data_5VL8 # _model_server_result.job_id cEzPPDQYbxDfVsrBXs9NkA _model_server_result.datetime_utc '2024-10-11 16:33:08' _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 5vl8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5VL8 # _exptl.entry_id 5VL8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 590.24 _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](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 5VL8 _cell.length_a 57.58 _cell.length_b 57.58 _cell.length_c 183.57 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VL8 _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 57.58 57.58 0 3 'crystal symmetry operation' 10_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 57.58 57.58 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 2.576 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C27 H38 Cu N6 O3 S' _chem_comp.formula_weight 590.24 _chem_comp.id S32 _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](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 C24 C25 S32 doub 277 n y C24 C23 S32 sing 278 n y C25 C26 S32 sing 279 n y C23 N6 S32 doub 280 n y C26 C22 S32 doub 281 n y N6 C22 S32 sing 282 n y N6 CU1 S32 sing 283 n n C22 C21 S32 sing 284 n n O3 CU1 S32 sing 285 n n CU1 N5 S32 sing 286 n n CU1 N4 S32 sing 287 n n C16 C17 S32 doub 288 n y C16 N5 S32 sing 289 n y C21 C20 S32 sing 290 n n C17 C18 S32 sing 291 n y N5 C15 S32 doub 292 n y C12 N4 S32 sing 293 n n C12 C27 S32 sing 294 n n C20 N4 S32 sing 295 n n N4 C13 S32 sing 296 n n C11 C27 S32 sing 297 n n C11 N3 S32 sing 298 n n C18 C19 S32 doub 299 n y O2 C10 S32 doub 300 n n C15 C19 S32 sing 301 n y C15 C14 S32 sing 302 n n C10 N3 S32 sing 303 n n C10 C9 S32 sing 304 n n C13 C14 S32 sing 305 n n C9 C8 S32 sing 306 n n C8 C7 S32 sing 307 n n C7 C6 S32 sing 308 n n C6 C5 S32 sing 309 n n C5 C4 S32 sing 310 n n C5 S1 S32 sing 311 n n N2 C4 S32 sing 312 n n N2 C1 S32 sing 313 n n C4 C2 S32 sing 314 n n S1 C3 S32 sing 315 n n C1 O1 S32 doub 316 n n C1 N1 S32 sing 317 n n C2 C3 S32 sing 318 n n C2 N1 S32 sing 319 n n N2 H1 S32 sing 320 n n N1 H2 S32 sing 321 n n C2 H3 S32 sing 322 n n C4 H4 S32 sing 323 n n C3 H5 S32 sing 324 n n C3 H6 S32 sing 325 n n C5 H7 S32 sing 326 n n C6 H8 S32 sing 327 n n C6 H9 S32 sing 328 n n C7 H10 S32 sing 329 n n C7 H11 S32 sing 330 n n C8 H12 S32 sing 331 n n C8 H13 S32 sing 332 n n C9 H14 S32 sing 333 n n C9 H15 S32 sing 334 n n N3 H16 S32 sing 335 n n C11 H17 S32 sing 336 n n C11 H18 S32 sing 337 n n C27 H19 S32 sing 338 n n C27 H20 S32 sing 339 n n C12 H21 S32 sing 340 n n C12 H22 S32 sing 341 n n C13 H23 S32 sing 342 n n C13 H24 S32 sing 343 n n C14 H25 S32 sing 344 n n C14 H26 S32 sing 345 n n C19 H27 S32 sing 346 n n C18 H28 S32 sing 347 n n C17 H29 S32 sing 348 n n C16 H30 S32 sing 349 n n C20 H31 S32 sing 350 n n C20 H32 S32 sing 351 n n C21 H33 S32 sing 352 n n C21 H34 S32 sing 353 n n C26 H35 S32 sing 354 n n C25 H36 S32 sing 355 n n C24 H37 S32 sing 356 n n C23 H38 S32 sing 357 n n # _atom_sites.entry_id 5VL8 _atom_sites.fract_transf_matrix[1][1] 0.017367 _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] 0.017367 _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] 0.005448 _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 S32 A 1 201 1 S32 S32 . C 3 CU A 1 202 1 CU CU . D 4 GOL A 1 203 2 GOL GOL . E 5 HOH A 1 301 48 HOH HOH . E 5 HOH A 2 302 24 HOH HOH . E 5 HOH A 3 303 123 HOH HOH . E 5 HOH A 4 304 105 HOH HOH . E 5 HOH A 5 305 56 HOH HOH . E 5 HOH A 6 306 35 HOH HOH . E 5 HOH A 7 307 1 HOH HOH . E 5 HOH A 8 308 89 HOH HOH . E 5 HOH A 9 309 142 HOH HOH . E 5 HOH A 10 310 8 HOH HOH . E 5 HOH A 11 311 23 HOH HOH . E 5 HOH A 12 312 47 HOH HOH . E 5 HOH A 13 313 26 HOH HOH . E 5 HOH A 14 314 4 HOH HOH . E 5 HOH A 15 315 29 HOH HOH . E 5 HOH A 16 316 80 HOH HOH . E 5 HOH A 17 317 18 HOH HOH . E 5 HOH A 18 318 44 HOH HOH . E 5 HOH A 19 319 71 HOH HOH . E 5 HOH A 20 320 7 HOH HOH . E 5 HOH A 21 321 12 HOH HOH . E 5 HOH A 22 322 128 HOH HOH . E 5 HOH A 23 323 11 HOH HOH . E 5 HOH A 24 324 2 HOH HOH . E 5 HOH A 25 325 15 HOH HOH . E 5 HOH A 26 326 17 HOH HOH . E 5 HOH A 27 327 110 HOH HOH . E 5 HOH A 28 328 46 HOH HOH . E 5 HOH A 29 329 106 HOH HOH . E 5 HOH A 30 330 75 HOH HOH . E 5 HOH A 31 331 25 HOH HOH . E 5 HOH A 32 332 3 HOH HOH . E 5 HOH A 33 333 14 HOH HOH . E 5 HOH A 34 334 10 HOH HOH . E 5 HOH A 35 335 138 HOH HOH . E 5 HOH A 36 336 22 HOH HOH . E 5 HOH A 37 337 67 HOH HOH . E 5 HOH A 38 338 5 HOH HOH . E 5 HOH A 39 339 57 HOH HOH . E 5 HOH A 40 340 33 HOH HOH . E 5 HOH A 41 341 21 HOH HOH . E 5 HOH A 42 342 19 HOH HOH . E 5 HOH A 43 343 31 HOH HOH . E 5 HOH A 44 344 140 HOH HOH . E 5 HOH A 45 345 27 HOH HOH . E 5 HOH A 46 346 59 HOH HOH . E 5 HOH A 47 347 144 HOH HOH . E 5 HOH A 48 348 76 HOH HOH . E 5 HOH A 49 349 37 HOH HOH . E 5 HOH A 50 350 143 HOH HOH . E 5 HOH A 51 351 63 HOH HOH . E 5 HOH A 52 352 69 HOH HOH . E 5 HOH A 53 353 73 HOH HOH . E 5 HOH A 54 354 34 HOH HOH . E 5 HOH A 55 355 6 HOH HOH . E 5 HOH A 56 356 62 HOH HOH . E 5 HOH A 57 357 70 HOH HOH . E 5 HOH A 58 358 13 HOH HOH . E 5 HOH A 59 359 115 HOH HOH . E 5 HOH A 60 360 139 HOH HOH . E 5 HOH A 61 361 50 HOH HOH . E 5 HOH A 62 362 60 HOH HOH . E 5 HOH A 63 363 66 HOH HOH . E 5 HOH A 64 364 30 HOH HOH . E 5 HOH A 65 365 36 HOH HOH . E 5 HOH A 66 366 20 HOH HOH . E 5 HOH A 67 367 16 HOH HOH . E 5 HOH A 68 368 9 HOH HOH . E 5 HOH A 69 369 38 HOH HOH . E 5 HOH A 70 370 88 HOH HOH . E 5 HOH A 71 371 42 HOH HOH . E 5 HOH A 72 372 135 HOH HOH . E 5 HOH A 73 373 141 HOH HOH . E 5 HOH A 74 374 65 HOH HOH . E 5 HOH A 75 375 43 HOH HOH . E 5 HOH A 76 376 32 HOH HOH . E 5 HOH A 77 377 54 HOH HOH . E 5 HOH A 78 378 49 HOH HOH . E 5 HOH A 79 379 72 HOH HOH . E 5 HOH A 80 380 136 HOH HOH . E 5 HOH A 81 381 53 HOH HOH . E 5 HOH A 82 382 79 HOH HOH . E 5 HOH A 83 383 137 HOH HOH . E 5 HOH A 84 384 92 HOH HOH . E 5 HOH A 85 385 96 HOH HOH . E 5 HOH A 86 386 134 HOH HOH . E 5 HOH A 87 387 101 HOH HOH . E 5 HOH A 88 388 51 HOH HOH . E 5 HOH A 89 389 83 HOH HOH . E 5 HOH A 90 390 124 HOH HOH . E 5 HOH A 91 391 107 HOH HOH . E 5 HOH