data_1NKM # _model_server_result.job_id z1va4bdmb_Q4dmAfbQ_xsQ _model_server_result.datetime_utc '2024-10-19 03:45:48' _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 1nkm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":260}' # _entry.id 1NKM # _exptl.entry_id 1NKM _exptl.method 'X-RAY DIFFRACTION' # _entity.details 'Residue peptide of the Peptidomimetic Inhibitor was chemically synthesized.' _entity.formula_weight 717.939 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~1~-[(2S,3S)-3-hydroxy-4-oxo-4-{[(1R)-1-phenylpropyl]amino}butan-2-yl]-N~4~,N~4~-dimethyl-L-aspartamide _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 1NKM _cell.length_a 73.88 _cell.length_b 73.88 _cell.length_c 216.43 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NKM _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id OG _struct_conn.ptnr1_label_comp_id SER _struct_conn.ptnr1_label_seq_id 132 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id SER _struct_conn.ptnr1_auth_seq_id 132 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id C4 _struct_conn.ptnr2_label_comp_id 0FP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id 0FP _struct_conn.ptnr2_auth_seq_id 260 _struct_conn.ptnr2_symmetry 1_555 _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 1.443 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C37 H63 N7 O7' _chem_comp.formula_weight 717.939 _chem_comp.id 0FP _chem_comp.mon_nstd_flag . _chem_comp.name N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~1~-[(2S,3S)-3-hydroxy-4-oxo-4-{[(1R)-1-phenylpropyl]amino}butan-2-yl]-N~4~,N~4~-dimethyl-L-aspartamide _chem_comp.type peptide-like _chem_comp.pdbx_synonyms 'BILC 408' # 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 CA C 0FP sing 1 n n CA CB 0FP sing 2 n n CA HA2 0FP sing 3 n n CA HA 0FP sing 4 n n C O 0FP doub 5 n n C N 0FP sing 6 n n CB CG 0FP sing 7 n n CB HB1 0FP sing 8 n n CB HB2 0FP sing 9 n n CG CD 0FP sing 10 n n CG HG1 0FP sing 11 n n CG HG2 0FP sing 12 n n CD CE 0FP sing 13 n n CD HD1 0FP sing 14 n n CD HD2 0FP sing 15 n n CE NZ 0FP sing 16 n n CE HE1 0FP sing 17 n n CE HE2 0FP sing 18 n n NZ HZ1 0FP sing 19 n n NZ HZ2 0FP sing 20 n n N CA1 0FP sing 21 n n N H 0FP sing 22 n n CA1 CB1 0FP sing 23 n n CA1 C1 0FP sing 24 n n CA1 HA1 0FP sing 25 n n CB1 CG1 0FP sing 26 n n CB1 CG2 0FP sing 27 n n CB1 CG3 0FP sing 28 n n CG1 HG11 0FP sing 29 n n CG1 HG12 0FP sing 30 n n CG1 HG13 0FP sing 31 n n CG2 HG21 0FP sing 32 n n CG2 HG22 0FP sing 33 n n CG2 HG23 0FP sing 34 n n CG3 HG31 0FP sing 35 n n CG3 HG32 0FP sing 36 n n CG3 HG33 0FP sing 37 n n C1 O1 0FP doub 38 n n C1 N1 0FP sing 39 n n N1 CA2 0FP sing 40 n n N1 H1 0FP sing 41 n n CA2 CB2 0FP sing 42 n n CA2 C2 0FP sing 43 n n CA2 HA3 0FP sing 44 n n CB2 CG11 0FP sing 45 n n CB2 CG21 0FP sing 46 n n CB2 CG31 0FP sing 47 n n CG11 HG14 0FP sing 48 n n CG11 HG15 0FP sing 49 n n CG11 HG16 0FP sing 50 n n CG21 HG24 0FP sing 51 n n CG21 HG25 0FP sing 52 n n CG21 HG26 0FP sing 53 n n CG31 HG34 0FP sing 54 n n CG31 HG35 0FP sing 55 n n CG31 HG36 0FP sing 56 n n C2 O2 0FP doub 57 n n C2 N2 0FP sing 58 n n N2 CA3 0FP sing 59 n n N2 H2 0FP sing 60 n n CA3 CB3 0FP sing 61 n n CA3 C3 0FP sing 62 n n CA3 HA11 0FP sing 63 n n CB3 CG4 0FP sing 64 n n CB3 HB21 0FP sing 65 n n CB3 HB3 0FP sing 66 n n CG4 OD1 0FP doub 67 n n CG4 ND2 0FP sing 68 n n ND2 CE1 0FP sing 69 n n ND2 CE2 0FP sing 70 n n CE1 HE11 0FP sing 71 n n CE1 HE12 0FP sing 72 n n CE1 HE13 0FP sing 73 n n CE2 HE21 0FP sing 74 n n CE2 HE22 0FP sing 75 n n CE2 HE23 0FP sing 76 n n C3 O3 0FP doub 77 n n C3 N3 0FP sing 78 n n N3 CA4 0FP sing 79 n n N3 H3 0FP sing 80 n n CA4 C4 0FP sing 81 n n CA4 CB4 0FP sing 82 n n CA4 HA4 0FP sing 83 n n C4 O4 0FP sing 84 n n C4 C11 0FP sing 85 n n CB4 HB11 0FP sing 86 n n CB4 HB22 0FP sing 87 n n CB4 HB31 0FP sing 88 n n C11 O11 0FP doub 89 n n C11 N21 0FP sing 90 n n N21 C31 0FP sing 91 n n N21 HN2 0FP sing 92 n n C31 C311 0FP sing 93 n n C31 C41 0FP sing 94 n n C31 HC3 0FP sing 95 n n C311 C32 0FP sing 96 n n C311 H311 0FP sing 97 n n C311 H312 0FP sing 98 n n C32 H321 0FP sing 99 n n C32 H322 0FP sing 100 n n C32 H323 0FP sing 101 n n C41 C5 0FP doub 102 n y C41 C9 0FP sing 103 n y C5 C6 0FP sing 104 n y C5 HC5 0FP sing 105 n n C6 C7 0FP doub 106 n y C6 HC6 0FP sing 107 n n C7 C8 0FP sing 108 n y C7 HC7 0FP sing 109 n n C8 C9 0FP doub 110 n y C8 HC8 0FP sing 111 n n C9 HC9 0FP sing 112 n n C4 H62 0FP sing 113 n n O4 H63 0FP sing 114 n n # _atom_sites.entry_id 1NKM _atom_sites.fract_transf_matrix[1][1] 0.013535 _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] 0.013535 _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] 0.00462 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id 0FP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 260 _pdbx_nonpoly_scheme.auth_seq_num 260 _pdbx_nonpoly_scheme.pdb_mon_id 0FP _pdbx_nonpoly_scheme.auth_mon_id DNL _pdbx_nonpoly_scheme.pdb_ins_code . # 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 CA 0FP . . . C 2 64.823 5.539 33.151 1 72.26 ? CA 0FP 260 A 1 HETATM 2 C C 0FP . . . C 2 64.058 5.207 31.872 1 71.31 ? C 0FP 260 A 1 HETATM 3 O O 0FP . . . C 2 64.636 5.107 30.783 1 70.46 ? O 0FP 260 A 1 HETATM 4 C CB 0FP . . . C 2 63.998 5.145 34.388 1 73.27 ? CB 0FP 260 A 1 HETATM 5 C CG 0FP . . . C 2 64.713 5.433 35.716 1 74.46 ? CG 0FP 260 A 1 HETATM 6 C CD 0FP . . . C 2 63.969 4.889 36.93 1 73.59 ? CD 0FP 260 A 1 HETATM 7 C CE 0FP . . . C 2 64.855 4.955 38.173 1 73.3 ? CE 0FP 260 A 1 HETATM 8 N NZ 0FP . . . C 2 66.158 4.242 37.976 1 72.25 ? NZ 0FP 260 A 1 HETATM 9 N N 0FP . . . C 2 62.752 5.034 32.015 1 70.28 ? N 0FP 260 A 1 HETATM 10 C CA1 0FP . . . C 2 61.904 4.718 30.879 1 68.88 ? CA1 0FP 260 A 1 HETATM 11 C CB1 0FP . . . C 2 61.461 3.227 30.897 1 69.38 ? CB1 0FP 260 A 1 HETATM 12 C CG1 0FP . . . C 2 60.449 2.993 32.026 1 67.95 ? CG1 0FP 260 A 1 HETATM 13 C CG2 0FP . . . C 2 60.83 