data_5WBD # _model_server_result.job_id QR0w31xmEQ2LuX7xj9BjLQ _model_server_result.datetime_utc '2024-11-17 16:31:55' _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 5wbd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5WBD # _exptl.entry_id 5WBD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 576.213 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[N-(2-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}ethyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide](hydroxy)copper' _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 5WBD _cell.length_a 57.51 _cell.length_b 57.51 _cell.length_c 174.81 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WBD _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2,3,4 # 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' 8_665 -y+1,-x+1,-z 0 -1 0 -1 0 0 0 0 -1 57.51 57.51 0 3 'crystal symmetry operation' 10_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 57.51 57.51 0 4 'crystal symmetry operation' 15_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _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 'C26 H36 Cu N6 O3 S' _chem_comp.formula_weight 576.213 _chem_comp.id SI7 _chem_comp.mon_nstd_flag . _chem_comp.name '[N-(2-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}ethyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide](hydroxy)copper' _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 C17 C18 SI7 doub 283 n y C17 C16 SI7 sing 284 n y C18 C19 SI7 sing 285 n y C16 N5 SI7 doub 286 n y C19 C15 SI7 doub 287 n y N5 C15 SI7 sing 288 n y N5 CU1 SI7 sing 289 n n C23 C24 SI7 doub 290 n y C23 N6 SI7 sing 291 n y C15 C14 SI7 sing 292 n n CU1 N6 SI7 sing 293 n n CU1 N4 SI7 sing 294 n n C24 C25 SI7 sing 295 n y N6 C22 SI7 doub 296 n y C14 C13 SI7 sing 297 n n C25 C26 SI7 doub 298 n y C22 C26 SI7 sing 299 n y C22 C21 SI7 sing 300 n n N4 C13 SI7 sing 301 n n N4 C12 SI7 sing 302 n n N4 C20 SI7 sing 303 n n C12 C11 SI7 sing 304 n n C21 C20 SI7 sing 305 n n O2 C10 SI7 doub 306 n n C11 N3 SI7 sing 307 n n C10 N3 SI7 sing 308 n n C10 C9 SI7 sing 309 n n C9 C8 SI7 sing 310 n n C8 C7 SI7 sing 311 n n C7 C6 SI7 sing 312 n n C6 C5 SI7 sing 313 n n C5 C4 SI7 sing 314 n n C5 S1 SI7 sing 315 n n C4 N2 SI7 sing 316 n n C4 C2 SI7 sing 317 n n N2 C1 SI7 sing 318 n n S1 C3 SI7 sing 319 n n C1 O1 SI7 doub 320 n n C1 N1 SI7 sing 321 n n C2 C3 SI7 sing 322 n n C2 N1 SI7 sing 323 n n CU1 O3 SI7 sing 324 n n C23 H1 SI7 sing 325 n n C24 H2 SI7 sing 326 n n C25 H3 SI7 sing 327 n n C26 H4 SI7 sing 328 n n C21 H5 SI7 sing 329 n n C21 H6 SI7 sing 330 n n C20 H7 SI7 sing 331 n n C20 H8 SI7 sing 332 n n C16 H9 SI7 sing 333 n n C17 H10 SI7 sing 334 n n C18 H11 SI7 sing 335 n n C19 H12 SI7 sing 336 n n C14 H13 SI7 sing 337 n n C13 H14 SI7 sing 338 n n C12 H15 SI7 sing 339 n n C12 H16 SI7 sing 340 n n C11 H17 SI7 sing 341 n n C11 H18 SI7 sing 342 n n N3 H19 SI7 sing 343 n n C9 H20 SI7 sing 344 n n C9 H21 SI7 sing 345 n n C8 H22 SI7 sing 346 n n C8 H23 SI7 sing 347 n n C7 H24 SI7 sing 348 n n C7 H25 SI7 sing 349 n n C6 H26 SI7 sing 350 n n C6 H27 SI7 sing 351 n n C5 H28 SI7 sing 352 n n C4 H29 SI7 sing 353 n n N2 H30 SI7 sing 