data_1ORI # _model_server_result.job_id pMNRwin-5kN11yvhmEfUtA _model_server_result.datetime_utc '2024-12-03 13:09:38' _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 1ori # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":354}' # _entry.id 1ORI # _exptl.entry_id 1ORI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _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 1ORI _cell.length_a 88.27 _cell.length_b 88.27 _cell.length_c 145.14 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ORI _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 2 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 PQS monomeric 1 author_and_software_defined_assembly 1 PISA dimeric 2 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 1 1 A,B,C,D,E 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' 6_565 x,-y+1,-z+1/2 1 0 0 0 -1 0 0 0 -1 0 88.27 72.57 # _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 # _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 277 n n N HN1 SAH sing 278 n n N HN2 SAH sing 279 n n CA CB SAH sing 280 n n CA C SAH sing 281 n n CA HA SAH sing 282 n n CB CG SAH sing 283 n n CB HB1 SAH sing 284 n n CB HB2 SAH sing 285 n n CG SD SAH sing 286 n n CG HG1 SAH sing 287 n n CG HG2 SAH sing 288 n n SD C5' SAH sing 289 n n C O SAH doub 290 n n C OXT SAH sing 291 n n OXT HXT SAH sing 292 n n C5' C4' SAH sing 293 n n C5' "H5'1" SAH sing 294 n n C5' "H5'2" SAH sing 295 n n C4' O4' SAH sing 296 n n C4' C3' SAH sing 297 n n C4' H4' SAH sing 298 n n O4' C1' SAH sing 299 n n C3' O3' SAH sing 300 n n C3' C2' SAH sing 301 n n C3' H3' SAH sing 302 n n O3' HO3' SAH sing 303 n n C2' O2' SAH sing 304 n n C2' C1' SAH sing 305 n n C2' H2' SAH sing 306 n n O2' HO2' SAH sing 307 n n C1' N9 SAH sing 308 n n C1' H1' SAH sing 309 n n N9 C8 SAH sing 310 n y N9 C4 SAH sing 311 n y C8 N7 SAH doub 312 n y C8 H8 SAH sing 313 n n N7 C5 SAH sing 314 n y C5 C6 SAH sing 315 n y C5 C4 SAH doub 316 n y C6 N6 SAH sing 317 n n C6 N1 SAH doub 318 n y N6 HN61 SAH sing 319 n n N6 HN62 SAH sing 320 n n N1 C2 SAH sing 321 n y C2 N3 SAH doub 322 n y C2 H2 SAH sing 323 n n N3 C4 SAH sing 324 n y # _atom_sites.entry_id 1ORI _atom_sites.fract_transf_matrix[1][1] 0.011329 _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] 0.011329 _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] 0.00689 _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 SAH A 1 354 354 SAH SAH . C 3 UNL A 1 355 355 UNL UNK . D 3 UNL A 1 700 700 UNL UNK . E 4 HOH A 1 356 356 HOH H2O . E 4 HOH A 2 357 357 HOH H2O . E 4 HOH A 3 358 358 HOH H2O . E 4 HOH A 4 359 359 HOH H2O . E 4 HOH A 5 360 360 HOH H2O . E 4 HOH A 6 362 362 HOH H2O . E 4 HOH A 7 363 363 HOH H2O . E 4 HOH A 8 364 364 HOH H2O . E 4 HOH A 9 365 365 HOH H2O . E 4 HOH A 10 366 366 HOH H2O . E 4 HOH A 11 367 367 HOH H2O . E 4 HOH A 12 368 368 HOH H2O . E 4 HOH A 13 369 369 HOH H2O . E 4 HOH A 14 370 370 HOH H2O . E 4 HOH A 15 371 371 HOH H2O . E 4 HOH A 16 372 372 HOH H2O . E 4 HOH A 17 373 373 HOH H2O . E 4 HOH A 18 374 374 HOH H2O . E 4 HOH A 19 375 375 HOH H2O . E 4 HOH A 20 376 376 HOH H2O . E 4 HOH A 21 377 377 HOH H2O . E 4 HOH A 22 378 378 HOH H2O . E 4 HOH A 23 379 379 HOH H2O . E 4 HOH A 24 380 380 HOH H2O . E 4 HOH A 25 381 381 HOH H2O . E 4 HOH A 26 382 382 HOH H2O . E 4 HOH A 27 383 383 HOH H2O . E 4 HOH A 28 384 384 HOH H2O . E 4 HOH A 29 385 385 HOH H2O . E 4 HOH A 30 386 386 HOH H2O . E 4 HOH A 31 387 387 HOH H2O . E 4 HOH A 32 388 388 HOH H2O . E 4 HOH A 33 389 389 HOH H2O . E 4 HOH A 34 390 390 HOH H2O . E 4 HOH A 35 391 391 HOH H2O . E 4 HOH A 36 392 392 HOH H2O . E 4 HOH A 37 393 393 HOH H2O . E 4 HOH A 38 394 394 HOH H2O . E 4 HOH A 39 395 395 HOH H2O . E 4 HOH A 40 397 397 HOH H2O . E 4 HOH A 41 398 398 HOH H2O . E 4 HOH A 42 400 400 HOH H2O . E 4 HOH A 43 401 401 HOH H2O . E 4 HOH A 44 403 403 HOH H2O . E 4 HOH A 45 404 404 HOH H2O . E 4 HOH A 46 405 405 HOH H2O . E 4 HOH A 47 406 406 HOH H2O . E 4 HOH A 48 408 408 HOH H2O . E 4 HOH A 49 409 409 HOH H2O . E 4 HOH A 50 410 410 HOH H2O . E 4 HOH A 51 413 413 HOH H2O . E 4 HOH A 52 414 414 HOH H2O . E 4 HOH A 53 416 416 HOH H2O . E 4 HOH A 54 417 417 HOH H2O . E 4 HOH A 55 418 418 HOH H2O . E 4 HOH A 56 419 419 HOH H2O . E 4 HOH A 57 420 420 HOH H2O . E 4 HOH A 58 421 421 HOH H2O . E 4 HOH A 59 422 422 HOH H2O . E 4 HOH A 60 423 423 HOH H2O . E 4 HOH A 61 425 425 HOH H2O . E 4 HOH A 62 426 426 HOH H2O . E 4 HOH A 63 427 427 HOH H2O . E 4 HOH A 64 428 428 HOH H2O . E 4 HOH A 65 429 429 HOH H2O . E 4 HOH A 66 431 431 HOH H2O . E 4 HOH A 67 432 432 HOH H2O . E 4 HOH A 68 433 433 HOH H2O . E 4 HOH A 69 434 434 HOH H2O . E 4 HOH A 70 435 435 HOH H2O . E 4 HOH A 71 437 437 HOH H2O . E 4 HOH A 72 438 438 HOH H2O . E 4 HOH A 73 439 439 HOH H2O . E 4 HOH A 74 440 440 HOH H2O . E 4 HOH A 75 441 441 HOH H2O . E 4 HOH A 76 442 442 HOH H2O . E 4 HOH A 77 443 443 HOH H2O . E 4 HOH A 78 444 444 HOH H2O . E 4 HOH A 79 448 448 HOH H2O . E 4 HOH A 80 449 449 HOH H2O . E 4 HOH A 81 450 450 HOH H2O . E 4 HOH A 82 454 454 HOH H2O . E 4 HOH A 83 455 455 HOH H2O . E 4 HOH A 84 456 456 HOH H2O . E 4 HOH A 85 457 457 HOH H2O . E 4 HOH A 86 458 458 HOH H2O . E 4 HOH A 87 459 459 HOH H2O . E 4 HOH A 88 460 460 HOH H2O . E 4 HOH A 89 463 463 HOH H2O . E 4 HOH A 90 465 465 HOH H2O . E 4 HOH A 91 466 466 HOH H2O . E 4 HOH A 92 467 467 HOH H2O . E 4 HOH A 93 469 469 HOH H2O . E 4 HOH A 94 470 470 HOH H2O . E 4 HOH A 95 471 471 HOH H2O . E 4 HOH A 96 472 472 HOH H2O . E 4 HOH A 97 474 474 HOH H2O . E 4 HOH A 98 477 477 HOH H2O . E 4 HOH A 99 478 478 HOH H2O . E 4 HOH A 100 479 479 HOH H2O . E 4 HOH A 101 480 480 HOH H2O . E 4 HOH A 102 481 481 HOH H2O . E 4 HOH A 103 484 484 HOH H2O . E 4 HOH A 104 487 