data_1A85 # _model_server_result.job_id m4K1AGnDADmihAgGaeWsEA _model_server_result.datetime_utc '2024-10-19 15:50:34' _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 1a85 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1}' # _entry.id 1A85 # _exptl.entry_id 1A85 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 393.437 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N~1~-(3-aminobenzyl)-N~2~-[(2R)-2-(hydroxycarbamoyl)-4-methylpentanoyl]-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 1A85 _cell.length_a 33.14 _cell.length_b 69.43 _cell.length_c 72.62 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1A85 _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,D,E,F _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 4 _struct_asym.id F _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 metalc ? metalc1 F OH 0DY . A 0DY 1 1_555 E ZN ZN . A ZN 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc2 F O1 0DY . A 0DY 1 1_555 E ZN ZN . A ZN 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc3 A O ASP 53 A ASP 137 1_555 B CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc4 A NE2 HIS 63 A HIS 147 1_555 D ZN ZN . A ZN 998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc5 A OD2 ASP 65 A ASP 149 1_555 D ZN ZN . A ZN 998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.914 ? metalc ? metalc6 A OD1 ASP 70 A ASP 154 1_555 C CA CA . A CA 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc7 A O GLY 71 A GLY 155 1_555 C CA CA . A CA 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc8 A O ASN 73 A ASN 157 1_555 C CA CA . A CA 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc9 A O ILE 75 A ILE 159 1_555 C CA CA . A CA 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc10 A NE2 HIS 78 A HIS 162 1_555 D ZN ZN . A ZN 998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc11 A O GLY 85 A GLY 169 1_555 B CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc12 A O GLY 87 A GLY 171 1_555 B CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc13 A OD1 ASP 89 A ASP 173 1_555 B CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc14 A ND1 HIS 91 A HIS 175 1_555 D ZN ZN . A ZN 998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc15 A OD2 ASP 93 A ASP 177 1_555 C CA CA . A CA 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc16 A OE2 GLU 96 A GLU 180 1_555 C CA CA . A CA 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc17 A NE2 HIS 113 A HIS 197 1_555 E ZN ZN . A ZN 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc18 A NE2 HIS 117 A HIS 201 1_555 E ZN ZN . A ZN 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc19 A NE2 HIS 123 A HIS 207 1_555 E ZN ZN . A ZN 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? # _chem_comp.formula 'C18 H27 N5 O5' _chem_comp.formula_weight 393.437 _chem_comp.id 0DY _chem_comp.mon_nstd_flag . _chem_comp.name N~1~-(3-aminobenzyl)-N~2~-[(2R)-2-(hydroxycarbamoyl)-4-methylpentanoyl]-L-aspartamide _chem_comp.type peptide-like _chem_comp.pdbx_synonyms HONH-iBM-Asn-NHBn(m-NH2) # 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 N OH 0DY sing 1 n n N C1 0DY sing 2 n n N HN 0DY sing 3 n n OH HOH 0DY sing 4 n n C1 O1 0DY doub 5 n n C1 CA 0DY sing 6 n n CA CB 0DY sing 7 n n CA C 0DY sing 8 n n CA HA 0DY sing 9 n n CB CG 0DY sing 10 n n CB HB1 0DY sing 11 n n CB HB2 0DY sing 12 n n CG CD1 0DY sing 13 n n CG CD2 0DY sing 14 n n CG HG 0DY sing 15 n n CD1 HD11 0DY sing 16 n n CD1 HD12 0DY sing 17 n n CD1 HD13 0DY sing 18 n n CD2 HD21 0DY sing 19 n n CD2 HD22 0DY sing 20 n n CD2 HD23 0DY sing 21 n n C O 0DY doub 22 n n N1 CA1 0DY sing 23 n n N1 H 0DY sing 24 n n CA1 C2 0DY sing 25 n n CA1 CB1 0DY sing 26 n n CA1 HA1 0DY sing 27 n n C2 O2 0DY doub 28 n n CB1 CG1 0DY sing 29 n n CB1 HB21 0DY sing 30 n n CB1 HB3 0DY sing 31 n n CG1 OD1 0DY doub 32 n n CG1 ND2 0DY sing 33 n n ND2 HD24 0DY sing 34 n n ND2 HD25 0DY sing 35 n n N2 CB2 0DY sing 36 n n N2 HN1 0DY sing 37 n n CB2 CG2 0DY sing 38 n n CB2 HB11 0DY sing 39 n n CB2 HB22 0DY sing 40 n n CG2 CD11 0DY doub 41 n y CG2 CD21 0DY sing 42 n y CD11 CE1 0DY sing 43 n y CD11 HD14 0DY sing 44 n n CE1 CZ 0DY doub 45 n y CE1 HC11 0DY sing 46 n n CD21 CE2 0DY doub 47 n y CD21 HC21 0DY sing 48 n n CE2 CZ 0DY sing 49 n y CE2 NE2 0DY sing 50 n n CZ HCZ1 0DY sing 51 n n NE2 HE21 0DY sing 52 n n NE2 HE22 0DY sing 53 n n C N1 0DY sing 54 n n C2 N2 0DY sing 55 n n # _atom_sites.entry_id 1A85 _atom_sites.fract_transf_matrix[1][1] 0.030175 _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] 0.014403 _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] 0.01377 _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 CA A 1 996 996 CA CA . C 2 CA A 1 997 997 CA CA . D 3 ZN A 1 998 998 ZN ZN . E 3 ZN A 1 999 999 ZN ZN . F 4 0DY A 1 1 1 0DY HMI . # 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 N N 0DY . . . F 4 25.697 59.973 53.918 1 12.7 ? N 0DY 1 A 1 HETATM 2 O OH 0DY . . . F 4 24.724 58.994 54.017 1 11.87 ? OH 0DY 1 A 1 HETATM 3 C C1 0DY . . . F 4 26.992 59.633 53.901 1 13.88 ? C1 0DY 1 A 1 HETATM 4 O O1 0DY . . . F 4 27.389 58.441 53.948 1 12.9 ? O1 0DY 1 A 1 HETATM 5 C CA 0DY . . . F 4 27.937 60.755 53.438 1 14.42 ? CA 0DY 1 A 1 HETATM 6 C CB 0DY . . . F 4 29.227 60.87 54.309 1 14.78 ? CB 0DY 1 A 1 HETATM 7 C CG 0DY . . . F 4 30.099 62.106 54.126 0 14.84 ? CG 0DY 1 A 1 HETATM 8 C CD1 0DY . . . F 4 29.775 63.073 55.243 0 14.91 ? CD1 0DY 1 A 1 HETATM 9 C CD2 0DY . . . F 4 31.553 61.693 54.166 0 14.91 ? CD2 0DY 1 A 1 HETATM 10 C C 0DY . . . F 4 28.279 60.497 51.986 1 14.95 ? C 0DY 1 A 1 HETATM 11 O O 0DY . . . F 4 27.804 61.206 51.098 1 14.61 ? O 0DY 1 A 1 HETATM 12 N N1 0DY . . . F 4 29.089 59.486 51.721 1 16.07 ? N1 0DY 1 A 1 HETATM 13 C CA1 0DY . . . F 4 29.443 59.233 50.336 1 16.97 ? CA1 0DY 1 A 1 HETATM 14 C C2 0DY . . . F 4 28.35 58.408 49.63 1 17.75 ? C2 0DY 1 A 1 HETATM 15 O O2 0DY . . . F 4 28.501 58.028 48.459 1 17.87 ? O2 0DY 1 A 1 HETATM 16 C CB1 0DY . . . F 4 30.799 58.559 50.213 1 16.82 ? CB1 0DY 1 A 1 HETATM 17 C CG1 0DY . . . F 4 31.22 58.371 48.754 1 17.54 ? CG1 0DY 1 A 1 HETATM 18 O OD1 0DY . . . F 4 31.567 57.266 48.361 1 18.37 ? OD1 0DY 1 A 1 HETATM 19 N ND2 0DY . . . F 4 31.23 59.458 47.956 1 16.18 ? ND2 0DY 1 A 1 HETATM 20 N N2 0DY . . . F 4 27.292 58.069 50.374 1 17.94 ? N2 0DY 1 A 1 HETATM 21 C CB2 0DY . . . F 4 26.143 57.342 49.848 1 18.63 ? CB2 0DY 1 A 1 HETATM 22 C CG2 0DY . . . F 4 26.056 55.924 49.388 1 18.78 ? CG2 0DY 1 A 1 HETATM 23 C CD11 0DY . . . F 4 26.846 54.916 49.995 1 18.44 ? CD11 0DY 1 A 1 HETATM 24 C CE1 0DY . . . F 4 26.685 53.572 49.681 1 18.28 ? CE1 0DY 1 A 1 HETATM 25 C CD21 0DY . . . F 4 25.111 55.557 48.427 1 19.14 ? CD21 0DY 1 A 1 HETATM 26 C CE2 0DY . . . F 4 24.948 54.209 48.114 1 19.53 ? CE2 0DY 1 A 1 HETATM 27 C CZ 0DY . . . F 4 25.73 53.213 48.724 1 19.36 ? CZ 0DY 1 A 1 HETATM 28 N NE2 0DY . . . F 4 23.98 53.909 47.273 1 20.83 ? NE2 0DY 1 A 1 HETATM 29 H HN 0DY . . . F 4 25.471 60.873 53.524 0 20 ? HN 0DY 1 A 1 HETATM 30 H HOH 0DY . . . F 4 23.84 59.483 53.964 0 20 ? HOH 0DY 1 A 1 HETATM 31 H H 0DY . . . F 4 29.406 58.921 52.411 0 20 ? H 0DY 1 A 1 HETATM 32 H HD24 0DY . . . F 4 31.516 59.315 47.03 0 20 ? HD24 0DY 1 A 1 HETATM 33 H HD25 0DY . . . F 4 30.987 60.325 48.314 0 20 ? HD25 0DY 1 A 1 HETATM 34 H HN1 0DY . . . F 4 27.256 58.334 51.307 0 20 ? HN1 0DY 1 A 1 HETATM 35 H HE21 0DY . . . F 4 23.403 54.615 46.936 0 20 ? HE21 0DY 1 A 1 HETATM 36 H HE22 0DY . . . F 4 23.853 52.955 47.079 0 20 ? HE22 0DY 1 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 36 #