354 n n C3 H31 SI7 sing 355 n n C3 H32 SI7 sing 356 n n C2 H33 SI7 sing 357 n n N1 H34 SI7 sing 358 n n C14 H36 SI7 sing 359 n n C13 H37 SI7 sing 360 n n # _atom_sites.entry_id 5WBD _atom_sites.fract_transf_matrix[1][1] 0.017388 _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] 0.017388 _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] 0.005721 _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 SI7 A 1 201 1 SI7 SI7 . C 3 ACT A 1 202 1 ACT ACT . D 4 HOH A 1 301 47 HOH HOH . D 4 HOH A 2 302 86 HOH HOH . D 4 HOH A 3 303 32 HOH HOH . D 4 HOH A 4 304 48 HOH HOH . D 4 HOH A 5 305 2 HOH HOH . D 4 HOH A 6 306 28 HOH HOH . D 4 HOH A 7 307 81 HOH HOH . D 4 HOH A 8 308 17 HOH HOH . D 4 HOH A 9 309 3 HOH HOH . D 4 HOH A 10 310 45 HOH HOH . D 4 HOH A 11 311 50 HOH HOH . D 4 HOH A 12 312 57 HOH HOH . D 4 HOH A 13 313 5 HOH HOH . D 4 HOH A 14 314 69 HOH HOH . D 4 HOH A 15 315 63 HOH HOH . D 4 HOH A 16 316 25 HOH HOH . D 4 HOH A 17 317 34 HOH HOH . D 4 HOH A 18 318 49 HOH HOH . D 4 HOH A 19 319 56 HOH HOH . D 4 HOH A 20 320 67 HOH HOH . D 4 HOH A 21 321 54 HOH HOH . D 4 HOH A 22 322 16 HOH HOH . D 4 HOH A 23 323 40 HOH HOH . D 4 HOH A 24 324 39 HOH HOH . D 4 HOH A 25 325 12 HOH HOH . D 4 HOH A 26 326 30 HOH HOH . D 4 HOH A 27 327 98 HOH HOH . D 4 HOH A 28 328 6 HOH HOH . D 4 HOH A 29 329 62 HOH HOH . D 4 HOH A 30 330 13 HOH HOH . D 4 HOH A 31 331 96 HOH HOH . D 4 HOH A 32 332 33 HOH HOH . D 4 HOH A 33 333 1 HOH HOH . D 4 HOH A 34 334 18 HOH HOH . D 4 HOH A 35 335 37 HOH HOH . D 4 HOH A 36 336 52 HOH HOH . D 4 HOH A 37 337 61 HOH HOH . D 4 HOH A 38 338 68 HOH HOH . D 4 HOH A 39 339 78 HOH HOH . D 4 HOH A 40 340 11 HOH HOH . D 4 HOH A 41 341 71 HOH HOH . D 4 HOH A 42 342 7 HOH HOH . D 4 HOH A 43 343 21 HOH HOH . D 4 HOH A 44 344 92 HOH HOH . D 4 HOH A 45 345 31 HOH HOH . D 4 HOH A 46 346 26 HOH HOH . D 4 HOH A 47 347 60 HOH HOH . D 4 HOH A 48 348 64 HOH HOH . D 4 HOH A 49 349 8 HOH HOH . D 4 HOH A 50 350 14 HOH HOH . D 4 HOH A 51 351 38 HOH HOH . D 4 HOH A 52 352 70 HOH HOH . D 4 HOH A 53 353 19 HOH HOH . D 4 HOH A 54 354 72 HOH HOH . D 4 HOH A 55 355 75 HOH HOH . D 4 HOH A 56 356 24 HOH HOH . D 4 HOH A 57 357 83 HOH HOH . D 4 HOH A 58 358 20 HOH HOH . D 4 HOH A 59 359 23 HOH HOH . D 4 HOH A 60 360 43 HOH HOH . D 4 HOH A 61 361 9 HOH HOH . D 4 HOH A 62 362 10 HOH HOH . D 4 HOH A 63 363 97 HOH HOH . D 4 HOH A 64 364 51 HOH HOH . D 4 HOH A 65 365 53 HOH HOH . D 4 HOH A 66 366 90 HOH HOH . D 4 HOH A 67 367 41 HOH HOH . D 4 HOH A 68 368 82 HOH HOH . D 4 HOH A 69 369 36 HOH HOH . D 4 HOH A 70 370 74 HOH HOH . D 4 HOH A 71 371 27 HOH HOH . D 4 HOH A 72 372 29 HOH HOH . D 4 HOH A 73 373 87 HOH HOH . D 4 HOH A 74 374 46 HOH HOH . D 4 HOH A 75 375 15 HOH HOH . D 4 HOH A 76 376 89 HOH HOH . D 4 HOH A 77 377 22 HOH HOH . D 4 HOH A 78 378 59 HOH HOH . D 4 HOH A 79 379 4 HOH HOH . D 4 HOH A 80 380 66 HOH HOH . D 4 HOH A 81 381 84 HOH HOH . D 4 HOH A 82 382 42 HOH HOH . D 4 HOH A 83 383 44 HOH HOH . D 4 HOH A 84 384 55 HOH HOH . D 4 HOH A 85 385 35 HOH HOH . D 4 HOH A 86 386 80 HOH HOH . D 4 HOH A 87 387 77 HOH HOH . D 4 HOH A 88 388 95 HOH HOH . D 4 HOH A 89 389 85 HOH HOH . D 4 HOH A 90 390 73 HOH