data_5VL5 # _model_server_result.job_id 52PGFjukzxjyDcQAYQTtew _model_server_result.datetime_utc '2025-07-17 11:59:11' _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 5vl5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5VL5 # _exptl.entry_id 5VL5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 633.268 _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}propyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide](azido)(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 5VL5 _cell.length_a 57.71 _cell.length_b 57.71 _cell.length_c 184.04 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VL5 _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 57.71 57.71 0 3 'crystal symmetry operation' 10_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 57.71 57.71 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 1_555 _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 2.648 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C27 H39 Cu N9 O3 S' _chem_comp.formula_weight 633.268 _chem_comp.id S31 _chem_comp.mon_nstd_flag . _chem_comp.name '[N-(3-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}propyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide](azido)(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 S31 doub 264 n y C17 C16 S31 sing 265 n y C18 C19 S31 sing 266 n y C16 N5 S31 doub 267 n y C19 C15 S31 doub 268 n y N7 N8 S31 doub 269 n n N5 C15 S31 sing 270 n y N5 CU1 S31 sing 271 n n N8 N9 S31 doub 272 n n C15 C14 S31 sing 273 n n N9 CU1 S31 sing 274 n n O3 CU1 S31 sing 275 n n CU1 N6 S31 sing 276 n n CU1 N4 S31 sing 277 n n C23 C24 S31 doub 278 n y C23 N6 S31 sing 279 n y C14 C13 S31 sing 280 n n C24 C25 S31 sing 281 n y N6 C22 S31 doub 282 n y C12 N4 S31 sing 283 n n C12 C27 S31 sing 284 n n C13 N4 S31 sing 285 n n N4 C20 S31 sing 286 n n C25 C26 S31 doub 287 n y C11 N3 S31 sing 288 n n C11 C27 S31 sing 289 n n O2 C10 S31 doub 290 n n C22 C26 S31 sing 291 n y C22 C21 S31 sing 292 n n C10 N3 S31 sing 293 n n C10 C9 S31 sing 294 n n C20 C21 S31 sing 295 n n C9 C8 S31 sing 296 n n C8 C7 S31 sing 297 n n C7 C6 S31 sing 298 n n C6 C5 S31 sing 299 n n C5 C4 S31 sing 300 n n C5 S1 S31 sing 301 n n N2 C4 S31 sing 302 n n N2 C1 S31 sing 303 n n C4 C2 S31 sing 304 n n S1 C3 S31 sing 305 n n C1 O1 S31 doub 306 n n C1 N1 S31 sing 307 n n C2 C3 S31 sing 308 n n C2 N1 S31 sing 309 n n C9 H1 S31 sing 310 n n C9 H2 S31 sing 311 n n C8 H3 S31 sing 312 n n C8 H4 S31 sing 313 n n C7 H5 S31 sing 314 n n C7 H6 S31 sing 315 n n C6 H7 S31 sing 316 n n C6 H8 S31 sing 317 n n C5 H9 S31 sing 318 n n C4 H10 S31 sing 319 n n N2 H11 S31 sing 320 n n C3 H12 S31 sing 321 n n C3 H13 S31 sing 322 n n C2 H14 S31 sing 323 n n N1 H15 S31 sing 324 n n N3 H16 S31 sing 325 n n C11 H17 S31 sing 326 n n C11 H18 S31 sing 327 n n C12 H19 S31 sing 328 n n C12 H20 S31 sing 329 n n C27 H21 S31 sing 330 n n C27 H22 S31 sing 331 n n C13 H23 S31 sing 332 n n C13 H24 S31 sing 333 n n C20 H25 S31 sing 334 n n C20 H26 S31 sing 335 n n C21 H27 S31 sing 336 n n C21 H28 S31 sing 337 n n C26 H29 S31 sing 338 n n C25 H30 S31 sing 339 n n C24 H31 S31 sing 340 n n C23 H32 S31 sing 341 n n N7 H33 S31 sing 342 n n C14 H34 S31 sing 343 n n C14 H35 S31 sing 344 n n C16 H36 S31 sing 345 n n C17 H37 S31 sing 346 n n C18 H38 S31 sing 347 n n C19 H39 S31 sing 348 n n # _atom_sites.entry_id 5VL5 _atom_sites.fract_transf_matrix[1][1] 0.017328 _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] 0.017328 _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] 0.005434 _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 S31 A 1 201 1 S31 S31 . C 3 CU A 1 202 1 CU CU . D 4 HOH A 1 301 149 HOH HOH . D 4 HOH A 2 302 105 HOH HOH . D 4 HOH A 3 303 13 HOH HOH . D 4 HOH A 4 304 58 HOH HOH . D 4 HOH A 5 305 110 HOH HOH . D 4 HOH A 6 306 2 HOH HOH . D 4 HOH A 7 307 22 HOH HOH . D 4 HOH A 8 308 51 HOH HOH . D 4 HOH A 9 309 85 HOH HOH . D 4 HOH A 10 310 100 HOH HOH . D 4 HOH A 11 311 35 HOH HOH . D 4 HOH A 12 312 44 HOH HOH . D 4 HOH A 13 313 25 HOH HOH . D 4 HOH A 14 314 33 HOH HOH . D 4 HOH A 15 315 28 HOH HOH . D 4 HOH A 16 316 61 HOH HOH . D 4 HOH A 17 317 78 HOH HOH . D 4 HOH A 18 318 3 HOH HOH . D 4 HOH A 19 319 152 HOH HOH . D 4 HOH A 20 320 1 HOH HOH . D 4 HOH A 21 321 79 HOH HOH . D 4 HOH A 22 322 7 HOH HOH . D 4 HOH A 23 323 65 HOH HOH . D 4 HOH A 24 324 19 HOH HOH . D 4 HOH A 25 325 66 HOH HOH . D 4 HOH A 26 326 11 HOH HOH . D 4 HOH A 27 327 31 HOH HOH . D 4 HOH A 28 328 141 HOH HOH . D 4 HOH A 29 329 6 HOH HOH . D 4 HOH A 30 330 73 HOH HOH . D 4 HOH A 31 331 124 HOH HOH . D 4 HOH A 32 332 71 HOH HOH . D 4 HOH A 33 333 8 HOH HOH . D 4 HOH A 34 334 17 HOH HOH . D 4 HOH A 35 335 37 HOH HOH . D 4 HOH A 36 337 27 HOH HOH . D 4 HOH A 37 338 112 HOH HOH . D 4 HOH A 38 339 5 HOH HOH . D 4 HOH A 39 340 140 HOH HOH . D 4 HOH A 40 341 36 HOH HOH . D 4 HOH A 41 342 12 HOH HOH . D 4 HOH A 42 343 39 HOH HOH . D 4 HOH A 43 344 46 HOH HOH . D 4 HOH A 44 345 47 HOH HOH . D 4 HOH A 45 346 122 HOH HOH . D 4 HOH A 46 347 81 HOH HOH . D 4 HOH A 47 348 16 HOH HOH . D 4 HOH A 48 349 26 HOH HOH . D 4 HOH A 49 350 123 HOH HOH . D 4 HOH A 50 351 59 HOH HOH . D 4 HOH A 51 352 23 HOH HOH . D 4 HOH A 52 353 63 HOH HOH . D 4 HOH A 53 354 15 HOH HOH . D 4 HOH A 54 355 80 HOH HOH . D 4 HOH A 55 356 52 HOH HOH . D 4 HOH A 56 357 82 HOH HOH . D 4 HOH A 57 358 20 HOH HOH . D 4 HOH A 58 359 30 HOH HOH . D 4 HOH A 59 360 54 HOH HOH . D 4 HOH A 60 361 49 HOH HOH . D 4 HOH A 61 362 4 HOH HOH . D 4 HOH A 62 363 34 HOH HOH . D 4 HOH A 63 364 42 HOH HOH . D 4 HOH A 64 365 32 HOH HOH . D 4 HOH A 65 366 9 HOH HOH . D 4 HOH A 66 367 77 HOH HOH . D 4 HOH A 67 368 57 HOH HOH . D 4 HOH A 68 369 67 HOH HOH . D 4 HOH A 69 370 148 HOH HOH . D 4 HOH A 70 371 24 HOH HOH . D 4 HOH A 71 372 29 HOH HOH . D 4 HOH A 72 373 38 HOH HOH . D 4 HOH A 73 374 41 HOH HOH . D 4 HOH A 74 375 72 HOH HOH . D 4 HOH A 75 376 151 HOH HOH . D 4 HOH A 76 377 120 HOH HOH . D 4 HOH A 77 378 18 HOH HOH . D 4 HOH A 78 379 143 HOH HOH . D 4 HOH A 79 380 90 HOH HOH . D 4 HOH A 80 381 62 HOH HOH . D 4 HOH A 81 382 101 HOH HOH . D 4 HOH A 82 383 43 HOH HOH . D 4 HOH A 83 384 60 HOH HOH . D 4 HOH A 84 385 40 HOH HOH . D 4 HOH A 85 386 146 HOH HOH . D 4 HOH A 86 387 147 HOH HOH . D 4 HOH A 87 388 121 HOH HOH . D 4 HOH A 88 389 142 HOH HOH . D 4 HOH A 89 390 136 HOH HOH . D 4 HOH A 90 391 150 HOH HOH . D 4 HOH A 91 392 89 HOH HOH . D 4 HOH A 92 393 135 HOH HOH . D 4 HOH A 93 394 131 HOH HOH . D 4 HOH A 94 395 69 HOH HOH . D 4 HOH A 95 396 125 HOH HOH . D 4 HOH A 96 397 21 HOH HOH . D 4 HOH A 97 398 106 HOH HOH . D 4 HOH A 98 399 117 HOH HOH . D 4 HOH A 99 400 129 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 O2 S31 . . . B 2 19.91 25.712 -15.046 1 18.73 ? O2 S31 201 A 1 HETATM 2 C C10 S31 . . . B 2 19.848 24.551 -14.405 1 16.52 ? C10 S31 201 A 1 HETATM 3 C C9 S31 . . . B 2 18.468 24.224 -13.742 1 17.81 ? C9 S31 201 A 1 HETATM 4 C C8 S31 . . . B 2 17.744 25.537 -13.325 1 17.56 ? C8 S31 201 A 1 HETATM 5 C C7 S31 . . . B 2 18.279 25.984 -11.963 1 16.07 ? C7 S31 201 A 1 HETATM 6 C C6 S31 . . . B 2 17.664 27.242 -11.452 1 14.96 ? C6 S31 201 A 1 HETATM 7 C C5 S31 . . . B 2 18.115 27.772 -10.095 1 13.26 ? C5 S31 201 A 1 HETATM 8 C C4 S31 . . . B 2 17.584 29.237 -9.697 1 11.64 ? C4 S31 201 A 1 HETATM 9 N N2 S31 . . . B 2 16.123 29.236 -9.776 1 12.24 ? N2 S31 201 A 1 HETATM 10 S S1 S31 . . . B 2 17.995 26.788 -8.648 1 15.79 ? S1 S31 201 A 1 HETATM 11 C C3 S31 . . . B 2 18.517 28.175 -7.726 1 16.36 ? C3 S31 201 A 1 HETATM 12 C C2 S31 . . . B 2 17.782 29.461 -8.135 1 12.66 ? C2 S31 201 A 1 HETATM 13 N N1 S31 . . . B 2 16.42 29.488 -7.569 1 12.65 ? N1 S31 201 A 1 HETATM 14 C C1 S31 . . . B 2 15.704 29.414 -8.594 1 12.24 ? C1 S31 201 A 1 HETATM 15 O O1 S31 . . . B 2 14.383 29.404 -8.302 1 14.52 ? O1 S31 201 A 1 HETATM 16 N N3 S31 . . . B 2 20.895 23.798 -14.207 1 19.25 ? N3 S31 201 A 1 HETATM 17 C C11 S31 . . . B 2 22.153 24.063 -15.053 1 22.4 ? C11 S31 201 A 1 HETATM 18 C C12 S31 . . . B 2 23.753 25.371 -15.578 1 30.56 ? C12 S31 201 A 1 HETATM 19 N N4 S31 . . . B 2 24.817 26.423 -15.448 1 33.08 ? N4 S31 201 A 1 HETATM 20 C C27 S31 . . . B 2 22.897 25.08 -14.204 1 26.95 ? C27 S31 201 A 1 HETATM 21 C C13 S31 . . . B 2 23.773 27.589 -15.495 1 30.85 ? C13 S31 201 A 1 HETATM 22 C C20 S31 . . . B 2 25.508 26.335 -14.288 1 31.17 ? C20 S31 201 A 1 HETATM 23 C C21 S31 . . . B 2 26.523 27.187 -14.154 1 36.26 ? C21 S31 201 A 1 HETATM 24 C C22 S31 . . . B 2 27.631 26.964 -14.884 1 39.99 ? C22 S31 201 A 1 HETATM 25 C C26 S31 . . . B 2 28.852 26.957 -14.29 1 42.92 ? C26 S31 201 A 1 HETATM 26 C C25 S31 . . . B 2 29.962 26.806 -15.061 1 43.26 ? C25 S31 201 A 1 HETATM 27 C C24 S31 . . . B 2 29.9 26.639 -16.409 1 41.65 ? C24 S31 201 A 1 HETATM 28 C C23 S31 . . . B 2 28.688 26.651 -17.01 1 42.97 ? C23 S31 201 A 1 HETATM 29 N N6 S31 . . . B 2 27.578 26.777 -16.238 1 38.46 ? N6 S31 201 A 1 HETATM 30 CU CU1 S31 . . . B 2 25.83 26.854 -17.28 1 34.57 ? CU1 S31 201 A 1 HETATM 31 N N8 S31 . . . B 2 25.457 29.682 -18.229 0.5 31.2 ? N8 S31 201 A 1 HETATM 32 N N9 S31 . . . B 2 25.519 28.596 -17.889 0.5 34.37 ? N9 S31 201 A 1 HETATM 33 N N7 S31 . . . B 2 25.389 30.782 -18.58 0.5 32.98 ? N7 S31 201 A 1 HETATM 34 N N5 S31 . . . B 2 24.047 26.982 -18.392 1 39.01 ? N5 S31 201 A 1 HETATM 35 C C15 S31 . . . B 2 22.829 27.378 -17.952 1 40.58 ? C15 S31 201 A 1 HETATM 36 C C14 S31 . . . B 2 22.548 27.725 -16.494 1 36.11 ? C14 S31 201 A 1 HETATM 37 C C16 S31 . . . B 2 24.27 26.684 -19.705 1 45.3 ? C16 S31 201 A 1 HETATM 38 C C17 S31 . . . B 2 23.257 26.736 -20.6 1 45.59 ? C17 S31 201 A 1 HETATM 39 C C18 S31 . . . B 2 22.028 27.108 -20.161 1 49.66 ? C18 S31 201 A 1 HETATM 40 C C19 S31 . . . B 2 21.816 27.438 -18.852 1 41.47 ? C19 S31 201 A 1 HETATM 41 O O3 S31 . . . B 2 26.219 24.666 -17.841 1 34.61 ? O3 S31 201 A 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 238 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 41 #