 SAH . . . C 3 10.262 -3.761 8.688 1 27.38 ? C6 SAH 1 A 1 HETATM 22 N N6 SAH . . . C 3 10.993 -4.775 8.21 1 23.3 ? N6 SAH 1 A 1 HETATM 23 N N1 SAH . . . C 3 8.945 -3.593 8.318 1 29.49 ? N1 SAH 1 A 1 HETATM 24 C C2 SAH . . . C 3 8.156 -2.576 8.77 1 28.5 ? C2 SAH 1 A 1 HETATM 25 N N3 SAH . . . C 3 8.617 -1.625 9.649 1 28.14 ? N3 SAH 1 A 1 HETATM 26 C C4 SAH . . . C 3 9.922 -1.787 10.03 1 22.91 ? C4 SAH 1 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #