data_3K5D # _model_server_result.job_id vIULLPAocf13k4VUwERTfw _model_server_result.datetime_utc '2025-01-07 14:10:12' _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 3k5d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":393}' # _entry.id 3K5D # _exptl.entry_id 3K5D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 544.791 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-acetyl-L-leucyl-N-[(4S,5S,7R)-8-(butylamino)-5-hydroxy-2,7-dimethyl-8-oxooctan-4-yl]-L-methioninamide _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 104.16 _cell.angle_gamma 90 _cell.entry_id 3K5D _cell.length_a 82.547 _cell.length_b 101.299 _cell.length_c 102.218 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3K5D _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G 1 1 B,E,H 2 1 C,F,I 3 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N 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 disulf ? disulf1 A SG CYS 171 A CYS 155 1_555 A SG CYS 375 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 233 A CYS 217 1_555 A SG CYS 398 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 285 A CYS 269 1_555 A SG CYS 335 A CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 B SG CYS 171 B CYS 155 1_555 B SG CYS 375 B CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 B SG CYS 233 B CYS 217 1_555 B SG CYS 398 B CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf6 B SG CYS 285 B CYS 269 1_555 B SG CYS 335 B CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf7 C SG CYS 171 C CYS 155 1_555 C SG CYS 375 C CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf8 C SG CYS 233 C CYS 217 1_555 C SG CYS 398 C CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf9 C SG CYS 285 C CYS 269 1_555 C SG CYS 335 C CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? # _chem_comp.formula 'C27 H52 N4 O5 S' _chem_comp.formula_weight 544.791 _chem_comp.id XLI _chem_comp.mon_nstd_flag . _chem_comp.name N-acetyl-L-leucyl-N-[(4S,5S,7R)-8-(butylamino)-5-hydroxy-2,7-dimethyl-8-oxooctan-4-yl]-L-methioninamide _chem_comp.type peptide-like _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 C O XLI doub 376 n n C CH3 XLI sing 377 n n C N XLI sing 378 n n CH3 H1 XLI sing 379 n n CH3 H2 XLI sing 380 n n CH3 H3 XLI sing 381 n n N CA XLI sing 382 n n N H XLI sing 383 n n CA C1 XLI sing 384 n n CA CB XLI sing 385 n n CA HA XLI sing 386 n n C1 O1 XLI doub 387 n n C1 N1 XLI sing 388 n n CB CG XLI sing 389 n n CB HB2 XLI sing 390 n n CB HB3 XLI sing 391 n n CG CD1 XLI sing 392 n n CG CD2 XLI sing 393 n n CG HG XLI sing 394 n n CD1 HD11 XLI sing 395 n n CD1 HD12 XLI sing 396 n n CD1 HD13 XLI sing 397 n n CD2 HD21 XLI sing 398 n n CD2 HD22 XLI sing 399 n n CD2 HD23 XLI sing 400 n n N1 CA1 XLI sing 401 n n N1 H4 XLI sing 402 n n CA1 C2 XLI sing 403 n n CA1 CB1 XLI sing 404 n n CA1 HA1 XLI sing 405 n n C2 O2 XLI doub 406 n n C2 N2 XLI sing 407 n n CB1 CG1 XLI sing 408 n n CB1 HB21 XLI sing 409 n n CB1 HB31 XLI sing 410 n n CG1 SD XLI sing 411 n n CG1 HG2 XLI sing 412 n n CG1 HG3 XLI sing 413 n n SD CE XLI sing 414 n n CE HE1 XLI sing 415 n n CE HE2 XLI sing 416 n n CE HE3 XLI sing 417 n n N2 CA2 XLI sing 418 n n N2 H5 XLI sing 419 n n CA2 C3 XLI sing 420 n n CA2 CB2 XLI sing 421 n n CA2 HA2 XLI sing 422 n n C3 O3 XLI sing 423 n n C3 CM XLI sing 424 n n CB2 CG2 XLI sing 425 n n CB2 HB22 XLI sing 426 n n CB2 HB32 XLI sing 427 n n CG2 CD11 XLI sing 428 n n CG2 CD21 XLI sing 429 n n CG2 HG1 XLI sing 430 n n CD11 HD14 XLI sing 431 n n CD11 HD15 XLI sing 432 n n CD11 HD16 XLI sing 433 n n CD21 HD24 XLI sing 434 n n CD21 HD25 XLI sing 435 n n CD21 HD26 XLI sing 436 n n CM CA3 XLI sing 437 n n CM HM2 XLI sing 438 n n CM HM3 XLI sing 439 n n CA3 CB3 XLI sing 440 n n CA3 C4 XLI sing 441 n n CA3 HA3 XLI sing 442 n n CB3 HB1 XLI sing 443 n n CB3 HB23 XLI sing 444 n n CB3 HB33 XLI sing 445 n n C4 O4 XLI doub 446 n n C4 N3 XLI sing 447 n n C11 N3 XLI sing 448 n n C11 C21 XLI sing 449 n n C11 H11 XLI sing 450 n n C11 H12 XLI sing 451 n n N3 HN2 XLI sing 452 n n C21 C31 XLI sing 453 n n C21 H21 XLI sing 454 n n C21 H22 XLI sing 455 n n C31 C41 XLI sing 456 n n C31 H31 XLI sing 457 n n C31 H32 XLI sing 458 n n C41 H41 XLI sing 459 n n C41 H42 XLI sing 460 n n C41 H43 XLI sing 461 n n C3 H51 XLI sing 462 n n O3 H52 XLI sing 463 n n # _atom_sites.entry_id 3K5D _atom_sites.fract_transf_matrix[1][1] 0.012114 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003056 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009872 _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] 0.010089 _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 D 2 XLI A 1 393 1 XLI LI1 . E 2 XLI B 1 393 1 XLI LI1 . F 2 XLI C 1 393 1 XLI LI1 . G 3 HOH A 1 394 1 HOH HOH . G 3 HOH A 2 395 2 HOH HOH . G 3 HOH A 3 396 3 HOH HOH . G 3 HOH A 4 397 4 HOH HOH . G 3 HOH A 5 398 14 HOH HOH . G 3 HOH A 6 399 15 HOH HOH . G 3 HOH A 7 400 16 HOH HOH . G 3 HOH A 8 401 17 HOH HOH . G 3 HOH A 9 402 18 HOH HOH . G 3 HOH A 10 403 19 HOH HOH . G 3 HOH A 11 404 20 HOH HOH . G 3 HOH A 12 405 21 HOH HOH . G 3 HOH A 13 406 22 HOH HOH . G 3 HOH A 14 407 23 HOH HOH . G 3 HOH A 15 408 24 HOH HOH . G 3 HOH A 16 409 25 HOH HOH . G 3 HOH A 17 410 26 HOH HOH . G 3 HOH A 18 411 27 HOH HOH . G 3 HOH A 19 412 28 HOH HOH . G 3 HOH A 20 413 29 HOH HOH . G 3 HOH A 21 414 30 HOH HOH . G 3 HOH A 22 415 31 HOH HOH . G 3 HOH A 23 416 32 HOH HOH . G 3 HOH A 24 417 33 HOH HOH . G 3 HOH A 25 418 34 HOH HOH . H 3 HOH B 1 394 5 HOH HOH . H 3 HOH B 2 395 6 HOH HOH . H 3 HOH B 3 396 7 HOH HOH . H 3 HOH B 4 397 8 HOH HOH . H 3 HOH B 5 398 9 HOH HOH . H 3 HOH B 6 399 10 HOH HOH . H 3 HOH B 7 400 35 HOH HOH . H 3 HOH B 8 401 36 HOH HOH . H 3 HOH B 9 402 37 HOH HOH . H 3 HOH B 10 403 38 HOH HOH . H 3 HOH B 11 404 39 HOH HOH . H 3 HOH B 12 405 40 HOH HOH . H 3 HOH B 13 406 41 HOH HOH . H 3 HOH B 14 407 42 HOH HOH . H 3 HOH B 15 408 43 HOH HOH . H 3 HOH B 16 409 44 HOH HOH . H 3 HOH B 17 410 45 HOH HOH . H 3 HOH B 18 411 46 HOH HOH . H 3 HOH B 19 412 47 HOH HOH . H 3 HOH B 20 413 48 HOH HOH . H 3 HOH B 21 414 49 HOH HOH . H 3 HOH B 22 415 50 HOH HOH . H 3 HOH B 23 416 51 HOH HOH . H 3 HOH B 24 417 52 HOH HOH . H 3 HOH B 25 418 53 HOH HOH . H 3 HOH B 26 419 54 HOH HOH . I 3 HOH C 1 394 11 HOH HOH . I 3 HOH C 2 395 12 HOH HOH . I 3 HOH C 3 396 13 HOH HOH . I 3 HOH C 4 397 55 HOH HOH . I 3 HOH C 5 398 56 HOH HOH . I 3 HOH C 6 399 57 HOH HOH . I 3 HOH C 7 400 58 HOH HOH . I 3 HOH C 8 401 59 HOH HOH . I 3 HOH C 9 402 60 HOH HOH . I 3 HOH C 10 403 61 HOH HOH . I 3 HOH C 11 404 62 HOH HOH . I 3 HOH C 12 405 63 HOH HOH . I 3 HOH C 13 406 64 HOH HOH . I 3 HOH C 14 407 65 HOH HOH . I 3 HOH C 15 408 66 HOH HOH . I 3 HOH C 16 409 67 HOH HOH . I 3 HOH C 17 410 68 HOH HOH . I 3 HOH C 18 411 69 HOH HOH . I 3 HOH C 19 412 70 HOH HOH . I 3 HOH C 20 413 71 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 C XLI . . . E 2 23.789 -35.055 -0.634 1 44.04 ? C XLI 393 B 1 HETATM 2 O O XLI . . . E 2 23.237 -34.972 -1.755 1 43.84 ? O XLI 393 B 1 HETATM 3 C CH3 XLI . . . E 2 24.332 -33.82 -0.009 1 50.33 ? CH3 XLI 393 B 1 HETATM 4 N N XLI . . . E 2 23.931 -36.202 0.063 1 42.5 ? N XLI 393 B 1 HETATM 5 C CA XLI . . . E 2 23.452 -37.454 -0.503 1 48.83 ? CA XLI 393 B 1 HETATM 6 C C1 XLI . . . E 2 21.963 -37.639 -0.259 1 45.36 ? C1 XLI 393 B 1 HETATM 7 O O1 XLI . . . E 2 21.49 -37.216 0.787 1 44.79 ? O1 XLI 393 B 1 HETATM 8 C CB XLI . . . E 2 24.33 -38.716 -0.194 1 46.87 ? CB XLI 393 B 1 HETATM 9 C CG XLI . . . E 2 24.407 -39.209 1.281 1 43.01 ? CG XLI 393 B 1 HETATM 10 C CD1 XLI . . . E 2 25.023 -38.13 2.203 1 54.52 ? CD1 XLI 393 B 1 HETATM 11 C CD2 XLI . . . E 2 25.264 -40.481 1.379 1 48.79 ? CD2 XLI 393 B 1 HETATM 12 N N1 XLI . . . E 2 21.242 -38.263 -1.225 1 43.13 ? N1 XLI 393 B 1 HETATM 13 C CA1 XLI . . . E 2 19.815 -38.489 -1.113 1 43.08 ? CA1 XLI 393 B 1 HETATM 14 C C2 XLI . . . E 2 19.557 -39.977 -1.257 1 41.45 ? C2 XLI 393 B 1 HETATM 15 O O2 XLI . . . E 2 19.036 -40.419 -2.28 1 45.18 ? O2 XLI 393 B 1 HETATM 16 C CB1 XLI . . . E 2 18.984 -37.666 -2.146 1 41.94 ? CB1 XLI 393 B 1 HETATM 17 C CG1 XLI . . . E 2 19.028 -36.146 -1.823 1 51.79 ? CG1 XLI 393 B 1 HETATM 18 S SD XLI . . . E 2 18.381 -35.217 -3.245 1 55.91 ? SD XLI 393 B 1 HETATM 19 C CE XLI . . . E 2 19.923 -34.935 -4.169 1 49.3 ? CE XLI 393 B 1 HETATM 20 N N2 XLI . . . E 2 19.919 -40.781 -0.218 1 35.36 ? N2 XLI 393 B 1 HETATM 21 C CA2 XLI . . . E 2 19.733 -42.237 -0.227 1 30.78 ? CA2 XLI 393 B 1 HETATM 22 C C3 XLI . . . E 2 18.486 -42.65 0.62 1 31.19 ? C3 XLI 393 B 1 HETATM 23 O O3 XLI . . . E 2 18.764 -42.57 2.024 1 42.42 ? O3 XLI 393 B 1 HETATM 24 C CB2 XLI . . . E 2 21.048 -42.955 0.196 1 32.26 ? CB2 XLI 393 B 1 HETATM 25 C CG2 XLI . . . E 2 22.3 -42.655 -0.681 1 32.59 ? CG2 XLI 393 B 1 HETATM 26 C CD11 XLI . . . E 2 23.529 -43.376 -0.05 1 33.17 ? CD11 XLI 393 B 1 HETATM 27 C CD21 XLI . . . E 2 22.144 -43.13 -2.157 1 37.1 ? CD21 XLI 393 B 1 HETATM 28 C CM XLI . . . E 2 17.105 -42.001 0.283 1 36.45 ? CM XLI 393 B 1 HETATM 29 C CA3 XLI . . . E 2 15.852 -42.902 0.513 1 31.04 ? CA3 XLI 393 B 1 HETATM 30 C CB3 XLI . . . E 2 14.59 -42.013 0.709 1 30.33 ? CB3 XLI 393 B 1 HETATM 31 C C4 XLI . . . E 2 15.564 -43.846 -0.64 1 35.37 ? C4 XLI 393 B 1 HETATM 32 O O4 XLI . . . E 2 15.897 -43.528 -1.78 1 32.45 ? O4 XLI 393 B 1 HETATM 33 C C11 XLI . . . E 2 14.584 -46.016 -1.332 1 35.18 ? C11 XLI 393 B 1 HETATM 34 N N3 XLI . . . E 2 14.935 -45.014 -0.329 1 35.83 ? N3 XLI 393 B 1 HETATM 35 C C21 XLI . . . E 2 14.224 -47.373 -0.683 1 37.15 ? C21 XLI 393 B 1 HETATM 36 C C31 XLI . . . E 2 13.534 -48.328 -1.69 1 43.21 ? C31 XLI 393 B 1 HETATM 37 C C41 XLI . . . E 2 14.528 -48.896 -2.741 1 38.2 ? C41 XLI 393 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 37 #