data_1VID # _model_server_result.job_id XjqWjA8D176_dqGtNKWseg _model_server_result.datetime_utc '2024-11-23 05:38:29' _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 1vid # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 1VID # _exptl.entry_id 1VID _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 1VID _cell.length_a 51.3 _cell.length_b 51.3 _cell.length_c 168.5 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VID _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 A OD1 ASP 141 A ASP 141 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc2 A OD2 ASP 169 A ASP 169 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc3 A OD1 ASN 170 A ASN 170 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc4 B MG MG . A MG 300 1_555 D O1 DNC . A DNC 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc5 B MG MG . A MG 300 1_555 D O2 DNC . A DNC 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc6 B MG MG . A MG 300 1_555 E O HOH . A HOH 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? # _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 295 n n N HN1 SAM sing 296 n n N HN2 SAM sing 297 n n CA C SAM sing 298 n n CA CB SAM sing 299 n n CA HA SAM sing 300 n n C O SAM doub 301 n n C OXT SAM sing 302 n n CB CG SAM sing 303 n n CB HB1 SAM sing 304 n n CB HB2 SAM sing 305 n n CG SD SAM sing 306 n n CG HG1 SAM sing 307 n n CG HG2 SAM sing 308 n n SD CE SAM sing 309 n n SD C5' SAM sing 310 n n CE HE1 SAM sing 311 n n CE HE2 SAM sing 312 n n CE HE3 SAM sing 313 n n C5' C4' SAM sing 314 n n C5' "H5'1" SAM sing 315 n n C5' "H5'2" SAM sing 316 n n C4' O4' SAM sing 317 n n C4' C3' SAM sing 318 n n C4' H4' SAM sing 319 n n O4' C1' SAM sing 320 n n C3' O3' SAM sing 321 n n C3' C2' SAM sing 322 n n C3' H3' SAM sing 323 n n O3' HO3' SAM sing 324 n n C2' O2' SAM sing 325 n n C2' C1' SAM sing 326 n n C2' H2' SAM sing 327 n n O2' HO2' SAM sing 328 n n C1' N9 SAM sing 329 n n C1' H1' SAM sing 330 n n N9 C8 SAM sing 331 n y N9 C4 SAM sing 332 n y C8 N7 SAM doub 333 n y C8 H8 SAM sing 334 n n N7 C5 SAM sing 335 n y C5 C6 SAM sing 336 n y C5 C4 SAM doub 337 n y C6 N6 SAM sing 338 n n C6 N1 SAM doub 339 n y N6 HN61 SAM sing 340 n n N6 HN62 SAM sing 341 n n N1 C2 SAM sing 342 n y C2 N3 SAM doub 343 n y C2 H2 SAM sing 344 n n N3 C4 SAM sing 345 n y # _atom_sites.entry_id 1VID _atom_sites.fract_transf_matrix[1][1] 0.019493 _atom_sites.fract_transf_matrix[1][2] 0.011254 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022509 _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] 0.005935 _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 MG A 1 300 300 MG MG . C 3 SAM A 1 301 301 SAM SAM . D 4 DNC A 1 302 302 DNC DNC . E 5 HOH A 1 350 350 HOH HOH . E 5 HOH A 2 351 351 HOH HOH . E 5 HOH A 3 352 352 HOH HOH . E 5 HOH A 4 353 353 HOH HOH . E 5 HOH A 5 354 354 HOH HOH . E 5 HOH A 6 355 355 HOH HOH . E 5 HOH A 7 356 356 HOH HOH . E 5 HOH A 8 357 357 HOH HOH . E 5 HOH A 9 358 358 HOH HOH . E 5 HOH A 10 359 359 HOH HOH . E 5 HOH A 11 360 360 HOH HOH . E 5 HOH A 12 361 361 HOH HOH . E 5 HOH A 13 362 362 HOH HOH . E 5 HOH A 14 363 363 HOH HOH . E 5 HOH A 15 364 364 HOH HOH . E 5 HOH A 16 365 365 HOH HOH . E 5 HOH A 17 366 366 HOH HOH . E 5 HOH A 18 367 367 HOH HOH . E 5 HOH A 19 368 368 HOH HOH . E 5 HOH A 20 369 369 HOH HOH . E 5 HOH A 21 370 370 HOH HOH . E 5 HOH A 22 371 371 HOH HOH . E 5 HOH A 23 372 372 HOH HOH . E 5 HOH A 24 373 373 HOH HOH . E 5 HOH A 25 374 374 HOH HOH . E 5 HOH A 26 375 375 HOH HOH . E 5 HOH A 27 376 376 HOH HOH . E 5 HOH A 28 377 377 HOH HOH . E 5 HOH A 29 378 378 HOH HOH . E 5 HOH A 30 379 379 HOH HOH . E 5 HOH A 31 380 380 HOH HOH . E 5 HOH A 32 381 381 HOH HOH . E 5 HOH A 33 382 382 HOH HOH . E 5 HOH A 34 383 383 HOH HOH . E 5 HOH A 35 384 384 HOH HOH . E 5 HOH A 36 385 385 HOH HOH . E 5 HOH A 37 386 386 HOH HOH . E 5 HOH A 38 387 387 HOH HOH . E 5 HOH A 39 388 388 HOH HOH . E 5 HOH A 40 389 389 HOH HOH . E 5 HOH A 41 390 390 HOH HOH . E 5 HOH A 42 391 391 HOH HOH . E 5 HOH A 43 392 392 HOH HOH . E 5 HOH A 44 393 393 HOH HOH . E 5 HOH A 45 394 394 HOH HOH . E 5 HOH A 46 395 395 HOH HOH . E 5 HOH A 47 396 396 HOH HOH . E 5 HOH A 48 397 397 HOH HOH . E 5 HOH A 49 398 398 HOH HOH . E 5 HOH A 50 399 399 HOH HOH . E 5 HOH A 51 400 400 HOH HOH . E 5 HOH A 52 401 401 HOH HOH . E 5 HOH A 53 402 402 HOH HOH . E 5 HOH A 54 403 403 HOH HOH . E 5 HOH A 55 404 404 HOH HOH . E 5 HOH A 56 405 405 HOH HOH . E 5 HOH A 57 406 406 HOH HOH . E 5 HOH A 58 407 407 HOH HOH . E 5 HOH A 59 408 408 HOH HOH . E 5 HOH A 60 409 409 HOH HOH . E 5 HOH A 61 410 410 HOH HOH . E 5 HOH A 62 411 411 HOH HOH . E 5 HOH A 63 412 412 HOH HOH . E 5 HOH A 64 413 413 HOH HOH . E 5 HOH A 65 414 414 HOH HOH . E 5 HOH A 66 415 415 HOH HOH . E 5 HOH A 67 416 416 HOH HOH . E 5 HOH A 68 417 417 HOH HOH . E 5 HOH A 69 418 418 HOH HOH . E 5 HOH A 70 419 419 HOH HOH . E 5 HOH A 71 420 420 HOH HOH . E 5 HOH A 72 421 421 HOH HOH . E 5 HOH A 73 422 422 HOH HOH . E 5 HOH A 74 423 423 HOH HOH . E 5 HOH A 75 424 424 HOH HOH . E 5 HOH A 76 425 425 HOH HOH . E 5 HOH A 77 426 426 HOH HOH . E 5 HOH A 78 427 427 HOH HOH . E 5 HOH A 79 428 428 HOH HOH . E 5 HOH A 80 429 429 HOH HOH . E 5 HOH A 81 430 430 HOH HOH . E 5 HOH A 82 431 431 HOH HOH . E 5 HOH A 83 432 432 HOH HOH . E 5 HOH A 84 433 433 HOH HOH . E 5 HOH A 85 434 434 HOH HOH . E 5 HOH A 86 435 435 HOH HOH . E 5 HOH A 87 436 436 HOH HOH . E 5 HOH A 88 437 437 HOH HOH . E 5 HOH A 89 438 438 HOH HOH . E 5 HOH A 90 439 439 HOH HOH . E 5 HOH A 91 440 440 HOH HOH . E 5 HOH A 92 441 441 HOH HOH . E 5 HOH A 93 442 442 HOH HOH . E 5 HOH A 94 443 443 HOH HOH . E 5 HOH A 95 444 444 HOH HOH . E 5 HOH A 96 445 445 HOH HOH . E 5 HOH A 97 446 446 HOH HOH . E 5 HOH A 98 447 447 HOH HOH . E 5 HOH A 99 448 448 HOH HOH . E 5 HOH A 100 450 450 HOH HOH . E 5 HOH A 101 451 451 HOH HOH . E 5 HOH A 102 452 452 HOH HOH . E 5 HOH A 103 453 453 HOH HOH . E 5 HOH A 104 454 454 HOH HOH . E 5 HOH A 105 455 455 HOH HOH . E 5 HOH A 106 456 456 HOH HOH . E 5 HOH A 107 457 457 HOH HOH . E 5 HOH A 108 458 458 HOH HOH . E 5 HOH A 109 459 459 HOH HOH . E 5 HOH A 110 460 460 HOH HOH . E 5 HOH A 111 461 461 HOH HOH . E 5 HOH A 112 462 462 HOH HOH . E 5 HOH A 113 463 463 HOH HOH . E 5 HOH A 114 464 464 HOH HOH . E 5 HOH A 115 465 465 HOH HOH . E 5 HOH A 116 466 466 HOH HOH . E 5 HOH A 117 467 467 HOH HOH . E 5 HOH A 118 468 468 HOH HOH . E 5 HOH A 119 469 469 HOH HOH . E 5 HOH A 120 470 470 HOH HOH . E 5 HOH A 121 471 471 HOH HOH . E 5 HOH A 122 472 472 HOH HOH . E 5 HOH A 123 473 473 HOH HOH . E 5 HOH A 124 474 474 HOH HOH . E 5 HOH A 125 475 475 HOH HOH . E 5 HOH A 126 476 476 HOH HOH . E 5 HOH A 127 477 477 HOH HOH . E 5 HOH A 128 478 478 HOH HOH . E 5 HOH A 129 479 479 HOH HOH . E 5 HOH A 130 480 480 HOH HOH . E 5 HOH A 131 481 481 HOH HOH . E 5 HOH A 132 482 482 HOH HOH . E 5 HOH A 133 483 483 HOH HOH . E 5 HOH A 134 484 484 HOH HOH . E 5 HOH A 135 485 485 HOH HOH . E 5 HOH A 136 486 486 HOH HOH . E 5 HOH A 137 487 487 HOH HOH . E 5 HOH A 138 488 488 HOH HOH . E 5 HOH A 139 489 489 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 -21.548 65.546 44.034 1 11.23 ? N SAM 301 A 1 HETATM 2 C CA SAM . . . C 3 -22.585 64.834 43.465 1 11.46 ? CA SAM 301 A 1 HETATM 3 C C SAM . . . C 3 -23.769 65.716 43.39 1 12.76 ? C SAM 301 A 1 HETATM 4 O O SAM . . . C 3 -24.093 66.484 44.313 1 13.98 ? O SAM 301 A 1 HETATM 5 O OXT SAM . . . C 3 -24.414 65.689 42.366 1 13.96 ? OXT SAM 301 A 1 HETATM 6 C CB SAM . . . C 3 -22.597 63.629 44.254 1 13.29 ? CB SAM 301 A 1 HETATM 7 C CG SAM . . . C 3 -21.999 62.311 44.054 1 13.08 ? CG SAM 301 A 1 HETATM 8 S SD SAM . . . C 3 -22.494 60.825 44.965 1 13.46 ? SD SAM 301 A 1 HETATM 9 C CE SAM . . . C 3 -22.624 61.328 46.635 1 10.75 ? CE SAM 301 A 1 HETATM 10 C C5' SAM . . . C 3 -20.799 60.37 44.563 1 14.74 ? C5' SAM 301 A 1 HETATM 11 C C4' SAM . . . C 3 -20.098 59.461 43.603 1 14.43 ? C4' SAM 301 A 1 HETATM 12 O O4' SAM . . . C 3 -18.777 59.211 43.652 1 15.64 ? O4' SAM 301 A 1 HETATM 13 C C3' SAM . . . C 3 -20.934 58.424 42.857 1 14.8 ? C3' SAM 301 A 1 HETATM 14 O O3' SAM . . . C 3 -21.393 58.816 41.604 1 14.23 ? O3' SAM 301 A 1 HETATM 15 C C2' SAM . . . C 3 -19.851 57.225 42.935 1 14.97 ? C2' SAM 301 A 1 HETATM 16 O O2' SAM . . . C 3 -19.708 56.335 41.847 1 17.9 ? O2' SAM 301 A 1 HETATM 17 C C1' SAM . . . C 3 -18.561 57.995 43.152 1 15.68 ? C1' SAM 301 A 1 HETATM 18 N N9 SAM . . . C 3 -17.269 57.906 43.785 1 14.72 ? N9 SAM 301 A 1 HETATM 19 C C8 SAM . . . C 3 -17.007 57.103 44.816 1 12.31 ? C8 SAM 301 A 1 HETATM 20 N N7 SAM . . . C 3 -15.785 56.739 45.114 1 14.66 ? N7 SAM 301 A 1 HETATM 21 C C5 SAM . . . C 3 -15.17 57.324 44.117 1 15.26 ? C5 SAM 301 A 1 HETATM 22 C C6 SAM . . . C 3 -13.754 57.465 43.904 1 15.04 ? C6 SAM 301 A 1 HETATM 23 N N6 SAM . . . C 3 -12.823 56.863 44.664 1 16.21 ? N6 SAM 301 A 1 HETATM 24 N N1 SAM . . . C 3 -13.302 58.218 42.904 1 14.78 ? N1 SAM 301 A 1 HETATM 25 C C2 SAM . . . C 3 -14.259 58.741 42.097 1 14.28 ? C2 SAM 301 A 1 HETATM 26 N N3 SAM . . . C 3 -15.595 58.635 42.134 1 14.97 ? N3 SAM 301 A 1 HETATM 27 C C4 SAM . . . C 3 -16.068 58.016 43.24 1 14.12 ? C4 SAM 301 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #