data_3EWD # _model_server_result.job_id lIHcBhBeGc4XOFF-mzrDSw _model_server_result.datetime_utc '2025-08-31 15:53:49' _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 3ewd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":372}' # _entry.id 3EWD # _exptl.entry_id 3EWD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 314.361 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (8R)-3-(5-S-methyl-5-thio-beta-D-ribofuranosyl)-3,6,7,8-tetrahydroimidazo[4,5-d][1,3]diazepin-8-ol _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 3EWD _cell.length_a 41.905 _cell.length_b 86.975 _cell.length_c 106.103 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EWD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 NE2 HIS 42 A HIS 42 1_555 B ZN ZN . A ZN 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc2 A NE2 HIS 44 A HIS 44 1_555 B ZN ZN . A ZN 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc3 A NE2 HIS 225 A HIS 225 1_555 B ZN ZN . A ZN 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc4 A OD1 ASP 309 A ASP 309 1_555 B ZN ZN . A ZN 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc5 B ZN ZN . A ZN 371 1_555 C O8 MCF . A MCF 372 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? # _chem_comp.formula 'C12 H18 N4 O4 S' _chem_comp.formula_weight 314.361 _chem_comp.id MCF _chem_comp.mon_nstd_flag . _chem_comp.name (8R)-3-(5-S-methyl-5-thio-beta-D-ribofuranosyl)-3,6,7,8-tetrahydroimidazo[4,5-d][1,3]diazepin-8-ol _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 C8 O8 MCF sing 218 n n O8 HO8 MCF sing 219 n n C7 C8 MCF sing 220 n n C8 C9 MCF sing 221 n n C8 H8 MCF sing 222 n n C7 N6 MCF sing 223 n n C7 H7 MCF sing 224 n n C7 H7A MCF sing 225 n n N6 C5 MCF sing 226 n n N6 HN6 MCF sing 227 n n C5 N4 MCF doub 228 n n C5 H5 MCF sing 229 n n N4 C10 MCF sing 230 n n C9 C10 MCF doub 231 n y C10 N3 MCF sing 232 n y C9 N1 MCF sing 233 n y N1 C2 MCF doub 234 n y C2 N3 MCF sing 235 n y C2 H2 MCF sing 236 n n N3 C1S MCF sing 237 n n O4S C1S MCF sing 238 n n C1S C2S MCF sing 239 n n C1S H1S MCF sing 240 n n C2S C3S MCF sing 241 n n C2S O2S MCF sing 242 n n C2S H2S MCF sing 243 n n O2S HO2S MCF sing 244 n n O4S C4S MCF sing 245 n n C5S C4S MCF sing 246 n n C4S C3S MCF sing 247 n n C4S H4S MCF sing 248 n n C3S O3S MCF sing 249 n n C3S H3S MCF sing 250 n n O3S HO3S MCF sing 251 n n C5S S5S MCF sing 252 n n C5S H5S MCF sing 253 n n C5S H5SA MCF sing 254 n n S5S C6S MCF sing 255 n n C6S H6S MCF sing 256 n n C6S H6SA MCF sing 257 n n C6S H6SB MCF sing 258 n n # _atom_sites.entry_id 3EWD _atom_sites.fract_transf_matrix[1][1] 0.023864 _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] 0.011498 _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] 0.009425 _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 ZN A 1 371 1 ZN ZN . C 3 MCF A 1 372 2 MCF MCF . D 4 HOH A 1 373 1 HOH HOH . D 4 HOH A 2 374 2 HOH HOH . D 4 HOH A 3 375 3 HOH HOH . D 4 HOH A 4 376 4 HOH HOH . D 4 HOH A 5 377 5 HOH HOH . D 4 HOH A 6 378 6 HOH HOH . D 4 HOH A 7 379 7 HOH HOH . D 4 HOH A 8 380 8 HOH HOH . D 4 HOH A 9 381 9 HOH HOH . D 4 HOH A 10 382 10 HOH HOH . D 4 HOH A 11 383 11 HOH HOH . D 4 HOH A 12 384 12 HOH HOH . D 4 HOH A 13 385 13 HOH HOH . D 4 HOH A 14 386 14 HOH HOH . D 4 HOH A 15 387 15 HOH HOH . D 4 HOH A 16 388 16 HOH HOH . D 4 HOH A 17 389 17 HOH HOH . D 4 HOH A 18 390 18 HOH HOH . D 4 HOH A 19 391 19 HOH HOH . D 4 HOH A 20 392 20 HOH HOH . D 4 HOH A 21 393 21 HOH HOH . D 4 HOH A 22 394 22 HOH HOH . D 4 HOH A 23 395 23 HOH HOH . D 4 HOH A 24 396 24 HOH HOH . D 4 HOH A 25 397 25 HOH HOH . D 4 HOH A 26 398 26 HOH HOH . D 4 HOH A 27 399 27 HOH HOH . D 4 HOH A 28 400 28 HOH HOH . D 4 HOH A 29 401 29 HOH HOH . D 4 HOH A 30 402 30 HOH HOH . D 4 HOH A 31 403 31 HOH HOH . D 4 HOH A 32 404 32 HOH HOH . D 4 HOH A 33 405 33 HOH HOH . D 4 HOH A 34 406 34 HOH HOH . D 4 HOH A 35 407 35 HOH HOH . D 4 HOH A 36 408 36 HOH HOH . D 4 HOH A 37 409 37 HOH HOH . D 4 HOH A 38 410 38 HOH HOH . D 4 HOH A 39 411 39 HOH HOH . D 4 HOH A 40 412 40 HOH HOH . D 4 HOH A 41 413 41 HOH HOH . D 4 HOH A 42 414 42 HOH HOH . D 4 HOH A 43 415 43 HOH HOH . D 4 HOH A 44 416 44 HOH HOH . D 4 HOH A 45 417 45 HOH HOH . D 4 HOH A 46 418 46 HOH HOH . D 4 HOH A 47 419 47 HOH HOH . D 4 HOH A 48 420 48 HOH HOH . D 4 HOH A 49 421 49 HOH HOH . D 4 HOH A 50 422 50 HOH HOH . D 4 HOH A 51 423 51 HOH HOH . D 4 HOH A 52 424 52 HOH HOH . D 4 HOH A 53 425 53 HOH HOH . D 4 HOH A 54 426 54 HOH HOH . D 4 HOH A 55 427 55 HOH HOH . D 4 HOH A 56 428 56 HOH HOH . D 4 HOH A 57 429 57 HOH HOH . D 4 HOH A 58 430 58 HOH HOH . D 4 HOH A 59 431 59 HOH HOH . D 4 HOH A 60 432 60 HOH HOH . D 4 HOH A 61 433 61 HOH HOH . D 4 HOH A 62 434 62 HOH HOH . D 4 HOH A 63 435 63 HOH HOH . D 4 HOH A 64 436 64 HOH HOH . D 4 HOH A 65 437 65 HOH HOH . D 4 HOH A 66 438 66 HOH HOH . D 4 HOH A 67 439 67 HOH HOH . D 4 HOH A 68 440 68 HOH HOH . D 4 HOH A 69 441 69 HOH HOH . D 4 HOH A 70 442 70 HOH HOH . D 4 HOH A 71 443 71 HOH HOH . D 4 HOH A 72 444 72 HOH HOH . D 4 HOH A 73 445 73 HOH HOH . D 4 HOH A 74 446 74 HOH HOH . D 4 HOH A 75 447 75 HOH HOH . D 4 HOH A 76 448 76 HOH HOH . D 4 HOH A 77 449 77 HOH HOH . D 4 HOH A 78 450 78 HOH HOH . D 4 HOH A 79 451 79 HOH HOH . D 4 HOH A 80 452 80 HOH HOH . D 4 HOH A 81 453 81 HOH HOH . D 4 HOH A 82 454 82 HOH HOH . D 4 HOH A 83 455 83 HOH HOH . D 4 HOH A 84 456 84 HOH HOH . D 4 HOH A 85 457 85 HOH HOH . D 4 HOH A 86 458 86 HOH HOH . D 4 HOH A 87 459 87 HOH HOH . D 4 HOH A 88 460 88 HOH HOH . D 4 HOH A 89 461 89 HOH HOH . D 4 HOH A 90 462 90 HOH HOH . D 4 HOH A 91 463 91 HOH HOH . D 4 HOH A 92 464 92 HOH HOH . D 4 HOH A 93 465 93 HOH HOH . D 4 HOH A 94 466 94 HOH HOH . D 4 HOH A 95 467 95 HOH HOH . D 4 HOH A 96 468 96 HOH HOH . D 4 HOH A 97 469 97 HOH HOH . D 4 HOH A 98 470 98 HOH HOH . D 4 HOH A 99 471 99 HOH HOH . D 4 HOH A 100 472 100 HOH HOH . D 4 HOH A 101 473 101 HOH HOH . D 4 HOH A 102 474 102 HOH HOH . D 4 HOH A 103 475 103 HOH HOH . D 4 HOH A 104 476 104 HOH HOH . D 4 HOH A 105 477 105 HOH HOH . D 4 HOH A 106 478 106 HOH HOH . D 4 HOH A 107 479 107 HOH HOH . D 4 HOH A 108 480 108 HOH HOH . D 4 HOH A 109 481 109 HOH HOH . D 4 HOH A 110 482 110 HOH HOH . D 4 HOH A 111 483 111 HOH HOH . D 4 HOH A 112 484 112 HOH HOH . D 4 HOH A 113 485 113 HOH HOH . D 4 HOH A 114 486 