data_1DY8 # _model_server_result.job_id HYNNrKpxESBNIl94J7B8Hw _model_server_result.datetime_utc '2025-08-04 08:57:12' _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 1dy8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 1DY8 # _exptl.entry_id 1DY8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 527.558 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[(benzyloxy)carbonyl]-L-isoleucyl-N-[(1R)-1-(carboxycarbonyl)-3,3-difluoropropyl]-L-leucinamide _entity.pdbx_number_of_molecules 2 _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 1DY8 _cell.length_a 93.82 _cell.length_b 93.82 _cell.length_c 80.95 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DY8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS dimeric 2 software_defined_assembly 1 PQS dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,G,I 1 1 B,D,F,H,J 2 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 ? 3 E N N ? 3 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 97 A CYS 97 1_555 A SG CYS 145 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? covale ? covale1 A OG SER 139 A SER 139 1_555 E CC 0F7 . A 0F7 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale2 B OG SER 139 B SER 139 1_555 F CC 0F7 . B 0F7 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? # _chem_comp.formula 'C25 H35 F2 N3 O7' _chem_comp.formula_weight 527.558 _chem_comp.id 0F7 _chem_comp.mon_nstd_flag . _chem_comp.name N-[(benzyloxy)carbonyl]-L-isoleucyl-N-[(1R)-1-(carboxycarbonyl)-3,3-difluoropropyl]-L-leucinamide _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 C1 O1 0F7 doub 1 n n C1 O2 0F7 sing 2 n n O2 C2 0F7 sing 3 n n C2 C3 0F7 sing 4 n n C2 H21 0F7 sing 5 n n C2 H22 0F7 sing 6 n n C3 C4 0F7 doub 7 n y C3 C8 0F7 sing 8 n y C4 C5 0F7 sing 9 n y C4 H41 0F7 sing 10 n n C5 C6 0F7 doub 11 n y C5 H51 0F7 sing 12 n n C6 C7 0F7 sing 13 n y C6 H61 0F7 sing 14 n n C7 C8 0F7 doub 15 n y C7 H71 0F7 sing 16 n n C8 H81 0F7 sing 17 n n N CA 0F7 sing 18 n n N H 0F7 sing 19 n n CA C 0F7 sing 20 n n CA CB 0F7 sing 21 n n CA HA 0F7 sing 22 n n C O 0F7 doub 23 n n CB CG1 0F7 sing 24 n n CB CG2 0F7 sing 25 n n CB HB 0F7 sing 26 n n CG1 CD1 0F7 sing 27 n n CG1 HG12 0F7 sing 28 n n CG1 HG13 0F7 sing 29 n n CG2 HG21 0F7 sing 30 n n CG2 HG22 0F7 sing 31 n n CG2 HG23 0F7 sing 32 n n CD1 HD11 0F7 sing 33 n n CD1 HD12 0F7 sing 34 n n CD1 HD13 0F7 sing 35 n n N1 CA1 0F7 sing 36 n n N1 H1 0F7 sing 37 n n CA1 C9 0F7 sing 38 n n CA1 CB1 0F7 sing 39 n n CA1 HA1 0F7 sing 40 n n C9 O3 0F7 doub 41 n n CB1 CG 0F7 sing 42 n n CB1 HB2 0F7 sing 43 n n CB1 HB3 0F7 sing 44 n n CG CD11 0F7 sing 45 n n CG CD2 0F7 sing 46 n n CG HG 0F7 sing 47 n n CD11 HD14 0F7 sing 48 n n CD11 HD15 0F7 sing 49 n n CD11 HD16 0F7 sing 50 n n CD2 HD21 0F7 sing 51 n n CD2 HD22 0F7 sing 52 n n CD2 HD23 0F7 sing 53 n n N2 CA2 0F7 sing 54 n n N2 H11 0F7 sing 55 n n CA2 CC 0F7 sing 56 n n CA2 CB2 0F7 sing 57 n n CA2 HA2 0F7 sing 58 n n CC O4 0F7 doub 59 n n CC CD 0F7 sing 60 n n CB2 CG3 0F7 sing 61 n n CB2 HB21 0F7 sing 62 n n CB2 HB1 0F7 sing 63 n n CG3 F1 0F7 sing 64 n n CG3 F2 0F7 sing 65 n n CG3 HG1 0F7 sing 66 n n CD OE1 0F7 sing 67 n n CD OE2 0F7 doub 68 n n OE1 HE1 0F7 sing 69 n n C1 N 0F7 sing 70 n n C N1 0F7 sing 71 n n C9 N2 0F7 sing 72 n n # _atom_sites.entry_id 1DY8 _atom_sites.fract_transf_matrix[1][1] 0.010659 _atom_sites.fract_transf_matrix[1][2] 0.006154 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012308 _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] 0.012353 _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 E 3 0F7 A 1 401 401 0F7 0F7 . F 3 0F7 B 1 401 401 0F7 0F7 . G 4 HOH A 1 2001 2001 HOH HOH . G 4 HOH A 2 2002 2002 HOH HOH . G 4 HOH A 3 2003 2003 HOH HOH . G 4 HOH A 4 2004 2004 HOH HOH . G 4 HOH A 5 2005 2005 HOH HOH . G 4 HOH A 6 2006 2006 HOH HOH . G 4 HOH A 7 2007 2007 HOH HOH . G 4 HOH A 8 2008 2008 HOH HOH . G 4 HOH A 9 2009 2009 HOH HOH . G 4 HOH A 10 2010 2010 HOH HOH . G 4 HOH A 11 2011 2011 HOH HOH . G 4 HOH A 12 2012 2012 HOH HOH . G 4 HOH A 13 2013 2013 HOH HOH . G 4 HOH A 14 2014 2014 HOH HOH . G 4 HOH A 15 2015 2015 HOH HOH . G 4 HOH A 16 2016 2016 HOH HOH . G 4 HOH A 17 2017 2017 HOH HOH . G 4 HOH A 18 2018 2018 HOH HOH . G 4 HOH A 19 2019 2019 HOH HOH . G 4 HOH A 20 2020 2020 HOH HOH . G 4 HOH A 21 2021 2021 HOH HOH . G 4 HOH A 22 2022 2022 HOH HOH . G 4 HOH A 23 2023 2023 HOH HOH . G 4 HOH A 24 2024 2024 HOH HOH . G 4 HOH A 25 2025 2025 HOH HOH . G 4 HOH A 26 2026 2026 HOH HOH . G 4 HOH A 27 2027 2027 HOH HOH . G 4 HOH A 28 2028 2028 HOH HOH . G 4 HOH A 29 2029 2029 HOH HOH . G 4 HOH A 30 2030 2030 HOH HOH . G 4 HOH A 31 2031 2031 HOH HOH . G 4 HOH A 32 2032 2032 HOH HOH . G 4 HOH A 33 2033 2033 HOH HOH . G 4 HOH A 34 2034 2034 HOH HOH . G 4 HOH A 35 2035 2035 HOH HOH . G 4 HOH A 36 2036 2036 HOH HOH . G 4 HOH A 37 2037 2037 HOH HOH . G 4 HOH A 38 2038 2038 HOH HOH . G 4 HOH A 39 2039 2039 HOH HOH . G 4 HOH A 40 2040 2040 HOH HOH . G 4 HOH A 41 2041 2041 HOH HOH . G 4 HOH A 42 2042 2042 HOH HOH . G 4 HOH A 43 2043 2043 HOH HOH . H 4 HOH B 1 2001 2001 HOH HOH . H 4 HOH B 2 2002 2002 HOH HOH . H 4 HOH B 3 2003 2003 HOH HOH . H 4 HOH B 4 2004 2004 HOH HOH . H 4 HOH B 5 2005 2005 HOH HOH . H 4 HOH B 6 2006 2006 HOH HOH . H 4 HOH B 7 2007 2007 HOH HOH . H 4 HOH B 8 2008 2008 HOH HOH . H 4 HOH B 9 2009 2009 HOH HOH . H 4 HOH B 10 2010 2010 HOH HOH . H 4 HOH B 11 2011 2011 HOH HOH . H 4 HOH B 12 2012 2012 HOH HOH . H 4 HOH B 13 2013 2013 HOH HOH . H 4 HOH B 14 2014 2014 HOH HOH . H 4 HOH B 15 2015 2015 HOH HOH . H 4 HOH B 16 2016 2016 HOH HOH . H 4 HOH B 17 2017 2017 HOH HOH . H 4 HOH B 18 2018 2018 HOH HOH . H 4 HOH B 19 2019 2019 HOH HOH . H 4 HOH B 20 2020 2020 HOH HOH . H 4 HOH B 21 2021 2021 HOH HOH . H 4 HOH B 22 2022 2022 HOH HOH . H 4 HOH B 23 2023 2023 HOH HOH . H 4 HOH B 24 2024 2024 HOH HOH . H 4 HOH B 25 2025 2025 HOH HOH . H 4 HOH B 26 2026 2026 HOH HOH . H 4 HOH B 27 2027 2027 HOH HOH . H 4 HOH B 28 2028 2028 HOH HOH . H 4 HOH B 29 2029 2029 HOH HOH . H 4 HOH B 30 2030 2030 HOH HOH . H 4 HOH B 31 2031 2031 HOH HOH . H 4 HOH B 32 2032 2032 HOH HOH . H 4 HOH B 33 2033 2033 HOH HOH . H 4 HOH B 34 2034 2034 HOH HOH . H 4 HOH B 35 2035 2035 HOH HOH . H 4 HOH B 36 2036 2036 HOH HOH . H 4 HOH B 37 2037 2037 HOH HOH . H 4 HOH B 38 2038 2038 HOH HOH . H 4 HOH B 39 2039 2039 HOH HOH . H 4 HOH B 40 2040 2040 HOH HOH . H 4 HOH B 41 2041 2041 HOH HOH . H 4 HOH B 42 2042 2042 HOH HOH . H 4 HOH B 43 2043 2043 HOH HOH . H 4 HOH B 44 2044 2044 HOH HOH . H 4 HOH B 45 2045 2045 HOH HOH . H 4 HOH B 46 2046 2046 HOH HOH . H 4 HOH B 47 2047 2047 HOH HOH . H 4 HOH B 48 2048 2048 HOH HOH . I 4 HOH C 1 2001 2001 HOH HOH . I 4 HOH C 2 2002 2002 HOH HOH . J 4 HOH D 1 2001 2001 HOH HOH . J 4 HOH D 2 2003 2003 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 0F7 . . . E 3 56.919 -11.798 10.155 1 66.21 ? C1 0F7 401 A 1 HETATM 2 O O1 0F7 . . . E 3 56.87 -10.561 10.153 1 65.96 ? O1 0F7 401 A 1 HETATM 3 O O2 0F7 . . . E 3 56.341 -12.595 9.244 1 70.35 ? O2 0F7 401 A 1 HETATM 4 C C2 0F7 . . . E 3 54.945 -12.909 9.248 1 73.42 ? C2 0F7 401 A 1 HETATM 5 C C3 0F7 . . . E 3 54.512 -12.925 7.801 1 80.72 ? C3 0F7 401 A 1 HETATM 6 C C4 0F7 . . . E 3 55.343 -13.476 6.815 1 84.85 ? C4 0F7 401 A 1 HETATM 7 C C5 0F7 . . . E 3 54.976 -13.496 5.475 1 85.45 ? C5 0F7 401 A 1 HETATM 8 C C6 0F7 . . . E 3 53.756 -12.963 5.083 1 83.59 ? C6 0F7 401 A 1 HETATM 9 C C7 0F7 . . . E 3 52.917 -12.41 6.053 1 86.24 ? C7 0F7 401 A 1 HETATM 10 C C8 0F7 . . . E 3 53.29 -12.392 7.4 1 84.23 ? C8 0F7 401 A 1 HETATM 11 N N 0F7 . . . E 3 58.011 -12.41 10.716 1 57.98 ? N 0F7 401 A 1 HETATM 12 C CA 0F7 . . . E 3 59.331 -11.829 10.641 1 49.92 ? CA 0F7 401 A 1 HETATM 13 C C 0F7 . . . E 3 60.117 -12.189 9.365 1 48.25 ? C 0F7 401 A 1 HETATM 14 O O 0F7 . . . E 3 60.548 -13.313 9.046 1 56.07 ? O 0F7 401 A 1 HETATM 15 C CB 0F7 . . . E 3 60.121 -12.024 11.924 1 47.35 ? CB 0F7 401 A 1 HETATM 16 C CG1 0F7 . . . E 3 59.235 -11.641 13.122 1 41.6 ? CG1 0F7 401 A 1 HETATM 17 C CG2 0F7 . . . E 3 61.365 -11.15 11.815 1 42.05 ? CG2 0F7 401 A 1 HETATM 18 C CD1 0F7 . . . E 3 59.689 -12.32 14.423 1 36.09 ? CD1 0F7 401 A 1 HETATM 19 N N1 0F7 . . . E 3 60.389 -11.105 8.583 1 46.13 ? N1 0F7 401 A 1 HETATM 20 C CA1 0F7 . . . E 3 61.053 -11.214 7.254 1 44.91 ? CA1 0F7 401 A 1 HETATM 21 C C9 0F7 . . . E 3 62.485 -11.635 7.602 1 43.13 ? C9 0F7 401 A 1 HETATM 22 O O3 0F7 . . . E 3 63.138 -10.882 8.319 1 46.29 ? O3 0F7 401 A 1 HETATM 23 C CB1 0F7 . . . E 3 61.022 -9.836 6.583 1 44.12 ? CB1 0F7 401 A 1 HETATM 24 C CG 0F7 . . . E 3 59.656 -9.315 6.082 1 48.59 ? CG 0F7 401 A 1 HETATM 25 C CD11 0F7 . . . E 3 59.749 -7.936 5.419 1 44.4 ? CD11 0F7 401 A 1 HETATM 26 C CD2 0F7 . . . E 3 58.971 -10.259 5.116 1 51.11 ? CD2 0F7 401 A 1 HETATM 27 N N2 0F7 . . . E 3 63.008 -12.751 7.072 1 41.06 ? N2 0F7 401 A 1 HETATM 28 C CA2 0F7 . . . E 3 64.345 -13.146 7.526 1 38.56 ? CA2 0F7 401 A 1 HETATM 29 C CC 0F7 . . . E 3 65.357 -13.102 6.311 1 40.06 ? CC 0F7 401 A 1 HETATM 30 O O4 0F7 . . . E 3 65.202 -11.838 5.648 1 36.26 ? O4 0F7 401 A 1 HETATM 31 C CB2 0F7 . . . E 3 64.443 -14.666 7.876 1 40.74 ? CB2 0F7 401 A 1 HETATM 32 C CG3 0F7 . . . E 3 64.085 -15.077 9.308 1 46.59 ? CG3 0F7 401 A 1 HETATM 33 F F1 0F7 . . . E 3 62.792 -15.321 9.469 1 42.3 ? F1 0F7 401 A 1 HETATM 34 F F2 0F7 . . . E 3 64.302 -14.1 10.207 1 47.6 ? F2 0F7 401 A 1 HETATM 35 C CD 0F7 . . . E 3 66.77 -13.181 7 1 47.19 ? CD 0F7 401 A 1 HETATM 36 O OE1 0F7 . . . E 3 67.114 -12.41 7.885 1 55.11 ? OE1 0F7 401 A 1 HETATM 37 O OE2 0F7 . . . E 3 67.54 -14.048 6.608 1 54.5 ? OE2 0F7 401 A 1 # _model_server_stats.io_time_ms 99 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 805 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 37 #