HOH . D 4 HOH A 91 391 94 HOH HOH . D 4 HOH A 92 392 58 HOH HOH . D 4 HOH A 93 393 76 HOH HOH . D 4 HOH A 94 394 65 HOH HOH . D 4 HOH A 95 395 88 HOH HOH . D 4 HOH A 96 396 79 HOH HOH . D 4 HOH A 97 397 93 HOH HOH . D 4 HOH A 98 398 91 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 CU CU1 SI7 . . . B 2 24.164 25.396 -17.726 1 23.94 ? CU1 SI7 201 A 1 HETATM 2 N N6 SI7 . . . B 2 25.833 24.431 -17.28 1 27.27 ? N6 SI7 201 A 1 HETATM 3 C C23 SI7 . . . B 2 26.32 23.315 -18.012 1 31.4 ? C23 SI7 201 A 1 HETATM 4 C C24 SI7 . . . B 2 27.502 22.678 -17.633 1 31.98 ? C24 SI7 201 A 1 HETATM 5 C C25 SI7 . . . B 2 28.234 23.123 -16.524 1 30.67 ? C25 SI7 201 A 1 HETATM 6 C C26 SI7 . . . B 2 27.781 24.215 -15.78 1 26.28 ? C26 SI7 201 A 1 HETATM 7 C C22 SI7 . . . B 2 26.603 24.851 -16.157 1 23.56 ? C22 SI7 201 A 1 HETATM 8 C C21 SI7 . . . B 2 26.052 26.032 -15.401 1 23.58 ? C21 SI7 201 A 1 HETATM 9 C C20 SI7 . . . B 2 24.652 25.716 -14.914 1 23.52 ? C20 SI7 201 A 1 HETATM 10 N N4 SI7 . . . B 2 23.594 25.871 -15.872 1 21.79 ? N4 SI7 201 A 1 HETATM 11 N N5 SI7 . . . B 2 22.585 26.278 -18.528 1 25.6 ? N5 SI7 201 A 1 HETATM 12 C C16 SI7 . . . B 2 22.135 25.747 -19.77 1 26.09 ? C16 SI7 201 A 1 HETATM 13 C C17 SI7 . . . B 2 21.038 26.279 -20.452 1 25.15 ? C17 SI7 201 A 1 HETATM 14 C C18 SI7 . . . B 2 20.353 27.366 -19.901 1 23.04 ? C18 SI7 201 A 1 HETATM 15 C C19 SI7 . . . B 2 20.767 27.905 -18.68 1 23.76 ? C19 SI7 201 A 1 HETATM 16 C C15 SI7 . . . B 2 21.862 27.377 -17.998 1 24.58 ? C15 SI7 201 A 1 HETATM 17 C C14 SI7 . . . B 2 22.293 27.991 -16.684 1 27.65 ? C14 SI7 201 A 1 HETATM 18 C C13 SI7 . . . B 2 23.055 27.186 -15.641 1 26.18 ? C13 SI7 201 A 1 HETATM 19 C C12 SI7 . . . B 2 22.575 24.889 -15.575 1 20.55 ? C12 SI7 201 A 1 HETATM 20 C C11 SI7 . . . B 2 22.113 24.796 -14.119 1 17.32 ? C11 SI7 201 A 1 HETATM 21 N N3 SI7 . . . B 2 20.799 24.319 -13.842 1 12.72 ? N3 SI7 201 A 1 HETATM 22 C C10 SI7 . . . B 2 19.627 24.894 -14.117 1 11.13 ? C10 SI7 201 A 1 HETATM 23 O O2 SI7 . . . B 2 19.615 26.129 -14.745 1 11.01 ? O2 SI7 201 A 1 HETATM 24 C C9 SI7 . . . B 2 18.319 24.343 -13.609 1 10.39 ? C9 SI7 201 A 1 HETATM 25 C C8 SI7 . . . B 2 17.433 25.387 -12.979 1 9.86 ? C8 SI7 201 A 1 HETATM 26 C C7 SI7 . . . B 2 18.044 26.046 -11.751 1 9.2 ? C7 SI7 201 A 1 HETATM 27 C C6 SI7 . . . B 2 17.266 27.202 -11.152 1 9.73 ? C6 SI7 201 A 1 HETATM 28 C C5 SI7 . . . B 2 17.904 27.775 -9.898 1 8.98 ? C5 SI7 201 A 1 HETATM 29 C C4 SI7 . . . B 2 17.324 29.128 -9.491 1 8.11 ? C4 SI7 201 A 1 HETATM 30 N N2 SI7 . . . B 2 15.898 29.214 -9.485 1 8.56 ? N2 SI7 201 A 1 HETATM 31 S S1 SI7 . . . B 2 17.761 26.783 -8.434 1 9.25 ? S1 SI7 201 A 1 HETATM 32 C C3 SI7 . . . B 2 18.438 28.147 -7.537 1 9.02 ? C3 SI7 201 A 1 HETATM 33 C C2 SI7 . . . B 2 17.639 29.351 -8.01 1 8.29 ? C2 SI7 201 A 1 HETATM 34 N N1 SI7 . . . B 2 16.382 29.548 -7.399 1 8.97 ? N1 SI7 201 A 1 HETATM 35 C C1 SI7 . . . B 2 15.291 29.407 -8.238 1 8.71 ? C1 SI7 201 A 1 HETATM 36 O O1 SI7 . . . B 2 13.971 29.429 -8.004 1 9.7 ? O1 SI7 201 A 1 HETATM 37 O O3 SI7 . . . B 2 23.222 23.161 -18.267 1 26.3 ? O3 SI7 201 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 37 #