114 HOH HOH . D 4 HOH A 115 487 115 HOH HOH . D 4 HOH A 116 488 116 HOH HOH . D 4 HOH A 117 489 117 HOH HOH . D 4 HOH A 118 490 118 HOH HOH . D 4 HOH A 119 491 119 HOH HOH . D 4 HOH A 120 492 120 HOH HOH . D 4 HOH A 121 493 121 HOH HOH . D 4 HOH A 122 494 122 HOH HOH . D 4 HOH A 123 495 123 HOH HOH . D 4 HOH A 124 496 124 HOH HOH . D 4 HOH A 125 497 125 HOH HOH . D 4 HOH A 126 498 126 HOH HOH . D 4 HOH A 127 499 127 HOH HOH . D 4 HOH A 128 500 128 HOH HOH . D 4 HOH A 129 501 129 HOH HOH . D 4 HOH A 130 502 130 HOH HOH . D 4 HOH A 131 503 131 HOH HOH . D 4 HOH A 132 504 132 HOH HOH . D 4 HOH A 133 505 133 HOH HOH . D 4 HOH A 134 506 134 HOH HOH . D 4 HOH A 135 507 135 HOH HOH . D 4 HOH A 136 508 136 HOH HOH . D 4 HOH A 137 509 137 HOH HOH . D 4 HOH A 138 510 138 HOH HOH . D 4 HOH A 139 511 139 HOH HOH . D 4 HOH A 140 512 140 HOH HOH . D 4 HOH A 141 513 141 HOH HOH . D 4 HOH A 142 514 142 HOH HOH . D 4 HOH A 143 515 143 HOH HOH . D 4 HOH A 144 516 144 HOH HOH . D 4 HOH A 145 517 145 HOH HOH . D 4 HOH A 146 518 146 HOH HOH . D 4 HOH A 147 519 147 HOH HOH . D 4 HOH A 148 520 148 HOH HOH . D 4 HOH A 149 521 149 HOH HOH . D 4 HOH A 150 522 150 HOH HOH . D 4 HOH A 151 523 151 HOH HOH . D 4 HOH A 152 524 152 HOH HOH . D 4 HOH A 153 525 153 HOH HOH . D 4 HOH A 154 526 154 HOH HOH . D 4 HOH A 155 527 155 HOH HOH . D 4 HOH A 156 528 156 HOH HOH . D 4 HOH A 157 529 157 HOH HOH . D 4 HOH A 158 530 158 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 O O8 MCF . . . C 3 -9.528 -1.619 -25.026 1 13.39 ? O8 MCF 372 A 1 HETATM 2 C C8 MCF . . . C 3 -9.14 -2.98 -25.087 1 18.24 ? C8 MCF 372 A 1 HETATM 3 C C7 MCF . . . C 3 -7.935 -3.145 -25.997 1 19.06 ? C7 MCF 372 A 1 HETATM 4 N N6 MCF . . . C 3 -8.234 -2.563 -27.284 1 15.6 ? N6 MCF 372 A 1 HETATM 5 C C5 MCF . . . C 3 -9.014 -3.141 -28.182 1 17.45 ? C5 MCF 372 A 1 HETATM 6 N N4 MCF . . . C 3 -9.983 -3.956 -28.034 1 20.12 ? N4 MCF 372 A 1 HETATM 7 C C10 MCF . . . C 3 -10.451 -4.499 -26.854 1 22.47 ? C10 MCF 372 A 1 HETATM 8 C C9 MCF . . . C 3 -10.104 -4.03 -25.516 1 21.58 ? C9 MCF 372 A 1 HETATM 9 N N1 MCF . . . C 3 -10.806 -4.888 -24.703 1 23.2 ? N1 MCF 372 A 1 HETATM 10 C C2 MCF . . . C 3 -11.502 -5.757 -25.473 1 24.55 ? C2 MCF 372 A 1 HETATM 11 N N3 MCF . . . C 3 -11.315 -5.5 -26.774 1 25.64 ? N3 MCF 372 A 1 HETATM 12 C C1S MCF . . . C 3 -11.9 -6.291 -27.878 1 30.62 ? C1S MCF 372 A 1 HETATM 13 C C2S MCF . . . C 3 -11.142 -7.633 -27.766 1 32.71 ? C2S MCF 372 A 1 HETATM 14 O O2S MCF . . . C 3 -9.845 -7.637 -28.329 1 34.88 ? O2S MCF 372 A 1 HETATM 15 O O4S MCF . . . C 3 -13.278 -6.667 -27.686 1 31.8 ? O4S MCF 372 A 1 HETATM 16 C C4S MCF . . . C 3 -13.153 -8.003 -27.883 1 32.64 ? C4S MCF 372 A 1 HETATM 17 C C3S MCF . . . C 3 -12.01 -8.652 -28.44 1 34.33 ? C3S MCF 372 A 1 HETATM 18 O O3S MCF . . . C 3 -11.779 -8.394 -29.821 1 36.32 ? O3S MCF 372 A 1 HETATM 19 C C5S MCF . . . C 3 -14.283 -8.813 -27.375 1 35.38 ? C5S MCF 372 A 1 HETATM 20 S S5S MCF . . . C 3 -13.65 -8.946 -25.775 1 37.38 ? S5S MCF 372 A 1 HETATM 21 C C6S MCF . . . C 3 -14.583 -10.281 -25.038 1 37.45 ? C6S MCF 372 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #