data_1YPM # _model_server_result.job_id XqSxdMV2nX6du5I_4dkCBA _model_server_result.datetime_utc '2024-10-18 16:25:54' _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 1ypm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":5555}' # _entry.id 1YPM # _exptl.entry_id 1YPM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 489.568 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-(4-NITROBENZOYL)-L-LEUCYL-N-(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)-L-PROLINAMIDE _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 99.73 _cell.angle_gamma 90 _cell.entry_id 1YPM _cell.length_a 69.652 _cell.length_b 71.721 _cell.length_c 71.331 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YPM _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 D _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 3 L CYS 1 1_555 B SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf2 B SG CYS 28 H CYS 42 1_555 B SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 B SG CYS 173 H CYS 168 1_555 B SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? disulf ? disulf4 B SG CYS 201 H CYS 191 1_555 B SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? covale ? covale1 C C GLU 8 I GLU 8 1_555 C N TYS 9 I TYS 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 C C TYS 9 I TYS 9 1_555 C N LEU 10 I LEU 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? # _chem_comp.formula 'C23 H35 N7 O5' _chem_comp.formula_weight 489.568 _chem_comp.id RA4 _chem_comp.mon_nstd_flag . _chem_comp.name N-(4-NITROBENZOYL)-L-LEUCYL-N-(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)-L-PROLINAMIDE _chem_comp.type peptide-like _chem_comp.pdbx_synonyms 1-GUANIDINO-4-(N-NITRO-BENZOYLAMINO-L-LEUCYL-L-PROLYLAMINO)BUTANE # _atom_sites.entry_id 1YPM _atom_sites.fract_transf_matrix[1][1] 0.014357 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002462 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013943 _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] 0.014224 _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 D 4 RA4 H 1 5555 5555 RA4 RA4 . E 5 HOH L 1 9004 9004 HOH HOH . E 5 HOH L 2 9015 9015 HOH HOH . E 5 HOH L 3 9042 9042 HOH HOH . E 5 HOH L 4 9049 9049 HOH HOH . E 5 HOH L 5 9060 9060 HOH HOH . E 5 HOH L 6 9062 9062 HOH HOH . E 5 HOH L 7 9066 9066 HOH HOH . E 5 HOH L 8 9072 9072 HOH HOH . E 5 HOH L 9 9081 9081 HOH HOH . E 5 HOH L 10 9086 9086 HOH HOH . E 5 HOH L 11 9087 9087 HOH HOH . E 5 HOH L 12 9096 9096 HOH HOH . E 5 HOH L 13 9109 9109 HOH HOH . E 5 HOH L 14 9111 9111 HOH HOH . E 5 HOH L 15 9114 9114 HOH HOH . E 5 HOH L 16 9130 9130 HOH HOH . E 5 HOH L 17 9137 9137 HOH HOH . E 5 HOH L 18 9139 9139 HOH HOH . E 5 HOH L 19 9153 9153 HOH HOH . F 5 HOH H 1 9001 9001 HOH HOH . F 5 HOH H 2 9002 9002 HOH HOH . F 5 HOH H 3 9003 9003 HOH HOH . F 5 HOH H 4 9005 9005 HOH HOH . F 5 HOH H 5 9006 9006 HOH HOH . F 5 HOH H 6 9007 9007 HOH HOH . F 5 HOH H 7 9008 9008 HOH HOH . F 5 HOH H 8 9009 9009 HOH HOH . F 5 HOH H 9 9010 9010 HOH HOH . F 5 HOH H 10 9011 9011 HOH HOH . F 5 HOH H 11 9012 9012 HOH HOH . F 5 HOH H 12 9013 9013 HOH HOH . F 5 HOH H 13 9014 9014 HOH HOH . F 5 HOH H 14 9016 9016 HOH HOH . F 5 HOH H 15 9017 9017 HOH HOH . F 5 HOH H 16 9018 9018 HOH HOH . F 5 HOH H 17 9019 9019 HOH HOH . F 5 HOH H 18 9020 9020 HOH HOH . F 5 HOH H 19 9021 9021 HOH HOH . F 5 HOH H 20 9022 9022 HOH HOH . F 5 HOH H 21 9023 9023 HOH HOH . F 5 HOH H 22 9024 9024 HOH HOH . F 5 HOH H 23 9025 9025 HOH HOH . F 5 HOH H 24 9026 9026 HOH HOH . F 5 HOH H 25 9027 9027 HOH HOH . F 5 HOH H 26 9028 9028 HOH HOH . F 5 HOH H 27 9029 9029 HOH HOH . F 5 HOH H 28 9030 9030 HOH HOH . F 5 HOH H 29 9031 9031 HOH HOH . F 5 HOH H 30 9032 9032 HOH HOH . F 5 HOH H 31 9033 9033 HOH HOH . F 5 HOH H 32 9034 9034 HOH HOH . F 5 HOH H 33 9035 9035 HOH HOH . F 5 HOH H 34 9036 9036 HOH HOH . F 5 HOH H 35 9037 9037 HOH HOH . F 5 HOH H 36 9038 9038 HOH HOH . F 5 HOH H 37 9039 9039 HOH HOH . F 5 HOH H 38 9040 9040 HOH HOH . F 5 HOH H 39 9041 9041 HOH HOH . F 5 HOH H 40 9043 9043 HOH HOH . F 5 HOH H 41 9045 9045 HOH HOH . F 5 HOH H 42 9046 9046 HOH HOH . F 5 HOH H 43 9047 9047 HOH HOH . F 5 HOH H 44 9048 9048 HOH HOH . F 5 HOH H 45 9050 9050 HOH HOH . F 5 HOH H 46 9051 9051 HOH HOH . F 5 HOH H 47 9052 9052 HOH HOH . F 5 HOH H 48 9053 9053 HOH HOH . F 5 HOH H 49 9054 9054 HOH HOH . F 5 HOH H 50 9055 9055 HOH HOH . F 5 HOH H 51 9056 9056 HOH HOH . F 5 HOH H 52 9057 9057 HOH HOH . F 5 HOH H 53 9058 9058 HOH HOH . F 5 HOH H 54 9059 9059 HOH HOH . F 5 HOH H 55 9061 9061 HOH HOH . F 5 HOH H 56 9063 9063 HOH HOH . F 5 HOH H 57 9064 9064 HOH HOH . F 5 HOH H 58 9065 9065 HOH HOH . F 5 HOH H 59 9067 9067 HOH HOH . F 5 HOH H 60 9068 9068 HOH HOH . F 5 HOH H 61 9069 9069 HOH HOH . F 5 HOH H 62 9070 9070 HOH HOH . F 5 HOH H 63 9071 9071 HOH HOH . F 5 HOH H 64 9073 9073 HOH HOH . F 5 HOH H 65 9074 9074 HOH HOH . F 5 HOH H 66 9075 9075 HOH HOH . F 5 HOH H 67 9076 9076 HOH HOH . F 5 HOH H 68 9077 9077 HOH HOH . F 5 HOH H 69 9078 9078 HOH HOH . F 5 HOH H 70 9079 9079 HOH HOH . F 5 HOH H 71 9080 9080 HOH HOH . F 5 HOH H 72 9082 9082 HOH HOH . F 5 HOH H 73 9083 9083 HOH HOH . F 5 HOH H 74 9084 9084 HOH HOH . F 5 HOH H 75 9085 9085 HOH HOH . F 5 HOH H 76 9089 9089 HOH HOH . F 5 HOH H 77 9090 9090 HOH HOH . F 5 HOH H 78 9091 9091 HOH HOH . F 5 HOH H 79 9092 9092 HOH HOH . F 5 HOH H 80 9093 9093 HOH HOH . F 5 HOH H 81 9094 9094 HOH HOH . F 5 HOH H 82 9095 9095 HOH HOH . F 5 HOH H 83 9097 9097 HOH HOH . F 5 HOH H 84 9098 9098 HOH HOH . F 5 HOH H 85 9099 9099 HOH HOH . F 5 HOH H 86 9100 9100 HOH HOH . F 5 HOH H 87 9101 9101 HOH HOH . F 5 HOH H 88 9102 9102 HOH HOH . F 5 HOH H 89 9103 9103 HOH HOH . F 5 HOH H 90 9104 9104 HOH HOH . F 5 HOH H 91 9105 9105 HOH HOH . F 5 HOH H 92 9106 9106 HOH HOH . F 5 HOH H 93 9107 9107 HOH HOH . F 5 HOH H 94 9108 9108 HOH HOH . F 5 HOH H 95 9110 9110 HOH HOH . F 5 HOH H 96 9112 9112 HOH HOH . F 5 HOH H 97 9113 9113 HOH HOH . F 5 HOH H 98 9115 9115 HOH HOH . F 5 HOH H 99 9116 9116 HOH HOH . F 5 HOH H 100 9117 9117 HOH HOH . F 5 HOH H 101 9118 9118 HOH HOH . F 5 HOH H 102 9119 9119 HOH HOH . F 5 HOH H 103 9121 9121 HOH HOH . F 5 HOH H 104 9122 9122 HOH HOH . F 5 HOH H 105 9123 9123 HOH HOH . F 5 HOH H 106 9124 9124 HOH HOH . F 5 HOH H 107 9125 9125 HOH HOH . F 5 HOH H 108 9126 9126 HOH HOH . F 5 HOH H 109 9127 9127 HOH HOH . F 5 HOH H 110 9128 9128 HOH HOH . F 5 HOH H 111 9129 9129 HOH HOH . F 5 HOH H 112 9131 9131 HOH HOH . F 5 HOH H 113 9132 9132 HOH HOH . F 5 HOH H 114 9133 9133 HOH HOH . F 5 HOH H 115 9134 9134 HOH HOH . F 5 HOH H 116 9135 9135 HOH HOH . F 5 HOH H 117 9136 9136 HOH HOH . F 5 HOH H 118 9138 9138 HOH HOH . F 5 HOH H 119 9140 9140 HOH HOH . F 5 HOH H 120 9141 9141 HOH HOH . F 5 HOH H 121 9142 9142 HOH HOH . F 5 HOH H 122 9144 9144 HOH HOH . F 5 HOH H 123 9145 9145 HOH HOH . F 5 HOH H 124 9146 9146 HOH HOH . F 5 HOH H 125 9147 9147 HOH HOH . F 5 HOH H 126 9148 9148 HOH HOH . F 5 HOH H 127 9149 9149 HOH HOH . F 5 HOH H 128 9150 9150 HOH HOH . F 5 HOH H 129 9151 9151 HOH HOH . F 5 HOH H 130 9152 9152 HOH HOH . F 5 HOH H 131 9154 9154 HOH HOH . F 5 HOH H 132 9155 9155 HOH HOH . G 5 HOH I 1 9044 9044 HOH HOH . G 5 HOH I 2 9088 9088 HOH HOH . G 5 HOH I 3 9120 9120 HOH HOH . G 5 HOH I 4 9143 9143 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 C26 RA4 . . . D 4 18.868 -16.772 24.152 1 63.08 ? C26 RA4 5555 H 1 HETATM 2 O O25 RA4 . . . D 4 19.55 -17.157 25.096 1 70.83 ? O25 RA4 5555 H 1 HETATM 3 C C27 RA4 . . . D 4 17.464 -17.318 24.074 1 62.38 ? C27 RA4 5555 H 1 HETATM 4 C C28 RA4 . . . D 4 17.002 -18.044 