data_9NBK # _model_server_result.job_id urXm8TgxM_CDYjCd2CsW3w _model_server_result.datetime_utc '2025-06-28 00:55:35' _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 9nbk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 9NBK # _exptl.entry_id 9NBK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 344.446 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate' _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 9NBK _cell.length_a 42.5 _cell.length_b 48.9 _cell.length_c 101.5 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9NBK _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 disulf ? disulf1 A SG CYS 22 A CYS 22 1_555 A SG CYS 63 A CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf2 A SG CYS 56 A CYS 56 1_555 A SG CYS 95 A CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 A SG CYS 153 A CYS 153 1_555 A SG CYS 200 A CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 A SG CYS 25 A CYS 25 1_555 B C2 E6D . A E6D 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.803 ? # _chem_comp.formula 'C17 H32 N2 O5' _chem_comp.formula_weight 344.446 _chem_comp.id E6D _chem_comp.mon_nstd_flag . _chem_comp.name 'ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate' _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 C23 O17 E6D sing 83 n n O18 C16 E6D doub 84 n n O17 C16 E6D sing 85 n n C16 C2 E6D sing 86 n n C2 C3 E6D sing 87 n n O1 C3 E6D sing 88 n n C3 C4 E6D sing 89 n n C4 O5 E6D doub 90 n n C4 N6 E6D sing 91 n n N6 C7 E6D sing 92 n n C7 C8 E6D sing 93 n n C7 C19 E6D sing 94 n n O9 C8 E6D doub 95 n n C8 N10 E6D sing 96 n n C19 C20 E6D sing 97 n n C22 C20 E6D sing 98 n n C20 C21 E6D sing 99 n n N10 C11 E6D sing 100 n n C12 C11 E6D sing 101 n n C12 C13 E6D sing 102 n n C13 C15 E6D sing 103 n n C13 C14 E6D sing 104 n n C14 H1 E6D sing 105 n n C14 H2 E6D sing 106 n n C14 H3 E6D sing 107 n n C13 H4 E6D sing 108 n n C15 H5 E6D sing 109 n n C15 H6 E6D sing 110 n n C15 H7 E6D sing 111 n n C12 H8 E6D sing 112 n n C12 H9 E6D sing 113 n n C11 H10 E6D sing 114 n n C11 H11 E6D sing 115 n n N10 H12 E6D sing 116 n n C7 H13 E6D sing 117 n n C19 H14 E6D sing 118 n n C19 H15 E6D sing 119 n n C20 H16 E6D sing 120 n n C22 H17 E6D sing 121 n n C22 H18 E6D sing 122 n n C22 H19 E6D sing 123 n n C21 H20 E6D sing 124 n n C21 H21 E6D sing 125 n n C21 H22 E6D sing 126 n n N6 H23 E6D sing 127 n n C3 H24 E6D sing 128 n n O1 H25 E6D sing 129 n n C2 H26 E6D sing 130 n n C2 H27 E6D sing 131 n n C23 H28 E6D sing 132 n n C23 H29 E6D sing 133 n n C23 C24 E6D sing 134 n n C24 H30 E6D sing 135 n n C24 H31 E6D sing 136 n n C24 H32 E6D sing 137 n n # _atom_sites.entry_id 9NBK _atom_sites.fract_transf_matrix[1][1] 0.023529 _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] 0.02045 _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] 0.009852 _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 E6D A 1 301 301 E6D E6D . C 3 HOH A 1 401 96 HOH HOH . C 3 HOH A 2 402 103 HOH HOH . C 3 HOH A 3 403 25 HOH HOH . C 3 HOH A 4 404 97 HOH HOH . C 3 HOH A 5 405 58 HOH HOH . C 3 HOH A 6 406 39 HOH HOH . C 3 HOH A 7 407 98 HOH HOH . C 3 HOH A 8 408 23 HOH HOH . C 3 HOH A 9 409 87 HOH HOH . C 3 HOH A 10 410 89 HOH HOH . C 3 HOH A 11 411 91 HOH HOH . C 3 HOH A 12 412 68 HOH HOH . C 3 HOH A 13 413 63 HOH HOH . C 3 HOH A 14 414 86 HOH HOH . C 3 HOH A 15 415 83 HOH HOH . C 3 HOH A 16 416 110 HOH HOH . C 3 HOH A 17 417 11 HOH HOH . C 3 HOH A 18 418 19 HOH HOH . C 3 HOH A 19 419 100 HOH HOH . C 3 HOH A 20 420 9 HOH HOH . C 3 HOH A 21 421 47 HOH HOH . C 3 HOH A 22 422 82 HOH HOH . C 3 HOH A 23 423 37 HOH HOH . C 3 HOH A 24 424 18 HOH HOH . C 3 HOH A 25 425 2 HOH HOH . C 3 HOH A 26 426 4 HOH HOH . C 3 HOH A 27 427 67 HOH HOH . C 3 HOH A 28 428 74 HOH HOH . C 3 HOH A 29 429 104 HOH HOH . C 3 HOH A 30 430 8 HOH HOH . C 3 HOH A 31 431 48 HOH HOH . C 3 HOH A 32 432 62 HOH HOH . C 3 HOH A 33 433 79 HOH HOH . C 3 HOH A 34 434 29 HOH HOH . C 3 HOH A 35 435 10 HOH HOH . C 3 HOH A 36 436 88 HOH HOH . C 3 HOH A 37 437 60 HOH HOH . C 3 HOH A 38 438 71 HOH HOH . C 3 HOH A 39 439 33 HOH HOH . C 3 HOH A 40 440 56 HOH HOH . C 3 HOH A 41 441 102 HOH HOH . C 3 HOH A 42 442 73 HOH HOH . C 3 HOH A 43 443 16 HOH HOH . C 3 HOH A 44 444 52 HOH HOH . C 3 HOH A 45 445 1 HOH HOH . C 3 HOH A 46 446 53 HOH HOH . C 3 HOH A 47 447 94 HOH HOH . C 3 HOH A 48 448 76 HOH HOH . C 3 HOH A 49 449 21 HOH HOH . C 3 HOH A 50 450 43 HOH HOH . C 3 HOH A 51 451 30 HOH HOH . C 3 HOH A 52 452 78 HOH HOH . C 3 HOH A 53 453 108 HOH HOH . C 3 HOH A 54 454 42 HOH HOH . C 3 HOH A 55 455 65 HOH HOH . C 3 HOH A 56 456 107 HOH HOH . C 3 HOH A 57 457 66 HOH HOH . C 3 HOH A 58 458 40 HOH HOH . C 3 HOH A 59 459 38 HOH HOH . C 3 HOH A 60 460 14 HOH HOH . C 3 HOH A 61 461 64 HOH HOH . C 3 HOH A 62 462 106 HOH HOH . C 3 HOH A 63 463 32 HOH HOH . C 3 HOH A 64 464 34 HOH HOH . C 3 HOH A 65 465 15 HOH HOH . C 3 HOH A 66 466 77 HOH HOH . C 3 HOH A 67 467 5 HOH HOH . C 3 HOH A 68 468 27 HOH HOH . C 3 HOH A 69 469 35 HOH HOH . C 3 HOH A 70 470 51 HOH HOH . C 3 HOH A 71 471 45 HOH HOH . C 3 HOH A 72 472 20 HOH HOH . C 3 HOH A 73 473 49 HOH HOH . C 3 HOH A 74 474 22 HOH HOH . C 3 HOH A 75 475 44 HOH HOH . C 3 HOH A 76 476 26 HOH HOH . C 3 HOH A 77 477 85 HOH HOH . C 3 HOH A 78 478 93 HOH HOH . C 3 HOH A 79 479 54 HOH HOH . C 3 HOH A 80 480 7 HOH HOH . C 3 HOH