data_5VKX # _model_server_result.job_id knmIlAdYEs4792oPU8wUFA _model_server_result.datetime_utc '2025-07-16 11:20:28' _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 5vkx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5VKX # _exptl.entry_id 5VKX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 603.242 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[N-(3-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}ethyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide](azido)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 5VKX _cell.length_a 57.875 _cell.length_b 57.875 _cell.length_c 184.424 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VKX _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,E _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 57.875 57.875 0 3 'crystal symmetry operation' 10_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 57.875 57.875 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 # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NE2 _struct_conn.ptnr1_label_comp_id HIS _struct_conn.ptnr1_label_seq_id 87 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id HIS _struct_conn.ptnr1_auth_seq_id 87 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id CU _struct_conn.ptnr2_label_comp_id CU _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CU _struct_conn.ptnr2_auth_seq_id 202 _struct_conn.ptnr2_symmetry 5_554 _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 2.193 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C26 H37 Cu N9 O2 S' _chem_comp.formula_weight 603.242 _chem_comp.id S18 _chem_comp.mon_nstd_flag . _chem_comp.name '[N-(3-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}ethyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide](azido)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 C24 C25 S18 doub 277 n y C24 C23 S18 sing 278 n y C25 C26 S18 sing 279 n y C23 N6 S18 doub 280 n y C26 C22 S18 doub 281 n y N6 C22 S18 sing 282 n y N6 CU1 S18 sing 283 n n N9 N8 S18 doub 284 n n N8 N7 S18 doub 285 n n N7 CU1 S18 sing 286 n n C22 C21 S18 sing 287 n n CU1 N5 S18 sing 288 n n CU1 N4 S18 sing 289 n n C16 C17 S18 doub 290 n y C16 N5 S18 sing 291 n y C17 C18 S18 sing 292 n y N5 C15 S18 doub 293 n y C21 C20 S18 sing 294 n n C18 C19 S18 doub 295 n y C15 C19 S18 sing 296 n y C15 C14 S18 sing 297 n n N4 C20 S18 sing 298 n n N4 C12 S18 sing 299 n n N4 C13 S18 sing 300 n n C12 C11 S18 sing 301 n n C14 C13 S18 sing 302 n n O2 C10 S18 doub 303 n n C10 N3 S18 sing 304 n n C10 C9 S18 sing 305 n n C11 N3 S18 sing 306 n n C9 C8 S18 sing 307 n n C8 C7 S18 sing 308 n n C7 C6 S18 sing 309 n n C6 C5 S18 sing 310 n n C5 C4 S18 sing 311 n n C5 S1 S18 sing 312 n n N2 C4 S18 sing 313 n n N2 C1 S18 sing 314 n n C4 C2 S18 sing 315 n n S1 C3 S18 sing 316 n n C1 O1 S18 doub 317 n n C1 N1 S18 sing 318 n n C2 C3 S18 sing 319 n n C2 N1 S18 sing 320 n n N2 H1 S18 sing 321 n n N1 H2 S18 sing 322 n n C2 H3 S18 sing 323 n n C4 H4 S18 sing 324 n n C3 H5 S18 sing 325 n n C3 H6 S18 sing 326 n n C5 H7 S18 sing 327 n n C6 H8 S18 sing 328 n n C6 H9 S18 sing 329 n n C7 H10 S18 sing 330 n n C7 H11 S18 sing 331 n n C8 H12 S18 sing 332 n n C8 H13 S18 sing 333 n n C9 H14 S18 sing 334 n n C9 H15 S18 sing 335 n n N3 H16 S18 sing 336 n n C11 H17 S18 sing 337 n n C11 H18 S18 sing 338 n n C12 H19 S18 sing 339 n n C12 H20 S18 sing 340 n n C13 H21 S18 sing 341 n n C13 H22 S18 sing 342 n n C14 H23 S18 sing 343 n n C14 H24 S18 sing 344 n n C19 H25 S18 sing 345 n n C18 H26 S18 sing 346 n n C17 H27 S18 sing 347 n n C16 H28 S18 sing 348 n n N9 H29 S18 sing 349 n n C20 H30 S18 sing 350 n n C20 H31 S18 sing 351 n n C21 H32 S18 sing 352 n n C21 H33 S18 sing 353 n n C26 H34 S18 sing 354 n n C25 H35 S18 sing 355 n n C24 H36 S18 sing 356 n n C23 H37 S18 sing 357 n n # _atom_sites.entry_id 5VKX _atom_sites.fract_transf_matrix[1][1] 0.017279 _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] 0.017279 _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] 0.005422 _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 S18 A 1 201 1 S18 S18 . C 3 CU A 1 202 2 CU CU . D 4 GOL A 1 203 1 GOL GOL . E 5 HOH A 1 301 171 HOH HOH . E 5 HOH A 2 302 92 HOH HOH . E 5 HOH A 3 303 177 HOH HOH . E 5 HOH A 4 304 178 HOH HOH . E 5 HOH A 5 305 170 HOH HOH . E 5 HOH A 6 306 97 HOH HOH . E 5 HOH A 7 307 169 HOH HOH . E 5 HOH A 8 308 40 HOH HOH . E 5 HOH A 9 309 128 HOH HOH . E 5 HOH A 10 310 26 HOH HOH . E 5 HOH A 11 311 19 HOH HOH . E 5 HOH A 12 312 108 HOH HOH . E 5 HOH A 13 313 1 HOH HOH . E 5 HOH A 14 314 52 HOH HOH . E 5 HOH A 15 315 2 HOH HOH . E 5 HOH A 16 316 64 HOH HOH . E 5 HOH A 17 317 8 HOH HOH . E 5 HOH A 18 318 15 HOH HOH . E 5 HOH A 19 319 67 HOH HOH . E 5 HOH A 20 320 13 HOH HOH . E 5 HOH A 21 321 4 HOH HOH . E 5 HOH A 22 322 16 HOH HOH . E 5 HOH A 23 323 166 HOH HOH . E 5 HOH A 24 324 51 HOH HOH . E 5 HOH A 25 325 30 HOH HOH . E 5 HOH A 26 326 168 HOH HOH . E 5 HOH A 27 327 49 HOH HOH . E 5 HOH A 28 328 10 HOH HOH . E 5 HOH A 29 329 12 HOH HOH . E 5 HOH A 30 330 60 HOH HOH . E 5 HOH A 31 331 174 HOH HOH . E 5 HOH A 32 332 113 HOH HOH . E 5 HOH A 33 333 20 HOH HOH . E 5 HOH A 34 334 22 HOH HOH . E 5 HOH A 35 335 66 HOH HOH . E 5 HOH A 36 336 134 HOH HOH . E 5 HOH A 37 337 45 HOH HOH . E 5 HOH A 38 338 17 HOH HOH . E 5 HOH A 39 339 88 HOH HOH . E 5 HOH A 40 340 28 HOH HOH . E 5 HOH A 41 341 58 HOH HOH . E 5 HOH A 42 342 112 HOH HOH . E 5 HOH A 43 343 41 HOH HOH . E 5 HOH A 44 344 5 HOH HOH . E 5 HOH A 45 345 77 