data_1ADG # _model_server_result.job_id Bu1h3gfOUo8Yw76eE7otKg _model_server_result.datetime_utc '2025-02-27 07:17:46' _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 1adg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":378}' # _entry.id 1ADG # _exptl.entry_id 1ADG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 714.375 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'BETA-METHYLENE-SELENAZOLE-4-CARBOXYAMIDE-ADENINE DINUCLEOTIDE' _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 1ADG _cell.length_a 56.3 _cell.length_b 75.2 _cell.length_c 182.3 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ADG _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # 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' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 91.15 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 SG CYS 46 A CYS 46 1_555 B ZN ZN . A ZN 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? metalc ? metalc2 A NE2 HIS 67 A HIS 67 1_555 B ZN ZN . A ZN 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc3 A SG CYS 97 A CYS 97 1_555 C ZN ZN . A ZN 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc4 A SG CYS 100 A CYS 100 1_555 C ZN ZN . A ZN 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc5 A SG CYS 103 A CYS 103 1_555 C ZN ZN . A ZN 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc6 A SG CYS 111 A CYS 111 1_555 C ZN ZN . A ZN 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc7 A SG CYS 174 A CYS 174 1_555 B ZN ZN . A ZN 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc8 B ZN ZN . A ZN 376 1_555 E O HOH . A HOH 388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.617 ? # _chem_comp.formula 'C20 H27 N7 O13 P2 Se' _chem_comp.formula_weight 714.375 _chem_comp.id SAD _chem_comp.mon_nstd_flag . _chem_comp.name 'BETA-METHYLENE-SELENAZOLE-4-CARBOXYAMIDE-ADENINE DINUCLEOTIDE' _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 PA O1A SAD doub 277 n n PA O2A SAD sing 278 n n PA O5B SAD sing 279 n n PA C3 SAD sing 280 n n O2A HOA2 SAD sing 281 n n O5B C5B SAD sing 282 n n C5B C4B SAD sing 283 n n C5B H51A SAD sing 284 n n C5B H52A SAD sing 285 n n C4B O4B SAD sing 286 n n C4B C3B SAD sing 287 n n C4B H4B SAD sing 288 n n O4B C1B SAD sing 289 n n C3B O3B SAD sing 290 n n C3B C2B SAD sing 291 n n C3B H3B SAD sing 292 n n O3B HO3A SAD sing 293 n n C2B O2B SAD sing 294 n n C2B C1B SAD sing 295 n n C2B H2B SAD sing 296 n n O2B HO2A SAD sing 297 n n C1B N9A SAD sing 298 n n C1B H1B SAD sing 299 n n N9A C8A SAD sing 300 n y N9A C4A SAD sing 301 n y C8A N7A SAD doub 302 n y C8A H8A SAD sing 303 n n N7A C5A SAD sing 304 n y C5A C6A SAD sing 305 n y C5A C4A SAD doub 306 n y C6A N6A SAD sing 307 n n C6A N1A SAD doub 308 n y N6A H61A SAD sing 309 n n N6A H62A SAD sing 310 n n N1A C2A SAD sing 311 n y C2A N3A SAD doub 312 n y C2A H2A SAD sing 313 n n N3A C4A SAD sing 314 n y C3 PN SAD sing 315 n n C3 H31 SAD sing 316 n n C3 H32 SAD sing 317 n n PN O1N SAD doub 318 n n PN O2N SAD sing 319 n n PN O5D SAD sing 320 n n O2N HON2 SAD sing 321 n n O5D C5D SAD sing 322 n n C5D C4D SAD sing 323 n n C5D H51N SAD sing 324 n n C5D H52N SAD sing 325 n n C4D O4D SAD sing 326 n n C4D C3D SAD sing 327 n n