data_8OFE # _model_server_result.job_id etzzHebgsGVCov0Ts3EWPw _model_server_result.datetime_utc '2024-10-10 16:29:38' _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 8ofe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 8OFE # _exptl.entry_id 8OFE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 401.564 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R)-2-[[methanoyl(oxidanyl)amino]methyl]-N-[(2S)-3-methyl-1-oxidanylidene-1-[2-(sulfanylmethyl)pyrrolidin-1-yl]butan-2-yl]heptanamide _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 120 _cell.entry_id 8OFE _cell.length_a 54.62 _cell.length_b 54.62 _cell.length_c 231.73 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8OFE _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall 'P 61 2 (x,y,z+5/12)' _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 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 # 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 93 A CYS 90 1_555 C ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc2 A NE2 HIS 135 A HIS 132 1_555 C ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc3 A NE2 HIS 139 A HIS 136 1_555 C ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc4 B O1 VLK . A VLK 201 1_555 C ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc5 B O2 VLK . A VLK 201 1_555 C ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? # _chem_comp.formula 'C19 H35 N3 O4 S' _chem_comp.formula_weight 401.564 _chem_comp.id VLK _chem_comp.mon_nstd_flag . _chem_comp.name (2R)-2-[[methanoyl(oxidanyl)amino]methyl]-N-[(2S)-3-methyl-1-oxidanylidene-1-[2-(sulfanylmethyl)pyrrolidin-1-yl]butan-2-yl]heptanamide _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 C18 C17 VLK sing 348 n n O3 C9 VLK doub 349 n n C17 C10 VLK sing 350 n n C17 C19 VLK sing 351 n n N3 C11 VLK sing 352 n n C10 C11 VLK sing 353 n n C10 N2 VLK sing 354 n n C9 N2 VLK sing 355 n n C9 C6 VLK sing 356 n n C11 O4 VLK doub 357 n n C7 C6 VLK sing 358 n n C7 N1 VLK sing 359 n n C6 C5 VLK sing 360 n n C5 C4 VLK sing 361 n n N1 C8 VLK sing 362 n n N1 O1 VLK sing 363 n n C8 O2 VLK doub 364 n n C4 C3 VLK sing 365 n n C3 C2 VLK sing 366 n n C1 C2 VLK sing 367 n n C1 H1 VLK sing 368 n n C1 H2 VLK sing 369 n n C1 H3 VLK sing 370 n n C2 H5 VLK sing 371 n n C2 H4 VLK sing 372 n n C6 H12 VLK sing 373 n n C5 H10 VLK sing 374 n n C5 H11 VLK sing 375 n n C4 H8 VLK sing 376 n n C4 H9 VLK sing 377 n n C3 H6 VLK sing 378 n n C3 H7 VLK sing 379 n n C10 H18 VLK sing 380 n n C8 H16 VLK sing 381 n n C18 H31 VLK sing 382 n n C18 H30 VLK sing 383 n n C18 H32 VLK sing 384 n n C17 H29 VLK sing 385 n n C19 H35 VLK sing 386 n n C19 H33 VLK sing 387 n n C19 H34 VLK sing 388 n n C7 H14 VLK sing 389 n n C7 H13 VLK sing 390 n n N2 H17 VLK sing 391 n n O1 H15 VLK sing 392 n n N3 C14 VLK sing 393 n n C14 C12 VLK sing 394 n n C12 C15 VLK sing 395 n n C15 C16 VLK sing 396 n n C16 N3 VLK sing 397 n n C14 C13 VLK sing 398 n n C14 H19 VLK sing 399 n n C12 H20 VLK sing 400 n n C12 H21 VLK sing 401 n n C15 H22 VLK sing 402 n n C15 H23 VLK sing 403 n n C16 H24 VLK sing 404 n n C16 H25 VLK sing 405 n n C13 H27 VLK sing 406 n n C13 H28 VLK sing 407 n n C13 S1 VLK sing 408 n n S1 H26 VLK sing 409 n n # _atom_sites.entry_id 8OFE _atom_sites.fract_transf_matrix[1][1] 0.018308 _atom_sites.fract_transf_matrix[1][2] 0.01057 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021141 _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] 0.004315 _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 VLK A 1 201 201 VLK 205 . C 3 ZN A 1 202 1 ZN ZN . D 4 HOH A 1 301 76 HOH HOH . D 4 HOH A 2 302 143 HOH HOH . D 4 HOH A 3 303 79 HOH HOH . D 4 HOH A 4 304 64 HOH HOH . D 4 HOH A 5 305 93 HOH HOH . D 4 HOH A 6 306 140 HOH HOH . D 4 HOH A 7 307 136 HOH HOH . D 4 HOH A 8 308 132 HOH HOH . D 4 HOH A 9 309 137 HOH HOH . D 4 HOH A 10 310 39 HOH HOH . D 4 HOH A 11 311 53 HOH HOH . D 4 HOH A 12 312 58 HOH HOH . D 4 HOH A 13 313 36 HOH HOH . D 4 HOH A 14 314 23 HOH HOH . D 4 HOH A 15 315 123 HOH HOH . D 4 HOH A 16 316 90 HOH HOH . D 4 HOH A 17 317 98 HOH HOH . D 4 HOH A 18 318 41 HOH HOH . D 4 HOH A 19 319 44 HOH HOH . D 4 HOH A 20 320 26 HOH HOH . D 4 HOH A 21 321 73 HOH HOH . D 4 HOH A 22 322 43 HOH HOH . D 4 HOH A 23 323 48 HOH HOH . D 4 HOH A 24 324 40 HOH HOH . D 4 HOH A 25 325 88 HOH HOH . D 4 HOH A 26 326 30 HOH HOH . D 4 HOH A 27 327 49 HOH HOH . D 4 HOH A 28 328 125 HOH HOH . D 4 HOH A 29 329 42 HOH HOH . D 4 HOH A 30 330 22 HOH HOH . D 4 HOH A 31 331 25 HOH HOH . D 4 HOH A 32 332 105 HOH HOH . D 4 HOH A 33 333 28 HOH HOH . D 4 HOH A 34 334 5 HOH HOH . D 4 HOH A 35 335 45 HOH HOH . D 4 HOH A 36 336 38 HOH HOH . D 4 HOH A 37 337 50 HOH HOH . D 4 HOH A 38 338 144 HOH HOH . D 4 HOH A 39 339 55 HOH HOH . D 4 HOH A 40 340 68 HOH HOH . D 4 HOH A 41 341 31 HOH HOH . D 4 HOH A 42 342 119 HOH HOH . D 4 HOH A 43 343 37 HOH HOH . D 4 HOH A 44 344 3 HOH HOH . D 4 HOH A 45 345 52 HOH HOH . D 4 HOH A 46 346 74 HOH HOH . D 4 HOH A 47 347 67 HOH HOH . D 4 HOH A 48 348 51 HOH HOH . D 4 HOH A 49 349 75 HOH HOH . D 4 HOH A 50 350 4 HOH HOH . D 4 HOH A 51 351 54 HOH HOH . D 4 HOH A 52 352 32 HOH HOH . D 4 HOH A 53 353 10 HOH HOH . D 4 HOH A 54 354 15 HOH HOH . D 4 HOH A 55 355 66 HOH HOH . D 4 HOH A 56 356 12 HOH HOH . D 4 HOH A 57 357 47 HOH HOH . D 4 HOH A 58 358 60 HOH HOH . D 4 HOH A 59 359 24 HOH HOH . D 4 HOH A 60 360 80 HOH HOH . D 4 HOH A 61 361 11 HOH HOH . D 4 HOH A 62 362 77 HOH HOH . D 4 HOH A 63 363 17 HOH HOH . D 4 HOH A 64 364 110 HOH HOH . D 4 HOH A 65 365 69 HOH HOH . D 4 HOH A 66 366 27 HOH HOH . D 4 HOH A 67 367 104 HOH HOH . D 4 HOH A 68 368 59 HOH HOH . D 4 HOH A 69 369 102 HOH HOH . D 4 HOH A 70 370 34 HOH HOH . D 4 HOH A 71 371 16 HOH HOH . D 4 HOH A 72 372 65 HOH HOH . D 4 HOH A 73 373 6 HOH HOH . D 4 HOH A 74 374 111 HOH HOH . D 4 HOH A 75 375 57 HOH HOH . D 4 HOH A 76 376 9 HOH HOH . D 4 HOH A 77 377 20 HOH HOH . D 4 HOH A 78 378 71 HOH HOH . D 4 HOH A 79 379 21 HOH HOH . D 4 HOH A 80 380 13 HOH HOH . D 4 HOH A 81 381 2 HOH HOH . D 4 HOH A 82 382 33 HOH HOH . D 4 HOH A 83 383 100 HOH HOH . D 4 HOH A 84 384 8 HOH HOH . D 4 HOH A 85 385 46 HOH HOH . D 4 HOH A 86 386 142 HOH HOH . D 4 HOH A 87 387 141 HOH HOH . D 4 HOH A 88 388 19 HOH HOH . D 4 HOH A 89 389 18 HOH HOH . D 4 HOH A 90 390 117 HOH HOH . D 4 HOH A 91 391 139 HOH HOH . D 4 HOH A 92 392 61 HOH HOH . D 4 HOH A 93 393 99 HOH HOH . D 4 HOH A 94 394 114 HOH HOH . D 4 HOH A 95 395 14 HOH HOH . D 4 HOH A 96 396 84 HOH HOH . D 4 HOH A 97 397 138 HOH HOH . D 4 HOH A 98 398 63 HOH HOH . D 4 HOH A 99 399 83 HOH HOH . D 4 HOH A 100 400 86 HOH HOH . D 4 HOH A 101 401 35 HOH HOH . D 4 HOH A 102 402 106 HOH HOH . D 4 HOH A 103 403 62 HOH HOH . D 4 HOH A 104 404 89 HOH HOH . D 4 HOH A 105 405 108 HOH HOH . D 4 HOH A 106 406 56 HOH HOH . D 4 HOH A 107 407 95 HOH HOH . D 4 HOH A 108 408 107 HOH HOH . D 4 HOH A 109 409 97 HOH HOH . D 4 HOH A 110 410 133 HOH HOH . D 4 HOH A 111 411 70 HOH HOH . D 4 HOH A 112 412 134 HOH HOH . D 4 HOH A 113 413 135 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 C C1 VLK . . . B 2 -5.928 21.982 7.542 0.8 31.81 ? C1 VLK 201 A 1 HETATM 2 C C2 VLK . . . B 2 -4.657 21.403 8.126 0.8 28.89 ? C2 VLK 201 A 1 HETATM 3 C C6 VLK . . . B 2 -5.008 16.936 5.83 0.8 32.19 ? C6 VLK 201 A 1 HETATM 4 C C5 VLK . . . B 2 -4.06 18.117 6.051 0.8 31.79 ? C5 VLK 201 A 1 HETATM 5 C C4 VLK . . . B 2 -4.756 19.332 6.638 0.8 31.82 ? C4 VLK 201 A 1 HETATM 6 C C3 VLK . . . B 2 -3.898 20.466 7.194 0.8 29.23 ? C3 VLK 201 A 1 HETATM 7 C C11 VLK . . . B 2 -9.243 18.957 5.169 0.8 40.89 ? C11 VLK 201 A 1 HETATM 8 C C10 VLK . . . B 2 -8.493 17.8 4.519 0.8 35.96 ? C10 VLK 201 A 1 HETATM 9 C C8 VLK . . . B 2 -2.293 15.372 6.547 0.8 29.41 ? C8 VLK 201 A 1 HETATM 10 C C18 VLK . . . B 2 -8.647 15.57 3.403 0.8 39.59 ? C18 VLK 201 A 1 HETATM 11 C C17 VLK . . . B 2 -9.391 16.572 4.276 0.8 38.28 ? C17 VLK 201 A 1 HETATM 12 C C19 VLK . . . B 2 -9.845 15.917 5.567 0.8 39.09 ? C19 VLK 201 A 1 HETATM 13 C C7 VLK . . . B 2 -4.328 15.695 5.274 0.8 28.91 ? C7 VLK 201 A 1 HETATM 14 C C9 VLK . . . B 2 -6.115 17.325 4.858 0.8 31.98 ? C9 VLK 201 A 1 HETATM 15 N N1 VLK . . . B 2 -3.541 15.145 6.361 0.8 29.92 ? N1 VLK 201 A 1 HETATM 16 N N2 VLK . . . B 2 -7.341 17.485 5.359 0.8 34.2 ? N2 VLK 201 A 1 HETATM 17 N N3 VLK . . . B 2 -10.105 19.629 4.378 0.8 42.72 ? N3 VLK 201 A 1 HETATM 18 O O1 VLK . . . B 2 -4.135 14.406 7.383 0.8 31.35 ? O1 VLK 201 A 1 HETATM 19 O O2 VLK . . . B 2 -1.782 15.089 7.588 0.8 30.07 ? O2 VLK 201 A 1 HETATM 20 O O3 VLK . . . B 2 -5.87 17.479 3.675 0.8 31.9 ? O3 VLK 201 A 1 HETATM 21 O O4 VLK . . . B 2 -9.058 19.27 6.345 0.8 41.62 ? O4 VLK 201 A 1 HETATM 22 H H1 VLK . . . B 2 -6.333 22.595 8.184 0.8 38.17 ? H1 VLK 201 A 1 HETATM 23 H H2 VLK . . . B 2 -6.554 21.261 7.342 0.8 38.17 ? H2 VLK 201 A 1 HETATM 24 H H3 VLK . . . B 2 -5.718 22.466 6.72 0.8 38.17 ? H3 VLK 201 A 1 HETATM 25 H H5 VLK . . . B 2 -4.062 22.141 8.378 0.8 34.67 ? H5 VLK 201 A 1 HETATM 26 H H4 VLK . . . B 2 -4.884 20.91 8.944 0.8 34.67 ? H4 VLK 201 A 1 HETATM 27 H H12 VLK . . . B 2 -5.367 16.718 6.725 0.8 38.63 ? H12 VLK 201 A 1 HETATM 28 H H10 VLK . . . B 2 -3.652 18.365 5.194 0.8 38.15 ? H10 VLK 201 A 1 HETATM 29 H H11 VLK . . . B 2 -3.337 17.84 6.653 0.8 38.15 ? H11 VLK 201 A 1 HETATM 30 H H8 VLK . . . B 2 -5.339 19.019 7.364 0.8 38.18 ? H8 VLK 201 A 1 HETATM 31 H H9 VLK . . . B 2 -5.332 19.712 5.939 0.8 38.18 ? H9 VLK 201 A 1 HETATM 32 H H6 VLK . . . B 2 -3.536 20.989 6.445 0.8 35.08 ? H6 VLK 201 A 1 HETATM 33 H H7 VLK . . . B 2 -3.137 20.081 7.682 0.8 35.08 ? H7 VLK 201 A 1 HETATM 34 H H18 VLK . . . B 2 -8.162 18.112 3.638 0.8 43.16 ? H18 VLK 201 A 1 HETATM 35 H H16 VLK . . . B 2 -1.793 15.766 5.847 0.8 35.29 ? H16 VLK 201 A 1 HETATM 36 H H31 VLK . . . B 2 -8.421 15.985 2.554 0.8 47.5 ? H31 VLK 201 A 1 HETATM 37 H H30 VLK . . . B 2 -9.212 14.795 3.244 0.8 47.5 ? H30 VLK 201 A 1 HETATM 38 H H32 VLK . . . B 2 -7.832 15.29 3.853 0.8 47.5 ? H32 VLK 201 A 1 HETATM 39 H H29 VLK . . . B 2 -10.215 16.869 3.815 0.8 45.94 ? H29 VLK 201 A 1 HETATM 40 H H35 VLK . . . B 2 -9.068 15.619 6.07 0.8 46.91 ? H35 VLK 201 A 1 HETATM 41 H H33 VLK . . . B 2 -10.41 15.154 5.362 0.8 46.91 ? H33 VLK 201 A 1 HETATM 42 H H34 VLK . . . B 2 -10.347 16.559 6.097 0.8 46.91 ? H34 VLK 201 A 1 HETATM 43 H H14 VLK . . . B 2 -3.752 15.926 4.513 0.8 34.7 ? H14 VLK 201 A 1 HETATM 44 H H13 VLK . . . B 2 -4.993 15.042 4.965 0.8 34.7 ? H13 VLK 201 A 1 HETATM 45 H H17 VLK . . . B 2 -7.456 17.397 6.219 0.8 41.05 ? H17 VLK 201 A 1 HETATM 46 H H15 VLK . . . B 2 -3.513 13.903 7.767 0.8 37.62 ? H15 VLK 201 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 46 #