HOH HOH . E 5 HOH A 46 346 35 HOH HOH . E 5 HOH A 47 347 34 HOH HOH . E 5 HOH A 48 348 11 HOH HOH . E 5 HOH A 49 349 36 HOH HOH . E 5 HOH A 50 350 165 HOH HOH . E 5 HOH A 51 351 69 HOH HOH . E 5 HOH A 52 352 24 HOH HOH . E 5 HOH A 53 353 105 HOH HOH . E 5 HOH A 54 354 75 HOH HOH . E 5 HOH A 55 355 54 HOH HOH . E 5 HOH A 56 356 44 HOH HOH . E 5 HOH A 57 357 25 HOH HOH . E 5 HOH A 58 358 147 HOH HOH . E 5 HOH A 59 359 9 HOH HOH . E 5 HOH A 60 360 3 HOH HOH . E 5 HOH A 61 361 87 HOH HOH . E 5 HOH A 62 362 39 HOH HOH . E 5 HOH A 63 363 53 HOH HOH . E 5 HOH A 64 364 14 HOH HOH . E 5 HOH A 65 365 50 HOH HOH . E 5 HOH A 66 366 29 HOH HOH . E 5 HOH A 67 367 6 HOH HOH . E 5 HOH A 68 368 18 HOH HOH . E 5 HOH A 69 369 172 HOH HOH . E 5 HOH A 70 370 117 HOH HOH . E 5 HOH A 71 371 76 HOH HOH . E 5 HOH A 72 372 27 HOH HOH . E 5 HOH A 73 373 106 HOH HOH . E 5 HOH A 74 374 31 HOH HOH . E 5 HOH A 75 375 38 HOH HOH . E 5 HOH A 76 376 80 HOH HOH . E 5 HOH A 77 377 57 HOH HOH . E 5 HOH A 78 378 98 HOH HOH . E 5 HOH A 79 379 46 HOH HOH . E 5 HOH A 80 380 99 HOH HOH . E 5 HOH A 81 381 43 HOH HOH . E 5 HOH A 82 382 7 HOH HOH . E 5 HOH A 83 383 48 HOH HOH . E 5 HOH A 84 384 32 HOH HOH . E 5 HOH A 85 385 47 HOH HOH . E 5 HOH A 86 386 91 HOH HOH . E 5 HOH A 87 387 167 HOH HOH . E 5 HOH A 88 388 23 HOH HOH . E 5 HOH A 89 389 68 HOH HOH . E 5 HOH A 90 390 63 HOH HOH . E 5 HOH A 91 391 103 HOH HOH . E 5 HOH A 92 392 89 HOH HOH . E 5 HOH A 93 393 33 HOH HOH . E 5 HOH A 94 394 21 HOH HOH . E 5 HOH A 95 395 62 HOH HOH . E 5 HOH A 96 396 176 HOH HOH . E 5 HOH A 97 397 124 HOH HOH . E 5 HOH A 98 398 119 HOH HOH . E 5 HOH A 99 399 59 HOH HOH . E 5 HOH A 100 400 107 HOH HOH . E 5 HOH A 101 401 82 HOH HOH . E 5 HOH A 102 402 153 HOH HOH . E 5 HOH A 103 403 150 HOH HOH . E 5 HOH A 104 404 56 HOH HOH . E 5 HOH A 105 405 161 HOH HOH . E 5 HOH A 106 406 145 HOH HOH . E 5 HOH A 107 407 96 HOH HOH . E 5 HOH A 108 408 83 HOH HOH . E 5 HOH A 109 409 100 HOH HOH . E 5 HOH A 110 410 146 HOH HOH . E 5 HOH A 111 411 137 HOH HOH . E 5 HOH A 112 412 152 HOH HOH . E 5 HOH A 113 413 129 HOH HOH . E 5 HOH A 114 414 136 HOH HOH . E 5 HOH A 115 415 85 HOH HOH . E 5 HOH A 116 416 104 HOH HOH . E 5 HOH A 117 417 86 HOH HOH . E 5 HOH A 118 418 55 HOH HOH . E 5 HOH A 119 419 151 HOH HOH . E 5 HOH A 120 420 175 HOH HOH . E 5 HOH A 121 421 173 HOH HOH . E 5 HOH A 122 422 71 HOH HOH . E 5 HOH A 123 423 109 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 O1 S18 . . . B 2 14.36 29.561 -8.272 1 12.46 ? O1 S18 201 A 1 HETATM 2 C C1 S18 . . . B 2 15.643 29.441 -8.537 1 11.48 ? C1 S18 201 A 1 HETATM 3 N N2 S18 . . . B 2 16.059 29.245 -9.746 1 11.19 ? N2 S18 201 A 1 HETATM 4 N N1 S18 . . . B 2 16.484 29.626 -7.569 1 12.73 ? N1 S18 201 A 1 