data_3CBM # _model_server_result.job_id r-ZA9KWn2N9nWiqVyqtCnw _model_server_result.datetime_utc '2024-12-22 06:26:16' _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 3cbm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1}' # _entry.id 3CBM # _exptl.entry_id 3CBM _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 3CBM _cell.length_a 102.338 _cell.length_b 38.902 _cell.length_c 66.812 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CBM _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 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 covale ? covale1 A SG CYS 9 A CYS 119 1_555 E S2 BME . A BME 396 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.556 ? covale ? covale2 A SG CYS 90 A CYS 200 1_555 D S2 BME . A BME 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? covale ? covale3 A SG CYS 178 A CYS 288 1_555 F S2 BME . A BME 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? covale ? covale4 B C SER 4 B SER 301 1_555 B N MLZ 5 B MLZ 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 sing covale ? covale5 B C MLZ 5 B MLZ 302 1_555 B N LYS 6 B LYS 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 sing # _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 312 n n N HN1 SAH sing 313 n n N HN2 SAH sing 314 n n CA CB SAH sing 315 n n CA C SAH sing 316 n n CA HA SAH sing 317 n n CB CG SAH sing 318 n n CB HB1 SAH sing 319 n n CB HB2 SAH sing 320 n n CG SD SAH sing 321 n n CG HG1 SAH sing 322 n n CG HG2 SAH sing 323 n n SD C5' SAH sing 324 n n C O SAH doub 325 n n C OXT SAH sing 326 n n OXT HXT SAH sing 327 n n C5' C4' SAH sing 328 n n C5' "H5'1" SAH sing 329 n n C5' "H5'2" SAH sing 330 n n C4' O4' SAH sing 331 n n C4' C3' SAH sing 332 n n C4' H4' SAH sing 333 n n O4' C1' SAH sing 334 n n C3' O3' SAH sing 335 n n C3' C2' SAH sing 336 n n C3' H3' SAH sing 337 n n O3' HO3' SAH sing 338 n n C2' O2' SAH sing 339 n n C2' C1' SAH sing 340 n n C2' H2' SAH sing 341 n n O2' HO2' SAH sing 342 n n C1' N9 SAH sing 343 n n C1' H1' SAH sing 344 n n N9 C8 SAH sing 345 n y N9 C4 SAH sing 346 n y C8 N7 SAH doub 347 n y C8 H8 SAH sing 348 n n N7 C5 SAH sing 349 n y C5 C6 SAH sing 350 n y C5 C4 SAH doub 351 n y C6 N6 SAH sing 352 n n C6 N1 SAH doub 353 n y N6 HN61 SAH sing 354 n n N6 HN62 SAH sing 355 n n N1 C2 SAH sing 356 n y C2 N3 SAH doub 357 n y C2 H2 SAH sing 358 n n N3 C4 SAH sing 359 n y # _atom_sites.entry_id 3CBM _atom_sites.fract_transf_matrix[1][1] 0.009772 _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] 0.025706 _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] 0.014967 _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 HOH A 1 398 1 HOH TIP . G 5 HOH A 2 399 2 HOH TIP . G 5 HOH A 3 400 3 HOH TIP . G 5 HOH A 4 401 4 HOH TIP . G 5 HOH A 5 402 5 HOH TIP . G 5 HOH A 6 403 6 HOH TIP . G 5 HOH A 7 404 7 HOH TIP . G 5 HOH A 8 405 8 HOH TIP . G 5 HOH A 9 406 9 HOH TIP . G 5 HOH A 10 407 10 HOH TIP . G 5 HOH A 11 408 11 HOH TIP . G 5 HOH A 12 409 12 HOH TIP . G 5 HOH A 13 410 13 HOH TIP . G 5 HOH A 14 411 14 HOH TIP . G 5 HOH A 15 412 15 HOH TIP . G 5 HOH A 16 413 16 HOH TIP . G 5 HOH A 17 414 17 HOH TIP . G 5 HOH