data_2ZDL # _model_server_result.job_id omjIDeRuNV84QiBXmt1tYg _model_server_result.datetime_utc '2024-12-02 11:05:34' _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 2zdl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 2ZDL # _exptl.entry_id 2ZDL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 372.461 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclopentyloxy)ethanoyl)pyrrolidine-2-carboxamide _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 120 _cell.entry_id 2ZDL _cell.length_a 54.5 _cell.length_b 54.5 _cell.length_c 108.6 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZDL _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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,G,H _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 7 A CYS 22 1_555 A SG CYS 137 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 25 A CYS 42 1_555 A SG CYS 41 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf3 A SG CYS 109 A CYS 128 1_555 A SG CYS 210 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 A SG CYS 116 A CYS 136 1_555 A SG CYS 183 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf5 A SG CYS 148 A CYS 168 1_555 A SG CYS 162 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 A SG CYS 173 A CYS 191 1_555 A SG CYS 197 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? # _chem_comp.formula 'C20 H28 N4 O3' _chem_comp.formula_weight 372.461 _chem_comp.id 45U _chem_comp.mon_nstd_flag . _chem_comp.name (S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclopentyloxy)ethanoyl)pyrrolidine-2-carboxamide _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 C2 C3 45U sing 1 n n C2 C1 45U sing 2 n n C24 N23 45U sing 3 n n C24 C25 45U sing 4 n n C3 C4 45U sing 5 n n N23 C7 45U sing 6 n n C26 C25 45U doub 7 n y C26 C27 45U sing 8 n y C7 C1 45U sing 9 n n C7 O22 45U doub 10 n n C25 C30 45U sing 11 n y C1 N1 45U sing 12 n n C4 N1 45U sing 13 n n C27 C28 45U doub 14 n y N1 C14 45U sing 15 n n C30 C29 45U doub 16 n y C28 C29 45U sing 17 n y C28 C21 45U sing 18 n n C14 O32 45U doub 19 n n C14 C5 45U sing 20 n n N46 C21 45U sing 21 n n C21 N47 45U doub 22 n n C5 O21 45U sing 23 n n O21 C44 45U sing 24 n n C45 C44 45U sing 25 n n C45 C47 45U sing 26 n n C44 C49 45U sing 27 n n C49 C48 45U sing 28 n n C47 C48 45U sing 29 n n C5 H5 45U sing 30 n n C5 H5A 45U sing 31 n n C44 H44 45U sing 32 n n C49 H49 45U sing 33 n n C49 H49A 45U sing 34 n n C48 H48 45U sing 35 n n C48 H48A 45U sing 36 n n C47 H47 45U sing 37 n n C47 H47A 45U sing 38 n n C45 H45 45U sing 39 n n C45 H45A 45U sing 40 n n C1 H1 45U sing 41 n n C2 H2 45U sing 42 n n C2 H2A 45U sing 43 n n C3 H3 45U sing 44 n n C3 H3A 45U sing 45 n n C4 H4 45U sing 46 n n C4 H4A 45U sing 47 n n N23 HN23 45U sing 48 n n C24 H24 45U sing 49 n n C24 H24A 45U sing 50 n n C26 H26 45U sing 51 n n C27 H27 45U sing 52 n n N46 HN46 45U sing 53 n n N46 HN4A 45U sing 54 n n N47 HN47 45U sing 55 n n C29 H29 45U sing 56 n n C30 H30 45U sing 57 n n # _atom_sites.entry_id 2ZDL _atom_sites.fract_transf_matrix[1][1] 0.018349 _atom_sites.fract_transf_matrix[1][2] 0.010594 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021187 _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] 0.009208 _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 1 601 601 CA CA . C 3 SO4 A 1 701 701 SO4 SO4 . D 4 45U A 1 501 501 45U 45U . E 5 GOL A 1 901 901 GOL GOL . F 5 GOL A 1 902 902 GOL GOL . G 5 GOL A 1 903 903 GOL GOL . H 6 HOH A 1 1001 1001 HOH HOH . H 6 HOH A 2 1002 1002 HOH HOH . H 6 HOH A 3 1003 1003 HOH HOH . H 6 HOH A 4 1004 1004 HOH HOH . H 6 HOH A 5 1005 1005 HOH HOH . H 6 HOH A 6 1006 1006 HOH HOH . H 6 HOH A 7 1007 1007 HOH HOH . H 6 HOH A 8 1008 1008 HOH HOH . H 6 HOH A 9 1009 1009 HOH HOH . H 6 HOH A 10 1010 1010 HOH HOH . H 6 HOH A 11 1011 1011 HOH HOH . H 6 HOH A 12 1012 1012 HOH HOH . H 6 HOH A 13 1013 1013 HOH HOH . H 6 HOH A 14 1014 1014 HOH HOH . H 6 HOH A 15 1015 1015 HOH HOH . H 6 HOH A 16 1016 1016 HOH HOH . H 6 HOH A 17 1017 1017 HOH HOH . H 6 HOH A 18 1018 1018 HOH HOH . H 6 HOH A 19 1019 1019 HOH HOH . H 6 HOH A 20 1020 1020 HOH HOH . H 6 HOH A 21 1021 1021 HOH HOH . H 6 HOH A 22 1022 1022 HOH HOH . H 6 HOH A 23 1023 1023 HOH HOH . H 6 HOH A 24 1024 1024 HOH HOH . H 6 HOH A 25 1025 1025 HOH HOH . H 6 HOH A 26 1026 1026 HOH HOH . H 6 HOH A 27 1027 1027 HOH HOH . H 6 HOH A 28 1028 1028 HOH HOH . H 6 HOH A 29 1029 1029 HOH HOH . H 6 HOH A 30 1030 1030 HOH HOH . H 6 HOH A 31 1031 1031 HOH HOH . H 6 HOH A 32 1032 1032 HOH HOH . H 6 HOH A 33 1033 1033 HOH HOH . H 6 HOH A 34 1034 1034 HOH HOH . H 6 HOH A 35 1035 1035 HOH HOH . H 6 HOH A 36 1036 1036 HOH HOH . H 6 HOH A 37 1037 1037 HOH HOH . H 6 HOH A 38 1038 1038 HOH HOH . H 6 HOH A 39 1039 1039 HOH HOH . H 6 HOH A 40 1040 1040 HOH HOH . H 6 HOH A 41 1041 1041 HOH HOH . H 6 HOH A 42 1042 1042 HOH HOH . H 6 HOH A 43 1043 1043 HOH HOH . H 6 HOH A 44 1044 1044 HOH HOH . H 6 HOH A 45 1045 1045 HOH HOH . H 6 HOH A 46 1046 1046 HOH HOH . H 6 HOH A 47 1047 1047 HOH HOH . H 6 HOH A 48 1048 1048 HOH HOH . H 6 HOH A 49 1049 1049 HOH HOH . H 6 HOH A 50 1050 1050 HOH HOH . H 6 HOH A 51 1051 1051 HOH HOH . H 6 HOH A 52 1052 1052 HOH HOH . H 6 HOH A 53 1053 1053 HOH HOH . H 6 HOH A 54 1054 1054 HOH HOH . H 6 HOH A 55 1055 1055 HOH HOH . H 6 HOH A 56 1056 1056 HOH HOH . H 6 HOH A 57 1057 1057 HOH HOH . H 6 HOH A 58 1058 1058 HOH HOH . H 6 HOH A 59 1059 1059 HOH HOH . H 6 HOH A 60 1060 1060 HOH HOH . H 6 HOH A 61 1061 1061 HOH HOH . H 6 HOH A 62 1062 1062 HOH HOH . H 6 HOH A 63 1063 1063 HOH HOH . H 6 HOH A 64 1064 1064 HOH HOH . H 6 HOH A 65 1065 1065 HOH HOH . H 6 HOH A 66 1066 1066 HOH HOH . H 6 HOH A 67 1067 1067 HOH HOH . H 6 HOH A 68 1068 1068 HOH HOH . H 6 HOH A 69 1069 1069 HOH HOH . H 6 HOH A 70 1070 1070 HOH HOH . H 6 HOH A 71 1071 1071 HOH HOH . H 6 HOH A 72 1072 1072 HOH HOH . H 6 HOH A 73 1073 1073 HOH HOH . H 6 HOH A 74 1074 1074 HOH HOH . H 6 HOH A 75 1075 1075 HOH HOH . H 6 HOH A 76 1076 1076 HOH HOH . H 6 HOH A 77 1077 1077 HOH HOH . H 6 HOH A 78 1078 1078 HOH HOH . H 6 HOH A 79 1079 1079 HOH HOH . H 6 HOH A 80 1080 1080 HOH HOH . H 6 HOH A 81 1081 1081 HOH HOH . H 6 HOH A 82 1082 1082 HOH HOH . H 6 HOH A 83 1083 1083 HOH HOH . H 6 HOH A 84 1084 1084 HOH HOH . H 6 HOH A 85 1085 1085 HOH HOH . H 6 HOH A 86 1086 1086 HOH HOH . H 6 HOH A 87 1087 1087 HOH HOH . H 6 HOH A 88 1088 1088 HOH HOH . H 6 HOH A 89 1089 1089 HOH HOH . H 6 HOH A 90 1090 1090 HOH HOH . H 6 HOH A 91 1091 1091 HOH HOH . H 