data_8DGB # _model_server_result.job_id bZz7KiMKJZNVXnONjYhmnw _model_server_result.datetime_utc '2025-07-28 02:32:29' _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 8dgb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 8DGB # _exptl.entry_id 8DGB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 485.551 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 67 _cell.angle_beta 79.57 _cell.angle_gamma 88.8 _cell.entry_id 8DGB _cell.length_a 47.03 _cell.length_b 53.241 _cell.length_c 59.532 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DGB _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _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,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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D 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 covale ? covale1 A SG CYS 145 A CYS 145 1_555 C C21 B1S . A B1S 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.844 ? covale ? covale2 B SG CYS 145 B CYS 145 1_555 D C21 B1S . B B1S 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.817 ? # _chem_comp.formula 'C21 H31 N3 O8 S' _chem_comp.formula_weight 485.551 _chem_comp.id B1S _chem_comp.mon_nstd_flag . _chem_comp.name '(1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid' _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 C15 C14 B1S sing 70 n n C14 C16 B1S sing 71 n n C14 C13 B1S sing 72 n n C13 C12 B1S sing 73 n n N11 C12 B1S sing 74 n n N11 C9 B1S sing 75 n n C12 C17 B1S sing 76 n n O8 C9 B1S sing 77 n n O8 C7 B1S sing 78 n n C9 O10 B1S doub 79 n n C7 C1 B1S sing 80 n n C17 O18 B1S doub 81 n n C17 N19 B1S sing 82 n n N19 C20 B1S sing 83 n n C1 C2 B1S doub 84 n y C1 C6 B1S sing 85 n y C2 C3 B1S sing 86 n y O22 C21 B1S sing 87 n n C6 C5 B1S doub 88 n y C20 C21 B1S sing 89 n n C20 C24 B1S sing 90 n n C3 C4 B1S doub 91 n y C5 C4 B1S sing 92 n y C24 C25 B1S sing 93 n n C25 C26 B1S sing 94 n n C25 C29 B1S sing 95 n n C26 C27 B1S sing 96 n n C29 O30 B1S doub 97 n n C29 N28 B1S sing 98 n n C27 N28 B1S sing 99 n n C7 H1 B1S sing 100 n n C7 H2 B1S sing 101 n n C2 H3 B1S sing 102 n n C3 H4 B1S sing 103 n n C4 H5 B1S sing 104 n n C5 H6 B1S sing 105 n n C6 H7 B1S sing 106 n n N11 H8 B1S sing 107 n n C12 H9 B1S sing 108 n n C13 H10 B1S sing 109 n n C13 H11 B1S sing 110 n n C14 H12 B1S sing 111 n n C15 H13 B1S sing 112 n n C15 H14 B1S sing 113 n n C15 H15 B1S sing 114 n n C16 H16 B1S sing 115 n n C16 H17 B1S sing 116 n n C16 H18 B1S sing 117 n n N19 H19 B1S sing 118 n n C20 H20 B1S sing 119 n n C21 H21 B1S sing 120 n n O22 H23 B1S sing 121 n n C24 H24 B1S sing 122 n n C24 H25 B1S sing 123 n n C25 H26 B1S sing 124 n n C26 H27 B1S sing 125 n n C26 H28 B1S sing 126 n n C27 H29 B1S sing 127 n n C27 H30 B1S sing 128 n n N28 H31 B1S sing 129 n n C21 S1 B1S sing 130 n n S1 O1 B1S doub 131 n n S1 O3 B1S doub 132 n n S1 O2 B1S sing 133 n n O2 H22 B1S sing 134 n n # _atom_sites.entry_id 8DGB _atom_sites.fract_transf_matrix[1][1] 0.021263 _atom_sites.fract_transf_matrix[1][2] -0.000445 _atom_sites.fract_transf_matrix[1][3] -0.004065 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018787 _atom_sites.fract_transf_matrix[2][3] -0.00804 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.018578 _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 C 2 B1S A 1 401 401 B1S LIG . D 2 B1S B 1 401 401 B1S LIG . E 3 HOH A 1 501 73 HOH HOH . E 3 HOH A 2 502 4 HOH HOH . E 3 HOH A 3 503 14 HOH HOH . E 3 HOH A 4 504 9 HOH HOH . E 3 HOH A 5 505 61 HOH HOH . E 3 HOH A 6 506 85 HOH HOH . F 3 HOH B 1 501 47 HOH HOH . F 3 HOH B 2 502 15 HOH HOH . F 3 HOH B 3 503 100 HOH HOH . F 3 HOH B 4 504 40 HOH HOH . F 3 HOH B 5 505 17 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 C7 B1S . . . D 2 -20.79 3.601 13.271 1 63.73 ? C7 B1S 401 B 1 HETATM 2 O O8 B1S . . . D 2 -21.175 2.267 13.33 1 63.11 ? O8 B1S 401 B 1 HETATM 3 C C9 B1S . . . D 2 -20.164 1.395 13.721 1 62.13 ? C9 B1S 401 B 1 HETATM 4 O O10 B1S . . . D 2 -19.043 1.605 13.432 1 62.34 ? O10 B1S 401 B 1 HETATM 5 C C1 B1S . . . D 2 -20.96 4.237 14.644 1 64.46 ? C1 B1S 401 B 1 HETATM 6 C C2 B1S . . . D 2 -21.986 5.137 14.858 1 65.08 ? C2 B1S 401 B 1 HETATM 7 C C3 B1S . . . D 2 -22.145 5.721 16.1 1 65.15 ? C3 B1S 401 B 1 HETATM 8 C C4 B1S . . . D 2 -21.274 5.405 17.124 1 65.25 ? C4 B1S 401 B 1 HETATM 9 C C5 B1S . . . D 2 -20.247 4.506 16.912 1 65.1 ? C5 B1S 401 B 1 HETATM 10 C C6 B1S . . . D 2 -20.091 3.924 15.67 1 64.74 ? C6 B1S 401 B 1 HETATM 11 N N11 B1S . . . D 2 -20.518 0.234 14.494 1 61.43 ? N11 B1S 401 B 1 HETATM 12 C C12 B1S . . . D 2 -19.93 -1.057 14.232 1 60.6 ? C12 B1S 401 B 1 HETATM 13 C C17 B1S . . . D 2 -19.987 -1.41 12.757 1 59.61 ? C17 B1S 401 B 1 HETATM 14 O O18 B1S . . . D 2 -20.998 -1.296 12.161 1 59.13 ? O18 B1S 401 B 1 HETATM 15 C C13 B1S . . . D 2 -20.761 -2.076 14.986 1 60.94 ? C13 B1S 401 B 1 HETATM 16 C C14 B1S . . . D 2 -20.85 -1.574 16.416 1 61.74 ? C14 B1S 401 B 1 HETATM 17 C C15 B1S . . . D 2 -21.966 -2.307 17.147 1 62.36 ? C15 B1S 401 B 1 HETATM 18 C C16 B1S . . . D 2 -19.512 -1.84 17.094 1 61.81 ? C16 B1S 401 B 1 HETATM 19 N N19 B1S . . . D 2 -18.791 -1.899 12.105 1 58.85 ? N19 B1S 401 B 1 HETATM 20 C C20 B1S . . . D 2 -18.793 -2.27 10.705 1 57.92 ? C20 B1S 401 B 1 HETATM 21 C C21 B1S . . . D 2 -18.205 -3.669 10.552 1 57.05 ? C21 B1S 401 B 1 HETATM 22 O O22 B1S . . . D 2 -19.2 -4.651 10.803 1 57.27 ? O22 B1S 401 B 1 HETATM 23 C C24 B1S . . . D 2 -17.919 -1.324 9.88 1 57.85 ? C24 B1S 401 B 1 HETATM 24 C C25 B1S . . . D 2 -18.277 0.164 10.158 1 58.16 ? C25 B1S 401 B 1 HETATM 25 C C26 B1S . . . D 2 -19.499 0.498 9.379 1 58.02 ? C26 B1S 401 B 1 HETATM 26 C C27 B1S . . . D 2 -19.101 1.587 8.37 1 58.18 ? C27 B1S 401 B 1 HETATM 27 N N28 B1S . . . D 2 -17.641 1.934 8.64 1 58.37 ? N28 B1S 401 B 1 HETATM 28 C C29 B1S . . . D 2 -17.15 1.059 9.724 1 58.53 ? C29 B1S 401 B 1 HETATM 29 O O30 B1S . . . D 2 -16.059 1.082 10.169 1 58.33 ? O30 B1S 401 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 29 #