A 18 415 18 HOH TIP . G 5 HOH A 19 416 19 HOH TIP . G 5 HOH A 20 417 20 HOH TIP . G 5 HOH A 21 418 21 HOH TIP . G 5 HOH A 22 419 22 HOH TIP . G 5 HOH A 23 420 23 HOH TIP . G 5 HOH A 24 421 24 HOH TIP . G 5 HOH A 25 422 25 HOH TIP . G 5 HOH A 26 423 26 HOH TIP . G 5 HOH A 27 424 27 HOH TIP . G 5 HOH A 28 425 28 HOH TIP . G 5 HOH A 29 426 29 HOH TIP . G 5 HOH A 30 427 30 HOH TIP . G 5 HOH A 31 428 31 HOH TIP . G 5 HOH A 32 429 32 HOH TIP . G 5 HOH A 33 430 33 HOH TIP . G 5 HOH A 34 431 34 HOH TIP . G 5 HOH A 35 432 35 HOH TIP . G 5 HOH A 36 433 36 HOH TIP . G 5 HOH A 37 434 37 HOH TIP . G 5 HOH A 38 435 38 HOH TIP . G 5 HOH A 39 436 39 HOH TIP . G 5 HOH A 40 437 40 HOH TIP . G 5 HOH A 41 438 41 HOH TIP . G 5 HOH A 42 439 42 HOH TIP . G 5 HOH A 43 440 43 HOH TIP . G 5 HOH A 44 441 44 HOH TIP . G 5 HOH A 45 442 45 HOH TIP . G 5 HOH A 46 443 46 HOH TIP . G 5 HOH A 47 444 47 HOH TIP . G 5 HOH A 48 445 48 HOH TIP . G 5 HOH A 49 446 49 HOH TIP . G 5 HOH A 50 447 50 HOH TIP . G 5 HOH A 51 448 51 HOH TIP . G 5 HOH A 52 449 52 HOH TIP . G 5 HOH A 53 450 54 HOH TIP . G 5 HOH A 54 451 57 HOH TIP . G 5 HOH A 55 452 58 HOH TIP . G 5 HOH A 56 453 59 HOH TIP . G 5 HOH A 57 454 60 HOH TIP . G 5 HOH A 58 455 61 HOH TIP . G 5 HOH A 59 456 62 HOH TIP . G 5 HOH A 60 457 63 HOH TIP . G 5 HOH A 61 458 64 HOH TIP . G 5 HOH A 62 459 65 HOH TIP . G 5 HOH A 63 460 66 HOH TIP . G 5 HOH A 64 461 67 HOH TIP . G 5 HOH A 65 462 68 HOH TIP . G 5 HOH A 66 463 69 HOH TIP . G 5 HOH A 67 464 70 HOH TIP . G 5 HOH A 68 465 71 HOH TIP . G 5 HOH A 69 466 72 HOH TIP . G 5 HOH A 70 467 73 HOH TIP . G 5 HOH A 71 468 74 HOH TIP . G 5 HOH A 72 469 76 HOH TIP . G 5 HOH A 73 470 77 HOH TIP . G 5 HOH A 74 471 78 HOH TIP . G 5 HOH A 75 472 79 HOH TIP . G 5 HOH A 76 473 80 HOH TIP . G 5 HOH A 77 474 81 HOH TIP . G 5 HOH A 78 475 82 HOH TIP . G 5 HOH A 79 476 83 HOH TIP . G 5 HOH A 80 477 84 HOH TIP . G 5 HOH A 81 478 85 HOH TIP . G 5 HOH A 82 479 86 HOH TIP . G 5 HOH A 83 480 87 HOH TIP . G 5 HOH A 84 481 88 HOH TIP . G 5 HOH A 85 482 89 HOH TIP . G 5 HOH A 86 483 90 HOH TIP . G 5 HOH A 87 484 91 HOH TIP . G 5 HOH A 88 485 92 HOH TIP . G 5 HOH A 89 486 93 HOH TIP . G 5 HOH A 90 487 94 HOH TIP . G 5 HOH A 91 488 95 HOH TIP . G 5 HOH A 92 489 96 HOH TIP . G 5 HOH A 93 490 97 HOH TIP . G 5 HOH A 94 491 99 HOH TIP . G 5 HOH A 95 492 100 HOH TIP . G 5 HOH A 96 493 101 HOH TIP . G 5 HOH A 97 494 102 HOH TIP . G 5 HOH A 98 495 103 HOH TIP . G 5 HOH A 99 496 104 HOH TIP . G 5 HOH A 100 497 105 HOH TIP . G 5 HOH A 101 498 106 HOH TIP . G 5 HOH A 102 499 107 HOH TIP . G 5 HOH A 103 500 108 HOH TIP . G 5 HOH A 104 501 109 HOH TIP . G 5 HOH A 105 502 110 HOH TIP . G 5 HOH A 106 503 111 HOH TIP . G 5 HOH A 107 504 112 HOH TIP . G 5 HOH A 108 505 113 HOH TIP . G 5 HOH A 109 506 114 HOH TIP . G 5 HOH A 110 507 115 HOH TIP . G 5 HOH A 111 508 116 HOH TIP . G 5 HOH A 112 509 117 HOH TIP . G 5 HOH A 113 510 118 HOH TIP . G 5 HOH A 114 511 119 HOH TIP . G 5 HOH A 115 512 120 HOH TIP . G 5 HOH A 116 513 121 HOH TIP . G 5 HOH A 117 514 123 HOH TIP . G 5 HOH A 118 515 124 HOH TIP . G 5 HOH A 119 516 125 HOH TIP . G 5 HOH A 120 517 