A 81 481 28 HOH HOH . C 3 HOH A 82 482 59 HOH HOH . C 3 HOH A 83 483 50 HOH HOH . C 3 HOH A 84 484 109 HOH HOH . C 3 HOH A 85 485 6 HOH HOH . C 3 HOH A 86 486 61 HOH HOH . C 3 HOH A 87 487 31 HOH HOH . C 3 HOH A 88 488 36 HOH HOH . C 3 HOH A 89 489 13 HOH HOH . C 3 HOH A 90 490 80 HOH HOH . C 3 HOH A 91 491 92 HOH HOH . C 3 HOH A 92 492 81 HOH HOH . C 3 HOH A 93 493 90 HOH HOH . C 3 HOH A 94 494 41 HOH HOH . C 3 HOH A 95 495 69 HOH HOH . C 3 HOH A 96 496 84 HOH HOH . C 3 HOH A 97 497 72 HOH HOH . C 3 HOH A 98 498 75 HOH HOH . C 3 HOH A 99 499 55 HOH HOH . C 3 HOH A 100 500 95 HOH HOH . C 3 HOH A 101 501 70 HOH HOH . C 3 HOH A 102 502 12 HOH HOH . C 3 HOH A 103 503 105 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 C14 E6D . . . B 2 -3.988 13.066 25.059 0.65 58.55 ? C14 E6D 301 A 1 HETATM 2 C C13 E6D . . . B 2 -2.516 13.178 25.453 0.65 60.12 ? C13 E6D 301 A 1 HETATM 3 C C15 E6D . . . B 2 -2.284 12.615 26.854 0.65 58.55 ? C15 E6D 301 A 1 HETATM 4 C C12 E6D . . . B 2 -1.583 12.503 24.444 0.65 60.63 ? C12 E6D 301 A 1 HETATM 5 C C11 E6D . . . B 2 -1.679 13.067 23.029 0.65 66.15 ? C11 E6D 301 A 1 HETATM 6 N N10 E6D . . . B 2 -0.612 12.537 22.199 0.65 43.12 ? N10 E6D 301 A 1 HETATM 7 C C8 E6D . . . B 2 -0.739 11.448 21.441 0.65 45.24 ? C8 E6D 301 A 1 HETATM 8 O O9 E6D . . . B 2 -1.765 10.776 21.371 0.65 41.59 ? O9 E6D 301 A 1 HETATM 9 C C7 E6D . . . B 2 0.547 11.109 20.677 0.65 43.49 ? C7 E6D 301 A 1 HETATM 10 C C19 E6D . . . B 2 1.601 10.759 21.728 0.65 44.84 ? C19 E6D 301 A 1 HETATM 11 C C20 E6D . . . B 2 2.225 9.38 21.53 0.65 43.82 ? C20 E6D 301 A 1 HETATM 12 C C22 E6D . . . B 2 1.143 8.308 21.629 0.65 45.11 ? C22 E6D 301 A 1 HETATM 13 C C21 E6D . . . B 2 2.848 9.313 20.148 0.65 44.55 ? C21 E6D 301 A 1 HETATM 14 N N6 E6D . . . B 2 0.982 12.209 19.834 0.65 43.81 ? N6 E6D 301 A 1 HETATM 15 C C4 E6D . . . B 2 0.728 12.203 18.509 0.65 36.23 ? C4 E6D 301 A 1 HETATM 16 O O5 E6D . . . B 2 0.127 11.295 17.967 0.65 33.01 ? O5 E6D 301 A 1 HETATM 17 C C3 E6D . . . B 2 1.19 13.39 17.65 0.65 34.24 ? C3 E6D 301 A 1 HETATM 18 O O1 E6D . . . B 2 1.069 14.625 18.285 0.65 36.98 ? O1 E6D 301 A 1 HETATM 19 C C2 E6D . . . B 2 2.641 13.185 17.217 0.65 37.45 ? C2 E6D 301 A 1 HETATM 20 C C16 E6D . . . B 2 2.93 14.186 16.134 0.65 34.78 ? C16 E6D 301 A 1 HETATM 21 O O18 E6D . . . B 2 2.615 14.003 14.995 0.65 31.02 ? O18 E6D 301 A 1 HETATM 22 O O17 E6D . . . B 2 3.521 15.288 16.572 0.65 41.83 ? O17 E6D 301 A 1 HETATM 23 C C23 E6D . . . B 2 4.379 15.201 17.725 0.74 33.99 ? C23 E6D 301 A 1 HETATM 24 C C24 E6D . . . B 2 4.465 16.544 18.409 0.74 44.24 ? C24 E6D 301 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 24 #