2.864 29.548 1 68.28 ? CG2 0FP 260 A 1 HETATM 14 C CG3 0FP . . . C 2 62.679 2.338 31.144 1 69.39 ? CG3 0FP 260 A 1 HETATM 15 C C1 0FP . . . C 2 60.669 5.596 30.939 1 67.06 ? C1 0FP 260 A 1 HETATM 16 O O1 0FP . . . C 2 60.249 6.017 32.02 1 66.47 ? O1 0FP 260 A 1 HETATM 17 N N1 0FP . . . C 2 60.098 5.879 29.775 1 65.19 ? N1 0FP 260 A 1 HETATM 18 C CA2 0FP . . . C 2 58.894 6.699 29.704 1 63.3 ? CA2 0FP 260 A 1 HETATM 19 C CB2 0FP . . . C 2 59.228 8.172 29.276 1 63.22 ? CB2 0FP 260 A 1 HETATM 20 C CG11 0FP . . . C 2 60.106 8.166 28.013 1 62.03 ? CG11 0FP 260 A 1 HETATM 21 C CG21 0FP . . . C 2 57.931 8.938 28.993 1 62.94 ? CG21 0FP 260 A 1 HETATM 22 C CG31 0FP . . . C 2 59.967 8.879 30.413 1 61.49 ? CG31 0FP 260 A 1 HETATM 23 C C2 0FP . . . C 2 57.876 6.073 28.743 1 61.17 ? C2 0FP 260 A 1 HETATM 24 O O2 0FP . . . C 2 58.203 5.736 27.598 1 59.86 ? O2 0FP 260 A 1 HETATM 25 N N2 0FP . . . C 2 56.649 5.908 29.23 1 58.48 ? N2 0FP 260 A 1 HETATM 26 C CA3 0FP . . . C 2 55.582 5.322 28.432 1 56.66 ? CA3 0FP 260 A 1 HETATM 27 C CB3 0FP . . . C 2 54.976 4.106 29.141 1 55.66 ? CB3 0FP 260 A 1 HETATM 28 C CG4 0FP . . . C 2 55.955 2.957 29.303 1 54.58 ? CG4 0FP 260 A 1 HETATM 29 O OD1 0FP . . . C 2 56.939 2.841 28.562 1 52.29 ? OD1 0FP 260 A 1 HETATM 30 N ND2 0FP . . . C 2 55.669 2.074 30.266 1 54.18 ? ND2 0FP 260 A 1 HETATM 31 C CE1 0FP . . . C 2 54.505 2.191 31.122 1 51.83 ? CE1 0FP 260 A 1 HETATM 32 C CE2 0FP . . . C 2 56.536 0.931 30.458 1 54.12 ? CE2 0FP 260 A 1 HETATM 33 C C3 0FP . . . C 2 54.448 6.296 28.127 1 55.53 ? C3 0FP 260 A 1 HETATM 34 O O3 0FP . . . C 2 53.858 6.888 29.031 1 54.77 ? O3 0FP 260 A 1 HETATM 35 N N3 0FP . . . C 2 54.141 6.447 26.844 1 54.66 ? N3 0FP 260 A 1 HETATM 36 C CA4 0FP . . . C 2 53.049 7.314 26.41 1 52.74 ? CA4 0FP 260 A 1 HETATM 37 C C4 0FP . . . C 2 51.951 6.465 25.8 1 51.84 ? C4 0FP 260 A 1 HETATM 38 O O4 0FP . . . C 2 51.162 7.277 25.006 1 52.58 ? O4 0FP 260 A 1 HETATM 39 C CB4 0FP . . . C 2 53.543 8.307 25.376 1 52.93 ? CB4 0FP 260 A 1 HETATM 40 C C11 0FP . . . C 2 51.116 5.818 26.93 1 52.62 ? C11 0FP 260 A 1 HETATM 41 O O11 0FP . . . C 2 51.663 5.409 27.964 1 53.05 ? O11 0FP 260 A 1 HETATM 42 N N21 0FP . . . C 2 49.801 5.732 26.742 1 53.43 ? N21 0FP 260 A 1 HETATM 43 C C31 0FP . . . C 2 48.876 5.14 27.716 1 56 ? C31 0FP 260 A 1 HETATM 44 C C311 0FP . . . C 2 47.841 4.232 27.049 1 56.45 ? C311 0FP 260 A 1 HETATM 45 C C32 0FP . . . C 2 47.054 3.45 28.1 1 55.66 ? C32 0FP 260 A 1 HETATM 46 C C41 0FP . . . C 2 48.14 6.209 28.486 1 57.44 ? C41 0FP 260 A 1 HETATM 47 C C5 0FP . . . C 2 48.52 6.528 29.793 1 59.65 ? C5 0FP 260 A 1 HETATM 48 C C6 0FP . . . C 2 47.81 7.479 30.543 1 59.57 ? C6 0FP 260 A 1 HETATM 49 C C7 0FP . . . C 2 46.709 8.12 29.978 1 59.44 ? C7 0FP 260 A 1 HETATM 50 C C8 0FP . . . C 2 46.322 7.81 28.668 1 58.47 ? C8 0FP 260 A 1 HETATM 51 C C9 0FP . . . C 2 47.039 6.86 27.932 1 57.38 ? C9 0FP 260 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 51 #