126 HOH TIP . G 5 HOH A 121 518 127 HOH TIP . G 5 HOH A 122 519 128 HOH TIP . G 5 HOH A 123 520 129 HOH TIP . G 5 HOH A 124 521 130 HOH TIP . G 5 HOH A 125 522 132 HOH TIP . G 5 HOH A 126 523 133 HOH TIP . G 5 HOH A 127 524 134 HOH TIP . G 5 HOH A 128 525 135 HOH TIP . G 5 HOH A 129 526 136 HOH TIP . G 5 HOH A 130 527 137 HOH TIP . G 5 HOH A 131 528 138 HOH TIP . G 5 HOH A 132 529 139 HOH TIP . G 5 HOH A 133 530 140 HOH TIP . G 5 HOH A 134 531 141 HOH TIP . G 5 HOH A 135 532 143 HOH TIP . G 5 HOH A 136 533 144 HOH TIP . G 5 HOH A 137 534 146 HOH TIP . G 5 HOH A 138 535 147 HOH TIP . G 5 HOH A 139 536 148 HOH TIP . G 5 HOH A 140 537 149 HOH TIP . G 5 HOH A 141 538 150 HOH TIP . G 5 HOH A 142 539 151 HOH TIP . G 5 HOH A 143 540 152 HOH TIP . G 5 HOH A 144 541 153 HOH TIP . G 5 HOH A 145 542 154 HOH TIP . G 5 HOH A 146 543 155 HOH TIP . G 5 HOH A 147 544 156 HOH TIP . G 5 HOH A 148 545 157 HOH TIP . G 5 HOH A 149 546 158 HOH TIP . G 5 HOH A 150 547 159 HOH TIP . G 5 HOH A 151 548 160 HOH TIP . G 5 HOH A 152 549 161 HOH TIP . G 5 HOH A 153 550 162 HOH TIP . G 5 HOH A 154 551 163 HOH TIP . H 5 HOH B 1 75 75 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 12.316 3.507 10.394 1 20.21 ? N SAH 1 A 1 HETATM 2 C CA SAH . . . C 3 12.866 4.088 11.691 1 20.45 ? CA SAH 1 A 1 HETATM 3 C CB SAH . . . C 3 14.252 3.699 12.104 1 20.02 ? CB SAH 1 A 1 HETATM 4 C CG SAH . . . C 3 14.522 2.253 12.432 1 19.83 ? CG SAH 1 A 1 HETATM 5 S SD SAH . . . C 3 13.931 2.252 14.166 1 20.24 ? SD SAH 1 A 1 HETATM 6 C C SAH . . . C 3 12.748 5.652 11.565 1 21.54 ? C SAH 1 A 1 HETATM 7 O O SAH . . . C 3 12.26 6.176 10.548 1 23 ? O SAH 1 A 1 HETATM 8 O OXT SAH . . . C 3 13.168 6.29 12.605 1 21.7 ? OXT SAH 1 A 1 HETATM 9 C C5' SAH . . . C 3 12.838 0.878 14.216 1 21.29 ? C5' SAH 1 A 1 HETATM 10 C C4' SAH . . . C 3 11.373 1.179 13.693 1 22.44 ? C4' SAH 1 A 1 HETATM 11 O O4' SAH . . . C 3 11.403 1.232 12.266 1 21.03 ? O4' SAH 1 A 1 HETATM 12 C C3' SAH . . . C 3 10.327 0.159 14.003 1 23.1 ? C3' SAH 1 A 1 HETATM 13 O O3' SAH . . . C 3 9.662 0.496 15.209 1 24.72 ? O3' SAH 1 A 1 HETATM 14 C C2' SAH . . . C 3 9.407 0.196 12.727 1 23.23 ? C2' SAH 1 A 1 HETATM 15 O O2' SAH . . . C 3 8.413 1.214 12.821 1 23.56 ? O2' SAH 1 A 1 HETATM 16 C C1' SAH . . . C 3 10.377 0.433 11.566 1 22.18 ? C1' SAH 1 A 1 HETATM 17 N N9 SAH . . . C 3 10.913 -0.643 10.969 1 22.23 ? N9 SAH 1 A 1 HETATM 18 C C8 SAH . . . C 3 12.167 -1.234 10.987 1 22.61 ? C8 SAH 1 A 1 HETATM 19 N N7 SAH . . . C 3 12.319 -2.273 10.238 1 21.39 ? N7 SAH 1 A 1 HETATM 20 C C5 SAH . . . C 3 11.038 -2.436 9.636 1 23.16 ? C5 SAH 1 A 1 HETATM 21 C C6 SAH . . . C 3 10.544 -3.407 8.693 1 22.53 ? C6 SAH 1 A 1 HETATM 22 N N6 SAH . . . C 3 11.3 -4.394 8.196 1 23.69 ? N6 SAH 1 A 1 HETATM 23 N N1 SAH . . . C 3 9.224 -3.266 8.333 1 22.94 ? N1 SAH 1 A 1 HETATM 24 C C2 SAH . . . C 3 8.413 -2.273 8.807 1 23.77 ? C2 SAH 1 A 1 HETATM 25 N N3 SAH . . . C 3 8.856 -1.32 9.699 1 23.1 ? N3 SAH 1 A 1 HETATM 26 C C4 SAH . . . C 3 10.17 -1.461 10.071 1 22.79 ? C4 SAH 1 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 372 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #