data_3KFP # _model_server_result.job_id ORa8VLoGc84TtKCILjcYRw _model_server_result.datetime_utc '2024-11-05 00:29:14' _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 3kfp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":200}' # _entry.id 3KFP # _exptl.entry_id 3KFP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 909.077 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate' _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 3KFP _cell.length_a 62.39 _cell.length_b 62.39 _cell.length_c 82.06 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KFP _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 7_555 y,x,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 27.353333 # _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 covale ? covale1 A SG CYS 67 A CYS 67 1_555 F S2 BME . A BME 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? covale ? covale2 B C2 3TL . A 3TL 200 1_555 B C2 3TL . A 3TL 200 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? # _chem_comp.formula 'C50 H64 N6 O10' _chem_comp.formula_weight 909.077 _chem_comp.id 3TL _chem_comp.mon_nstd_flag . _chem_comp.name 'benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate' _chem_comp.type peptide-like _chem_comp.pdbx_synonyms 'TL-3, C2 symmetric inhibitor' # 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 C31 O8 3TL doub 1 n n C31 O9 3TL sing 2 n n C31 N4 3TL sing 3 n n O9 CA 3TL sing 4 n n CA C 3TL sing 5 n n CA HA1 3TL sing 6 n n CA HA2 3TL sing 7 n n C C13 3TL doub 8 n y C C17 3TL sing 9 n y C13 C14 3TL sing 10 n y C13 H13 3TL sing 11 n n C14 C15 3TL doub 12 n y C14 H14 3TL sing 13 n n C15 C16 3TL sing 14 n y C15 H15 3TL sing 15 n n C16 C17 3TL doub 16 n y C16 H16 3TL sing 17 n n C17 H17 3TL sing 18 n n N4 C18 3TL sing 19 n n N4 HN4 3TL sing 20 n n C18 C19 3TL sing 21 n n C18 C20 3TL sing 22 n n C18 H18 3TL sing 23 n n C19 O4 3TL doub 24 n n C19 N2 3TL sing 25 n n C20 H201 3TL sing 26 n n C20 H202 3TL sing 27 n n C20 H203 3TL sing 28 n n N2 C10 3TL sing 29 n n N2 HN2 3TL sing 30 n n C10 C11 3TL sing 31 n n C10 C12 3TL sing 32 n n C10 H10 3TL sing 33 n n C11 O2 3TL doub 34 n n C11 N1 3TL sing 35 n n C12 CG2 3TL sing 36 n n C12 CG1 3TL sing 37 n n C12 H12 3TL sing 38 n n CG2 HG21 3TL sing 39 n n CG2 HG22 3TL sing 40 n n CG2 HG23 3TL sing 41 n n CG1 HG11 3TL sing 42 n n CG1 HG12 3TL sing 43 n n CG1 HG13 3TL sing 44 n n C2 O1 3TL sing 45 n n C2 C1 3TL sing 46 n n C2 H2 3TL sing 47 n n C2 C52 3TL sing 48 n n O1 HO1 3TL sing 49 n n C1 N1 3TL sing 50 n n C1 C3 3TL sing 51 n n C1 H1 3TL sing 52 n n N1 HN1 3TL sing 53 n n C3 C4 3TL sing 54 n n C3 H31 3TL sing 55 n n C3 H32 3TL sing 56 n n C4 C5 3TL doub 57 n y C4 C9 3TL sing 58 n y C5 C6 3TL sing 59 n y C5 H5 3TL sing 60 n n C9 C8 3TL doub 61 n y C9 H9 3TL sing 62 n n C6 C7 3TL doub 63 n y C6 H6 3TL sing 64 n n C8 C7 3TL sing 65 n y C8 H8 3TL sing 66 n n C7 H7 3TL sing 67 n n N51 C51 3TL sing 68 n n N51 HN51 3TL sing 69 n n N51 C61 3TL sing 70 n n C51 C52 3TL sing 71 n n C51 C53 3TL sing 72 n n C51 H51 3TL sing 73 n n C52 O51 3TL sing 74 n n C52 H52 3TL sing 75 n n O51 HO51 3TL sing 76 n n C53 C54 3TL sing 77 n n C53 H531 3TL sing 78 n n C53 H532 3TL sing 79 n n C54 C55 3TL doub 80 n y C54 C59 3TL sing 81 n y C55 C56 3TL sing 82 n y C55 H55 3TL sing 83 n n C59 C58 3TL doub 84 n y C59 H59 3TL sing 85 n n C56 C57 3TL doub 86 n y C56 H56 3TL sing 87 n n C58 C57 3TL sing 88 n y C58 H58 3TL sing 89 n n C57 H57 3TL sing 90 n n N52 C60 3TL sing 91 n n N52 HN52 3TL sing 92 n n N52 C69 3TL sing 93 n n C60 C61 3TL sing 94 n n C60 C62 3TL sing 95 n n C60 H60 3TL sing 96 n n C61 O52 3TL doub 97 n n C62 CG6 3TL sing 98 n n C62 CG5 3TL sing 99 n n C62 H62 3TL sing 100 n n CG6 HG61 3TL sing 101 n n CG6 HG62 3TL sing 102 n n CG6 HG63 3TL sing 103 n n CG5 HG51 3TL sing 104 n n CG5 HG52 3TL sing 105 n n CG5 HG53 3TL sing 106 n n N54 C68 3TL sing 107 n n N54 HN54 3TL sing 108 n n N54 C81 3TL sing 109 n n C68 C69 3TL sing 110 n n C68 C70 3TL sing 111 n n C68 H68 3TL sing 112 n n C69 O54 3TL doub 113 n n C70 H701 3TL sing 114 n n C70 H702 3TL sing 115 n n C70 H703 3TL sing 116 n n C81 O58 3TL doub 117 n n C81 O59 3TL sing 118 n n O59 CA5 3TL sing 119 n n CA5 C50 3TL sing 120 n n CA5 HA51 3TL sing 121 n n CA5 HA52 3TL sing 122 n n C50 C63 3TL doub 123 n y C50 C67 3TL sing 124 n y C63 C64 3TL sing 125 n y C63 H63 3TL sing 126 n n C64 C65 3TL doub 127 n y C64 H64 3TL sing 128 n n C65 C66 3TL sing 129 n y C65 H65 3TL sing 130 n n C66 C67 3TL doub 131 n y C66 H66 3TL sing 132 n n C67 H67 3TL sing 133 n n # _atom_sites.entry_id 3KFP _atom_sites.fract_transf_matrix[1][1] 0.016028 _atom_sites.fract_transf_matrix[1][2] 0.009254 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018508 _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] 0.012186 _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 3TL A 1 200 200 3TL 3TL . C 3 DMS A 1 300 300 DMS DMS . D 3 DMS A 1 301 301 DMS DMS . E 3 DMS A 1 302 302 DMS DMS . F 4 BME A 1 303 303 BME BME . G 5 HOH A 1 305 305 HOH HOH . G 5 HOH A 2 306 306 HOH HOH . G 5 HOH A 3 307 307 HOH HOH . G 5 HOH A 4 309 309 HOH HOH . G 5 HOH A 5 310 310 HOH HOH . G 5 HOH A 6 312 312 HOH HOH . G 5 HOH A 7 313 313 HOH HOH . G 5 HOH A 8 314 314 HOH HOH . G 5 HOH A 9 315 315 HOH HOH . G 5 HOH A 10 316 316 HOH HOH . G 5 HOH A 11 317 317 HOH HOH . G 5 HOH A 12 318 318 HOH HOH . G 5 HOH A 13 319 319 HOH HOH . G 5 HOH A 14 320 320 HOH HOH . G 5 HOH A 15 321 321 HOH HOH . G 5 HOH A 16 322 322 HOH HOH . G 5 HOH A 17 324 324 HOH HOH . G 5 HOH A 18 325 325 HOH HOH . G 5 HOH A 19 326 326 HOH HOH . G 5 HOH A 20 327 327 HOH HOH . G 5 HOH A 21 328 328 HOH HOH . G 5 HOH A 22 329 329 HOH HOH . G 5 HOH A 23 330 330 HOH HOH . G 5 HOH A 24 332 332 HOH HOH . G 5 HOH A 25 333 333 HOH HOH . G 5 HOH A 26 334 334 HOH HOH . G 5 HOH A 27 335 335 HOH HOH . G 5 HOH A 28 336 336 HOH HOH . G 5 HOH A 29 337 337 HOH HOH . G 5 HOH A 30 338 338 HOH HOH . G 5 HOH A 31 339 339 HOH HOH . G 5 HOH A 32 340 340 HOH HOH . G 5 HOH A 33 342 342 HOH HOH . G 5 HOH A 34 343 343 HOH HOH . G 5 HOH A 35 344 344 HOH HOH . G 5 HOH A 36 345 345 HOH HOH . G 5 HOH A 37 346 346 HOH HOH . G 5 HOH A 38 347 347 HOH HOH . G 5 HOH A 39 348 348 HOH HOH . G 5 HOH A 40 349 349 HOH HOH . G 5 HOH A 41 351 351 HOH HOH . G 5 HOH A 42 352 352 HOH HOH . G 5 HOH A 43 353 353 HOH HOH . G 5 HOH A 44 354 354 HOH HOH . G 5 HOH A 45 355 355 HOH HOH . G 5 HOH A 46 356 356 HOH HOH . G 5 HOH A 47 357 357 HOH HOH . G 5 HOH A 48 358 358 HOH HOH . G 5 HOH A 49 359 359 HOH HOH . G 5 HOH A 50 360 360 HOH HOH . G 5 HOH A 51 361 361 HOH HOH . G 5 HOH A 52 362 362 HOH HOH . G 5 HOH A 53 363 363 HOH HOH . G 5 HOH A 54 364 364 HOH HOH . G 5 HOH A 55 365 365 HOH HOH . G 5 HOH A 56 366 366 HOH HOH . G 5 HOH A 57 367 367 HOH HOH . G 5 HOH A 58 368 368 HOH HOH . G 5 HOH A 59 369 369 HOH HOH . G 5 HOH A 60 370 370 HOH HOH . G 5 HOH A 61 371 371 HOH HOH . G 5 HOH A 62 372 372 HOH HOH . G 5 HOH A 63 373 373 HOH HOH . G 5 HOH A 64 374 374 HOH HOH . G 5 HOH A 65 375 375 HOH HOH . G 5 HOH A 66 376 376 HOH HOH . G 5 HOH A 67 377 377 HOH HOH . G 5 HOH A 68 378 378 HOH HOH . G 5 HOH A 69 379 379 HOH HOH . G 5 HOH A 70 380 380 HOH HOH . G 5 HOH A 71 381 381 HOH HOH . G 5 HOH A 72 382 382 HOH HOH . G 5 HOH A 73 383 383 HOH HOH . G 5 HOH A 74 384 384 HOH HOH . G 5 HOH A 75 385 385 HOH HOH . G 5 HOH A 76 386 386 HOH HOH . G 5 HOH A 77 387 387 HOH HOH . G 5 HOH A 78 388 388 HOH HOH . G 5 HOH A 79 389 389 HOH HOH . G 5 HOH A 80 390 390 HOH HOH . G 5 HOH A 81 391 391 HOH HOH . G 5 HOH A 82 392 392 HOH HOH . G 5 HOH A 83 393 393 HOH HOH . G 5 HOH A 84 394 394 HOH HOH . G 5 HOH A 85 395 395 HOH HOH . G 5 HOH A 86 396 396 HOH HOH . G 5 HOH A 87 397 397 HOH HOH . G 5 HOH A 88 398 398 HOH HOH . G 5 HOH A 89 399 399 HOH HOH . G 5 HOH A 90 400 400 HOH HOH . G 5 HOH A 91 401 401 HOH HOH . G 5 HOH A 92 402 402 HOH HOH . G 5 HOH A 93 403 403 HOH HOH . G 5 HOH A 94 404 404 HOH HOH . G 5 HOH A 95 405 405 HOH HOH . G 5 HOH A 96 406 406 HOH HOH . G 5 HOH A 97 407 407 HOH HOH . G 5 HOH A 98 408 408 HOH HOH . G 5 HOH A 99 409 409 HOH HOH . G 5 HOH A 100 410 410 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 C31 3TL . . . B 2 -11.619 -11.526 5.68 1 28.54 ? C31 3TL 200 A 1 HETATM 2 O O8 3TL . . . B 2 -10.624 -10.657 5.907 1 28.46 ? O8 3TL 200 A 1 HETATM 3 O O9 3TL . . . B 2 -11.961 -11.431 4.391 1 33.67 ? O9 3TL 200 A 1 HETATM 4 C CA 3TL . . . B 2 -11.609 -10.287 3.563 1 33.87 ? CA 3TL 200 A 1 HETATM 5 C C 3TL . . . B 2 -12.212 -8.936 3.795 1 35.19 ? C 3TL 200 A 1 HETATM 6 C C13 3TL . . . B 2 -11.556 -7.891 3.158 1 30.49 ? C13 3TL 200 A 1 HETATM 7 C C14 3TL . . . B 2 -12.095 -6.627 3.356 1 33.4 ? C14 3TL 200 A 1 HETATM 8 C C15 3TL . . . B 2 -13.233 -6.571 4.123 1 25.68 ? C15 3TL 200 A 1 HETATM 9 C C16 3TL . . . B 2 -13.826 -7.62 4.791 1 32.87 ? C16 3TL 200 A 1 HETATM 10 C C17 3TL . . . B 2 -13.332 -8.899 4.598 1 32.74 ? C17 3TL 200 A 1 HETATM 11 N N4 3TL . . . B 2 -12.345 -12.361 6.413 1 30.9 ? N4 3TL 200 A 1 HETATM 12 C C18 3TL . . . B 2 -12.076 -12.383 7.834 1 29.5 ? C18 3TL 200 A 1 HETATM 13 C C19 3TL . . . B 2 -11.426 -13.659 8.234 1 25.78 ? C19 3TL 200 A 1 HETATM 14 O O4 3TL . . . B 2 -11.971 -14.731 7.84 1 26.44 ? O4 3TL 200 A 1 HETATM 15 C C20 3TL . . . B 2 -13.457 -12.114 8.411 1 33.28 ? C20 3TL 200 A 1 HETATM 16 N N2 3TL . . . B 2 -10.399 -13.577 8.956 1 26.19 ? N2 3TL 200 A 1 HETATM 17 C C10 3TL . . . B 2 -9.619 -14.668 9.532 1 27.81 ? C10 3TL 200 A 1 HETATM 18 C C11 3TL . . . B 2 -9.616 -14.536 10.979 1 27.68 ? C11 3TL 200 A 1 HETATM 19 O O2 3TL . . . B 2 -8.719 -13.731 11.431 1 27.73 ? O2 3TL 200 A 1 HETATM 20 C C12 3TL . . . B 2 -8.333 -15.045 8.795 1 30.9 ? C12 3TL 200 A 1 HETATM 21 C CG2 3TL . . . B 2 -8.412 -15.293 7.286 1 32 ? CG2 3TL 200 A 1 HETATM 22 C CG1 3TL . . . B 2 -7.833 -16.34 9.402 1 31.63 ? CG1 3TL 200 A 1 HETATM 23 C C2 3TL . . . B 2 -10.529 -16.034 14.162 1 36.32 ? C2 3TL 200 A 1 HETATM 24 O O1 3TL . . . B 2 -11.286 -17.101 13.565 1 45.17 ? O1 3TL 200 A 1 HETATM 25 C C1 3TL . . . B 2 -10.727 -14.887 13.201 1 34.04 ? C1 3TL 200 A 1 HETATM 26 N N1 3TL . . . B 2 -10.445 -15.197 11.781 1 27.39 ? N1 3TL 200 A 1 HETATM 27 C C3 3TL . . . B 2 -12.061 -14.269 13.635 1 37.42 ? C3 3TL 200 A 1 HETATM 28 C C4 3TL . . . B 2 -12.21 -12.824 13.266 1 38.84 ? C4 3TL 200 A 1 HETATM 29 C C5 3TL . . . B 2 -12.976 -12.282 12.244 1 39.25 ? C5 3TL 200 A 1 HETATM 30 C C9 3TL . . . B 2 -11.498 -12.066 14.181 1 39.94 ? C9 3TL 200 A 1 HETATM 31 C C6 3TL . . . B 2 -13.008 -10.91 12.06 1 40.95 ? C6 3TL 200 A 1 HETATM 32 C C8 3TL . . . B 2 -11.518 -10.693 14.022 1 42.51 ? C8 3TL 200 A 1 HETATM 33 C C7 3TL . . . B 2 -12.242 -10.178 12.962 1 42.24 ? C7 3TL 200 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 33 #