C4D H4D SAD sing 328 n n O4D C1D SAD sing 329 n n C3D O3D SAD sing 330 n n C3D C2D SAD sing 331 n n C3D H3D SAD sing 332 n n O3D HO3N SAD sing 333 n n C2D O2D SAD sing 334 n n C2D C1D SAD sing 335 n n C2D H2D SAD sing 336 n n O2D HO2N SAD sing 337 n n C1D C2N SAD sing 338 n n C1D H1D SAD sing 339 n n C2N N3N SAD doub 340 n y C2N SE1N SAD sing 341 n y N3N C4N SAD sing 342 n y C4N C5N SAD doub 343 n y C4N C6N SAD sing 344 n n C5N SE1N SAD sing 345 n y C5N HN5 SAD sing 346 n n C6N O6N SAD doub 347 n n C6N N6N SAD sing 348 n n N6N H61N SAD sing 349 n n N6N H62N SAD sing 350 n n # _atom_sites.entry_id 1ADG _atom_sites.fract_transf_matrix[1][1] 0.017762 _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] 0.013298 _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] 0.005485 _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 1 376 376 ZN ZN . C 2 ZN A 1 377 377 ZN ZN . D 3 SAD A 1 378 1 SAD SAD . E 4 HOH A 1 379 1 HOH HOH . E 4 HOH A 2 380 3 HOH HOH . E 4 HOH A 3 381 7 HOH HOH . E 4 HOH A 4 382 18 HOH HOH . E 4 HOH A 5 383 33 HOH HOH . E 4 HOH A 6 384 34 HOH HOH . E 4 HOH A 7 385 39 HOH HOH . E 4 HOH A 8 386 42 HOH HOH . E 4 HOH A 9 387 46 HOH HOH . E 4 HOH A 10 388 161 HOH HOH . E 4 HOH A 11 389 200 HOH HOH . E 4 HOH A 12 390 223 HOH HOH . E 4 HOH A 13 391 228 HOH HOH . E 4 HOH A 14 392 400 HOH HOH . E 4 HOH A 15 393 404 HOH HOH . E 4 HOH A 16 394 407 HOH HOH . E 4 HOH A 17 395 410 HOH HOH . E 4 HOH A 18 396 411 HOH HOH . E 4 HOH A 19 397 412 HOH HOH . E 4 HOH A 20 398 414 HOH HOH . E 4 HOH A 21 399 418 HOH HOH . E 4 HOH A 22 400 420 HOH HOH . E 4 HOH A 23 401 421 HOH HOH . E 4 HOH A 24 402 500 HOH HOH . E 4 HOH A 25 403 501 HOH HOH . E 4 HOH A 26 404 502 HOH HOH . E 4 HOH A 27 405 503 HOH HOH . E 4 HOH A 28 406 504 HOH HOH . E 4 HOH A 29 407 505 HOH HOH . E 4 HOH A 30 408 506 HOH HOH . E 4 HOH A 31 409 507 HOH HOH . E 4 HOH A 32 410 508 HOH HOH . E 4 HOH A 33 411 509 HOH HOH . E 4 HOH A 34 412 510 HOH HOH . E 4 HOH A 35 413 511 HOH HOH . E 4 HOH A 36 414 5 HOH HOH . E 4 HOH A 37 415 9 HOH HOH . E 4 HOH A 38 416 23 HOH HOH . E 4 HOH A 39 417 39 HOH HOH A E 4 HOH A 40 418 66 HOH HOH . E 4 HOH A 41 419 67 HOH HOH . E 4 HOH A 42 420 88 HOH HOH . E 4 HOH A 43 421 144 HOH HOH . E 4 HOH A 44 422 146 HOH HOH . E 4 HOH A 45 423 149 HOH HOH . E 4 HOH A 46 424 150 HOH HOH . E 4 HOH A 47 425 154 HOH HOH . E 4 HOH A 48 426 206 HOH HOH . E 4 HOH A 49 427 208 HOH HOH . E 4 HOH A 50 428 210 HOH HOH . E 4 HOH A 51 429 213 HOH HOH . E 4 HOH A 52 430 215 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 P PA SAD . . . D 3 13.58 7.325 27.436 1 28.02 ? PA SAD 378 A 1 HETATM 2 O O1A SAD . . . D 3 13.055 5.924 27.284 1 26.28 ? O1A SAD 378 A 1 HETATM 3 O O2A SAD . . . D 3 14.986 7.668 27.012 1 26.08 ? O2A SAD 378 A 1 HETATM 4 O O5B SAD . . . D 3 13.292 7.734 28.978 1 24.96 ? O5B SAD 378 A 1 HETATM 5 C C5B SAD . . . D 3 13.61 6.804 30.038 1 22.8 ? C5B SAD 378 A 1 HETATM 6 C C4B SAD . . . D 3 14.996 7.119 30.622 1 19.69 ? C4B SAD 378 A 1 HETATM 7 O O4B SAD . . . D 3 15.157 6.409 31.849 1 18.36 ? O4B SAD 378 A 1 HETATM 8 C C3B SAD . . . D 3 16.18 6.679 29.755 1 18.94 ? C3B SAD 378 A 1 HETATM 9 O O3B SAD . . . D 3 17.1 7.778 29.593 1 16.67 ? O3B SAD 378 A 1 HETATM 