25.179 1 63.92 ? C28 RA4 5555 H 1 HETATM 5 C C29 RA4 . . . D 4 15.851 -18.825 25.081 1 63.54 ? C29 RA4 5555 H 1 HETATM 6 C C30 RA4 . . . D 4 15.137 -18.896 23.881 1 66.45 ? C30 RA4 5555 H 1 HETATM 7 C C34 RA4 . . . D 4 15.602 -18.169 22.783 1 67.46 ? C34 RA4 5555 H 1 HETATM 8 C C35 RA4 . . . D 4 16.761 -17.389 22.873 1 64.6 ? C35 RA4 5555 H 1 HETATM 9 N N31 RA4 . . . D 4 14.024 -19.664 23.814 1 71.75 ? N31 RA4 5555 H 1 HETATM 10 O O32 RA4 . . . D 4 13.592 -20.376 24.946 1 76.73 ? O32 RA4 5555 H 1 HETATM 11 O O33 RA4 . . . D 4 13.379 -19.757 22.795 1 78.32 ? O33 RA4 5555 H 1 HETATM 12 N N24 RA4 . . . D 4 19.295 -15.861 23.269 1 61.41 ? N24 RA4 5555 H 1 HETATM 13 C C23 RA4 . . . D 4 19.263 -14.448 23.538 1 44.9 ? C23 RA4 5555 H 1 HETATM 14 C C18 RA4 . . . D 4 18.645 -13.608 22.443 1 38.43 ? C18 RA4 5555 H 1 HETATM 15 O O17 RA4 . . . D 4 17.598 -13.077 22.829 1 44.23 ? O17 RA4 5555 H 1 HETATM 16 C C22 RA4 . . . D 4 20.596 -13.886 24.018 1 49.99 ? C22 RA4 5555 H 1 HETATM 17 C C21 RA4 . . . D 4 20.781 -13.907 25.532 1 57.42 ? C21 RA4 5555 H 1 HETATM 18 C C19 RA4 . . . D 4 21.335 -12.57 26.056 1 25.99 ? C19 RA4 5555 H 1 HETATM 19 C C20 RA4 . . . D 4 19.491 -14.31 26.258 1 68.95 ? C20 RA4 5555 H 1 HETATM 20 N N16 RA4 . . . D 4 19.303 -13.046 21.395 1 29.63 ? N16 RA4 5555 H 1 HETATM 21 C C12 RA4 . . . D 4 18.872 -11.802 20.775 1 21.48 ? C12 RA4 5555 H 1 HETATM 22 C C11 RA4 . . . D 4 17.436 -11.857 20.319 1 38.71 ? C11 RA4 5555 H 1 HETATM 23 O O10 RA4 . . . D 4 17.064 -12.804 19.632 1 48.19 ? O10 RA4 5555 H 1 HETATM 24 C C13 RA4 . . . D 4 19.759 -11.719 19.511 1 22.44 ? C13 RA4 5555 H 1 HETATM 25 C C14 RA4 . . . D 4 20.94 -12.685 19.768 1 23.12 ? C14 RA4 5555 H 1 HETATM 26 C C15 RA4 . . . D 4 20.379 -13.761 20.735 1 29.95 ? C15 RA4 5555 H 1 HETATM 27 N N9 RA4 . . . D 4 16.793 -10.758 20.415 1 28.26 ? N9 RA4 5555 H 1 HETATM 28 C C8 RA4 . . . D 4 15.432 -10.908 19.933 1 26.3 ? C8 RA4 5555 H 1 HETATM 29 C C7 RA4 . . . D 4 14.556 -9.949 20.768 1 35.35 ? C7 RA4 5555 H 1 HETATM 30 C C6 RA4 . . . D 4 13.293 -10.693 21.213 1 38.23 ? C6 RA4 5555 H 1 HETATM 31 C C5 RA4 . . . D 4 12.584 -9.902 22.342 1 30.19 ? C5 RA4 5555 H 1 HETATM 32 N N4 RA4 . . . D 4 11.998 -10.916 23.174 1 24.08 ? N4 RA4 5555 H 1 HETATM 33 C C2 RA4 . . . D 4 11.172 -10.577 24.064 1 31 ? C2 RA4 5555 H 1 HETATM 34 N N1 RA4 . . . D 4 10.885 -9.391 24.419 1 22.24 ? N1 RA4 5555 H 1 HETATM 35 N N3 RA4 . . . D 4 10.586 -11.562 24.648 1 25.53 ? N3 RA4 5555 H 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 35 #