HETATM 5 C C2 S18 . . . B 2 17.818 29.516 -8.169 1 11.69 ? C2 S18 201 A 1 HETATM 6 C C4 S18 . . . B 2 17.543 29.239 -9.73 1 10.95 ? C4 S18 201 A 1 HETATM 7 C C3 S18 . . . B 2 18.612 28.228 -7.681 1 12.91 ? C3 S18 201 A 1 HETATM 8 S S1 S18 . . . B 2 17.99 26.849 -8.617 1 12.82 ? S1 S18 201 A 1 HETATM 9 C C5 S18 . . . B 2 18.099 27.834 -10.145 1 12.6 ? C5 S18 201 A 1 HETATM 10 C C6 S18 . . . B 2 17.48 27.264 -11.434 1 12.14 ? C6 S18 201 A 1 HETATM 11 C C7 S18 . . . B 2 18.332 26.124 -11.959 1 12.69 ? C7 S18 201 A 1 HETATM 12 C C8 S18 . . . B 2 17.637 25.498 -13.221 1 13.72 ? C8 S18 201 A 1 HETATM 13 C C9 S18 . . . B 2 18.492 24.401 -13.872 1 14.84 ? C9 S18 201 A 1 HETATM 14 C C10 S18 . . . B 2 19.816 24.971 -14.346 1 15.14 ? C10 S18 201 A 1 HETATM 15 O O2 S18 . . . B 2 19.869 26.022 -14.997 1 15.6 ? O2 S18 201 A 1 HETATM 16 N N3 S18 . . . B 2 20.899 24.261 -14 1 16.75 ? N3 S18 201 A 1 HETATM 17 C C11 S18 . . . B 2 22.196 25.019 -14.041 1 20.78 ? C11 S18 201 A 1 HETATM 18 C C12 S18 . . . B 2 22.668 24.828 -15.493 1 22.54 ? C12 S18 201 A 1 HETATM 19 C C13 S18 . . . B 2 24.909 25.664 -14.698 1 30.17 ? C13 S18 201 A 1 HETATM 20 C C14 S18 . . . B 2 26.321 26.131 -15.133 1 34.28 ? C14 S18 201 A 1 HETATM 21 C C15 S18 . . . B 2 26.844 24.991 -15.965 1 30.61 ? C15 S18 201 A 1 HETATM 22 C C19 S18 . . . B 2 28.096 24.335 -15.466 1 42.86 ? C19 S18 201 A 1 HETATM 23 C C18 S18 . . . B 2 28.628 23.237 -16.237 1 39.11 ? C18 S18 201 A 1 HETATM 24 C C17 S18 . . . B 2 27.905 22.847 -17.43 1 43.14 ? C17 S18 201 A 1 HETATM 25 C C16 S18 . . . B 2 26.687 23.567 -17.839 1 46.85 ? C16 S18 201 A 1 HETATM 26 N N5 S18 . . . B 2 26.176 24.561 -17.087 1 40.25 ? N5 S18 201 A 1 HETATM 27 CU CU1 S18 . . . B 2 24.447 25.475 -17.868 1 32.42 ? CU1 S18 201 A 1 HETATM 28 N N7 S18 . . . B 2 23.855 23.67 -18.351 1 37.09 ? N7 S18 201 A 1 HETATM 29 N N8 S18 . . . B 2 22.871 23.09 -18.467 1 45.55 ? N8 S18 201 A 1 HETATM 30 N N9 S18 . . . B 2 21.925 22.477 -18.545 1 53.47 ? N9 S18 201 A 1 HETATM 31 N N4 S18 . . . B 2 23.923 25.72 -15.845 1 24.25 ? N4 S18 201 A 1 HETATM 32 C C20 S18 . . . B 2 23.662 27.195 -15.767 1 28.78 ? C20 S18 201 A 1 HETATM 33 C C21 S18 . . . B 2 22.507 27.809 -16.59 1 32.67 ? C21 S18 201 A 1 HETATM 34 C C22 S18 . . . B 2 22.283 27.412 -18.041 1 31.68 ? C22 S18 201 A 1 HETATM 35 N N6 S18 . . . B 2 22.852 26.384 -18.644 1 34.99 ? N6 S18 201 A 1 HETATM 36 C C26 S18 . . . B 2 21.161 28.11 -18.705 1 39.41 ? C26 S18 201 A 1 HETATM 37 C C25 S18 . . . B 2 20.783 27.715 -20.053 1 38.48 ? C25 S18 201 A 1 HETATM 38 C C24 S18 . . . B 2 21.532 26.669 -20.729 1 37.82 ? C24 S18 201 A 1 HETATM 39 C C23 S18 . . . B 2 22.622 26.039 -19.964 1 40.56 ? C23 S18 201 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 39 #