10 C C2B SAD . . . D 3 16.649 5.339 30.371 1 16.32 ? C2B SAD 378 A 1 HETATM 11 O O2B SAD . . . D 3 18.022 5.037 30.105 1 13.86 ? O2B SAD 378 A 1 HETATM 12 C C1B SAD . . . D 3 16.36 5.611 31.829 1 17.11 ? C1B SAD 378 A 1 HETATM 13 N N9A SAD . . . D 3 16.26 4.476 32.796 1 16.23 ? N9A SAD 378 A 1 HETATM 14 C C8A SAD . . . D 3 15.689 3.261 32.631 1 15.16 ? C8A SAD 378 A 1 HETATM 15 N N7A SAD . . . D 3 15.645 2.596 33.798 1 15.58 ? N7A SAD 378 A 1 HETATM 16 C C5A SAD . . . D 3 16.242 3.42 34.665 1 17.01 ? C5A SAD 378 A 1 HETATM 17 C C6A SAD . . . D 3 16.259 3.24 36.047 1 15.04 ? C6A SAD 378 A 1 HETATM 18 N N6A SAD . . . D 3 15.85 2.127 36.656 1 13.39 ? N6A SAD 378 A 1 HETATM 19 N N1A SAD . . . D 3 16.765 4.281 36.734 1 17.71 ? N1A SAD 378 A 1 HETATM 20 C C2A SAD . . . D 3 17.23 5.387 36.147 1 16.67 ? C2A SAD 378 A 1 HETATM 21 N N3A SAD . . . D 3 17.215 5.541 34.834 1 16.91 ? N3A SAD 378 A 1 HETATM 22 C C4A SAD . . . D 3 16.685 4.574 34.063 1 15.88 ? C4A SAD 378 A 1 HETATM 23 C C3 SAD . . . D 3 12.676 8.539 26.47 1 26.77 ? C3 SAD 378 A 1 HETATM 24 P PN SAD . . . D 3 12.143 10.049 27.299 1 27.03 ? PN SAD 378 A 1 HETATM 25 O O1N SAD . . . D 3 12.158 11.076 26.224 1 26.35 ? O1N SAD 378 A 1 HETATM 26 O O2N SAD . . . D 3 12.863 10.397 28.581 1 28.14 ? O2N SAD 378 A 1 HETATM 27 O O5D SAD . . . D 3 10.603 9.752 27.642 1 26.18 ? O5D SAD 378 A 1 HETATM 28 C C5D SAD . . . D 3 9.94 8.607 27.071 1 22.42 ? C5D SAD 378 A 1 HETATM 29 C C4D SAD . . . D 3 10.147 7.379 27.968 1 19.67 ? C4D SAD 378 A 1 HETATM 30 O O4D SAD . . . D 3 9.625 7.765 29.234 1 19.13 ? O4D SAD 378 A 1 HETATM 31 C C3D SAD . . . D 3 9.258 6.336 27.351 1 18.62 ? C3D SAD 378 A 1 HETATM 32 O O3D SAD . . . D 3 10.073 5.457 26.546 1 18.02 ? O3D SAD 378 A 1 HETATM 33 C C2D SAD . . . D 3 8.663 5.692 28.592 1 17.16 ? C2D SAD 378 A 1 HETATM 34 O O2D SAD . . . D 3 9.517 4.676 29.132 1 15.92 ? O2D SAD 378 A 1 HETATM 35 C C1D SAD . . . D 3 8.538 6.883 29.55 1 19.28 ? C1D SAD 378 A 1 HETATM 36 C C2N SAD . . . D 3 7.385 7.821 29.499 1 20.75 ? C2N SAD 378 A 1 HETATM 37 N N3N SAD . . . D 3 6.14 7.439 29.182 1 21.28 ? N3N SAD 378 A 1 HETATM 38 C C4N SAD . . . D 3 5.415 8.559 29.206 1 22.08 ? C4N SAD 378 A 1 HETATM 39 C C5N SAD . . . D 3 6.077 9.719 29.446 1 21.09 ? C5N SAD 378 A 1 HETATM 40 SE SE1N SAD . . . D 3 7.737 9.523 29.822 1 17.25 ? SE1N SAD 378 A 1 HETATM 41 C C6N SAD . . . D 3 3.952 8.461 29.001 1 22.88 ? C6N SAD 378 A 1 HETATM 42 O O6N SAD . . . D 3 3.188 9.441 29.054 1 24.26 ? O6N SAD 378 A 1 HETATM 43 N N6N SAD . . . D 3 3.574 7.213 28.767 1 21.47 ? N6N SAD 378 A 1 HETATM 44 H HO3A SAD . . . D 3 17.019 8.367 30.405 1 15 ? HO3A SAD 378 A 1 HETATM 45 H HO2A SAD . . . D 3 18.592 5.786 30.427 1 15 ? HO2A SAD 378 A 1 HETATM 46 H H61A SAD . . . D 3 15.494 1.37 36.108 1 15 ? H61A SAD 378 A 1 HETATM 47 H H62A SAD . . . D 3 15.898 2.053 37.656 1 15 ? H62A SAD 378 A 1 HETATM 48 H HO3N SAD . . . D 3 10.172 5.855 25.634 1 15 ? HO3N SAD 378 A 1 HETATM 49 H HO2N SAD . . . D 3 9.731 4.933 30.077 1 15 ? HO2N SAD 378 A 1 HETATM 50 H H61N SAD . . . D 3 4.295 6.523 28.735 1 15 ? H61N SAD 378 A 1 HETATM 51 H H62N SAD . . . D 3 2.601 6.986 28.729 1 15 ? H62N SAD 378 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 51 #