487 HOH H2O . E 4 HOH A 105 489 489 HOH H2O . E 4 HOH A 106 492 492 HOH H2O . E 4 HOH A 107 493 493 HOH H2O . E 4 HOH A 108 494 494 HOH H2O . E 4 HOH A 109 495 495 HOH H2O . E 4 HOH A 110 497 497 HOH H2O . E 4 HOH A 111 498 498 HOH H2O . E 4 HOH A 112 501 501 HOH H2O . E 4 HOH A 113 503 503 HOH H2O . E 4 HOH A 114 505 505 HOH H2O . E 4 HOH A 115 506 506 HOH H2O . E 4 HOH A 116 511 511 HOH H2O . E 4 HOH A 117 512 512 HOH H2O . E 4 HOH A 118 514 514 HOH H2O . E 4 HOH A 119 515 515 HOH H2O . E 4 HOH A 120 518 518 HOH H2O . E 4 HOH A 121 519 519 HOH H2O . E 4 HOH A 122 520 520 HOH H2O . E 4 HOH A 123 523 523 HOH H2O . E 4 HOH A 124 525 525 HOH H2O . E 4 HOH A 125 528 528 HOH H2O . E 4 HOH A 126 529 529 HOH H2O . E 4 HOH A 127 531 531 HOH H2O . E 4 HOH A 128 532 532 HOH H2O . E 4 HOH A 129 533 533 HOH H2O . # 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 . . . B 2 7.883 24.764 29.559 1 57.43 ? N SAH 354 A 1 HETATM 2 C CA SAH . . . B 2 7.219 25.359 30.722 1 57.77 ? CA SAH 354 A 1 HETATM 3 C CB SAH . . . B 2 7.801 26.748 31.012 1 58.95 ? CB SAH 354 A 1 HETATM 4 C CG SAH . . . B 2 8.254 27.517 29.772 1 61.47 ? CG SAH 354 A 1 HETATM 5 S SD SAH . . . B 2 8.632 29.262 30.153 1 62.87 ? SD SAH 354 A 1 HETATM 6 C C SAH . . . B 2 5.713 25.47 30.527 1 56.3 ? C SAH 354 A 1 HETATM 7 O O SAH . . . B 2 5.254 25.621 29.311 1 55.14 ? O SAH 354 A 1 HETATM 8 O OXT SAH . . . B 2 4.961 25.507 31.594 1 53.35 ? OXT SAH 354 A 1 HETATM 9 C C5' SAH . . . B 2 10.359 29.609 29.668 1 64.91 ? C5' SAH 354 A 1 HETATM 10 C C4' SAH . . . B 2 11.317 28.904 30.601 1 65 ? C4' SAH 354 A 1 HETATM 11 O O4' SAH . . . B 2 12.6 28.703 29.939 1 65.96 ? O4' SAH 354 A 1 HETATM 12 C C3' SAH . . . B 2 11.619 29.607 31.923 1 64.45 ? C3' SAH 354 A 1 HETATM 13 O O3' SAH . . . B 2 11.635 28.65 32.977 1 63.94 ? O3' SAH 354 A 1 HETATM 14 C C2' SAH . . . B 2 13.005 30.209 31.681 1 64.71 ? C2' SAH 354 A 1 HETATM 15 O O2' SAH . . . B 2 13.756 30.386 32.868 1 64.84 ? O2' SAH 354 A 1 HETATM 16 C C1' SAH . . . B 2 13.644 29.151 30.778 1 65.25 ? C1' SAH 354 A 1 HETATM 17 N N9 SAH . . . B 2 14.76 29.615 29.943 1 65.17 ? N9 SAH 354 A 1 HETATM 18 C C8 SAH . . . B 2 14.873 30.799 29.255 1 64.6 ? C8 SAH 354 A 1 HETATM 19 N N7 SAH . . . B 2 16.004 30.93 28.6 1 64.74 ? N7 SAH 354 A 1 HETATM 20 C C5 SAH . . . B 2 16.684 29.748 28.871 1 64.94 ? C5 SAH 354 A 1 HETATM 21 C C6 SAH . . . B 2 17.952 29.268 28.462 1 63.86 ? C6 SAH 354 A 1 HETATM 22 N N6 SAH . . . B 2 18.785 29.949 27.678 1 62.35 ? N6 SAH 354 A 1 HETATM 23 N N1 SAH . . . B 2 18.335 28.052 28.911 1 62.09 ? N1 SAH 354 A 1 HETATM 24 C C2 SAH . . . B 2 17.5 27.367 29.699 1 63.45 ? C2 SAH 354 A 1 HETATM 25 N N3 SAH . . . B 2 16.288 27.708 30.147 1 64.71 ? N3 SAH 354 A 1 HETATM 26 C C4 SAH . . . B 2 15.932 28.923 29.689 1 65.24 ? C4 SAH 354 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 26 #