A 92 392 58 HOH HOH . E 5 HOH A 93 393 122 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 S32 . . . B 2 14.245 29.343 -8.28 1 14.68 ? O1 S32 201 A 1 HETATM 2 C C1 S32 . . . B 2 15.579 29.334 -8.508 1 13.41 ? C1 S32 201 A 1 HETATM 3 N N2 S32 . . . B 2 16.062 29.111 -9.755 1 14.34 ? N2 S32 201 A 1 HETATM 4 N N1 S32 . . . B 2 16.493 29.426 -7.489 1 16.11 ? N1 S32 201 A 1 HETATM 5 C C2 S32 . . . B 2 17.819 29.364 -8.157 1 13.49 ? C2 S32 201 A 1 HETATM 6 C C4 S32 . . . B 2 17.526 29.175 -9.684 1 13.61 ? C4 S32 201 A 1 HETATM 7 C C3 S32 . . . B 2 18.561 28.1 -7.691 1 15.41 ? C3 S32 201 A 1 HETATM 8 S S1 S32 . . . B 2 17.978 26.702 -8.632 1 17.43 ? S1 S32 201 A 1 HETATM 9 C C5 S32 . . . B 2 18.117 27.812 -10.077 1 14.56 ? C5 S32 201 A 1 HETATM 10 C C6 S32 . . . B 2 17.509 27.145 -11.324 1 15.32 ? C6 S32 201 A 1 HETATM 11 C C7 S32 . . . B 2 18.345 26.06 -11.951 1 15.17 ? C7 S32 201 A 1 HETATM 12 C C8 S32 . . . B 2 17.676 25.405 -13.188 1 15.91 ? C8 S32 201 A 1 HETATM 13 C C9 S32 . . . B 2 18.396 24.142 -13.717 1 17.91 ? C9 S32 201 A 1 HETATM 14 C C10 S32 . . . B 2 19.753 24.551 -14.322 1 17.65 ? C10 S32 201 A 1 HETATM 15 O O2 S32 . . . B 2 19.806 25.67 -15.035 1 18.99 ? O2 S32 201 A 1 HETATM 16 N N3 S32 . . . B 2 20.871 23.721 -14.165 1 19.58 ? N3 S32 201 A 1 HETATM 17 C C11 S32 . . . B 2 22.023 23.937 -15.083 1 23.18 ? C11 S32 201 A 1 HETATM 18 C C27 S32 . . . B 2 23.012 25.041 -14.646 1 27.04 ? C27 S32 201 A 1 HETATM 19 C C12 S32 . . . B 2 23.983 25.04 -15.841 1 27.97 ? C12 S32 201 A 1 HETATM 20 C C13 S32 . . . B 2 25.466 26.328 -14.274 1 30.04 ? C13 S32 201 A 1 HETATM 21 C C14 S32 . . . B 2 26.496 27.434 -14.186 1 35.75 ? C14 S32 201 A 1 HETATM 22 C C15 S32 . . . B 2 27.764 27.09 -14.953 1 41.33 ? C15 S32 201 A 1 HETATM 23 C C19 S32 . . . B 2 28.998 27.058 -14.3 1 46.58 ? C19 S32 201 A 1 HETATM 24 C C18 S32 . . . B 2 30.147 26.794 -15.072 1 47 ? C18 S32 201 A 1 HETATM 25 C C17 S32 . . . B 2 30.094 26.56 -16.47 1 48.1 ? C17 S32 201 A 1 HETATM 26 C C16 S32 . . . B 2 28.846 26.601 -17.129 1 48.12 ? C16 S32 201 A 1 HETATM 27 N N5 S32 . . . B 2 27.698 26.859 -16.346 1 43.23 ? N5 S32 201 A 1 HETATM 28 CU CU1 S32 . . . B 2 25.813 26.75 -17.233 1 35.66 ? CU1 S32 201 A 1 HETATM 29 N N4 S32 . . . B 2 24.555 26.439 -15.495 1 30.22 ? N4 S32 201 A 1 HETATM 30 C C20 S32 . . . B 2 23.771 27.711 -15.497 1 33.69 ? C20 S32 201 A 1 HETATM 31 C C21 S32 . . . B 2 22.842 28.106 -16.683 1 43.38 ? C21 S32 201 A 1 HETATM 32 C C22 S32 . . . B 2 22.99 27.423 -18.079 1 45.73 ? C22 S32 201 A 1 HETATM 33 N N6 S32 . . . B 2 24.214 26.916 -18.539 1 41.5 ? N6 S32 201 A 1 HETATM 34 C C26 S32 . . . B 2 21.868 27.366 -18.947 1 45.98 ? C26 S32 201 A 1 HETATM 35 C C25 S32 . . . B 2 21.971 26.75 -20.217 1 51.05 ? C25 S32 201 A 1 HETATM 36 C C24 S32 . . . B 2 23.21 26.221 -20.653 1 51.84 ? C24 S32 201 A 1 HETATM 37 C C23 S32 . . . B 2 24.344 26.294 -19.803 1 49.29 ? C23 S32 201 A 1 HETATM 38 O O3 S32 . . . B 2 26.201 24.559 -17.845 1 35.81 ? O3 S32 201 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 38 #