6 HOH A 92 1092 1092 HOH HOH . H 6 HOH A 93 1093 1093 HOH HOH . H 6 HOH A 94 1094 1094 HOH HOH . H 6 HOH A 95 1095 1095 HOH HOH . H 6 HOH A 96 1096 1096 HOH HOH . H 6 HOH A 97 1097 1097 HOH HOH . H 6 HOH A 98 1098 1098 HOH HOH . H 6 HOH A 99 1099 1099 HOH HOH . H 6 HOH A 100 1100 1100 HOH HOH . H 6 HOH A 101 1101 1101 HOH HOH . H 6 HOH A 102 1102 1102 HOH HOH . H 6 HOH A 103 1103 1103 HOH HOH . H 6 HOH A 104 1104 1104 HOH HOH . H 6 HOH A 105 1105 1105 HOH HOH . H 6 HOH A 106 1106 1106 HOH HOH . H 6 HOH A 107 1107 1107 HOH HOH . H 6 HOH A 108 1108 1108 HOH HOH . H 6 HOH A 109 1109 1109 HOH HOH . H 6 HOH A 110 1110 1110 HOH HOH . H 6 HOH A 111 1111 1111 HOH HOH . H 6 HOH A 112 1112 1112 HOH HOH . H 6 HOH A 113 1113 1113 HOH HOH . H 6 HOH A 114 1114 1114 HOH HOH . H 6 HOH A 115 1115 1115 HOH HOH . H 6 HOH A 116 1116 1116 HOH HOH . H 6 HOH A 117 1117 1117 HOH HOH . H 6 HOH A 118 1118 1118 HOH HOH . H 6 HOH A 119 1119 1119 HOH HOH . H 6 HOH A 120 1120 1120 HOH HOH . H 6 HOH A 121 1121 1121 HOH HOH . H 6 HOH A 122 1122 1122 HOH HOH . H 6 HOH A 123 1123 1123 HOH HOH . H 6 HOH A 124 1124 1124 HOH HOH . H 6 HOH A 125 1125 1125 HOH HOH . H 6 HOH A 126 1126 1126 HOH HOH . H 6 HOH A 127 1127 1127 HOH HOH . H 6 HOH A 128 1128 1128 HOH HOH . H 6 HOH A 129 1129 1129 HOH HOH . H 6 HOH A 130 1130 1130 HOH HOH . H 6 HOH A 131 1131 1131 HOH HOH . H 6 HOH A 132 1132 1132 HOH HOH . H 6 HOH A 133 1133 1133 HOH HOH . H 6 HOH A 134 1134 1134 HOH HOH . H 6 HOH A 135 1135 1135 HOH HOH . H 6 HOH A 136 1136 1136 HOH HOH . H 6 HOH A 137 1137 1137 HOH HOH . H 6 HOH A 138 1138 1138 HOH HOH . H 6 HOH A 139 1139 1139 HOH HOH . H 6 HOH A 140 1140 1140 HOH HOH . H 6 HOH A 141 1141 1141 HOH HOH . H 6 HOH A 142 1142 1142 HOH HOH . H 6 HOH A 143 1143 1143 HOH HOH . H 6 HOH A 144 1144 1144 HOH HOH . H 6 HOH A 145 1145 1145 HOH HOH . H 6 HOH A 146 1146 1146 HOH HOH . H 6 HOH A 147 1147 1147 HOH HOH . H 6 HOH A 148 1148 1148 HOH HOH . H 6 HOH A 149 1149 1149 HOH HOH . H 6 HOH A 150 1150 1150 HOH HOH . H 6 HOH A 151 1151 1151 HOH HOH . H 6 HOH A 152 1152 1152 HOH HOH . H 6 HOH A 153 1153 1153 HOH HOH . H 6 HOH A 154 1154 1154 HOH HOH . H 6 HOH A 155 1155 1155 HOH HOH . H 6 HOH A 156 1156 1156 HOH HOH . H 6 HOH A 157 1157 1157 HOH HOH . H 6 HOH A 158 1158 1158 HOH HOH . H 6 HOH A 159 1159 1159 HOH HOH . H 6 HOH A 160 1160 1160 HOH HOH . H 6 HOH A 161 1161 1161 HOH HOH . H 6 HOH A 162 1162 1162 HOH HOH . H 6 HOH A 163 1163 1163 HOH HOH . H 6 HOH A 164 1164 1164 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 O O32 45U . . . D 4 -27.114 1.25 17.312 1 18.38 ? O32 45U 501 A 1 HETATM 2 C C14 45U . . . D 4 -28.289 1.268 16.975 1 25.87 ? C14 45U 501 A 1 HETATM 3 C C5 45U . . . D 4 -29.201 1.524 18.166 1 36.13 ? C5 45U 501 A 1 HETATM 4 O O21 45U . . . D 4 -30.21 0.579 18.295 1 38.93 ? O21 45U 501 A 1 HETATM 5 C C44 45U . . . D 4 -30.421 -0.513 19.154 1 36.05 ? C44 45U 501 A 1 HETATM 6 C C49 45U . . . D 4 -29.046 -1.222 19.219 1 32.98 ? C49 45U 501 A 1 HETATM 7 C C48 45U . . . D 4 -29.277 -2.699 19.53 1 33.29 ? C48 45U 501 A 1 HETATM 8 C C47 45U . . . D 4 -30.717 -2.998 19.228 1 24.38 ? C47 45U 501 A 1 HETATM 9 C C45 45U . . . D 4 -31.239 -1.715 18.513 1 30.8 ? C45 45U 501 A 1 HETATM 10 N N1 45U . . . D 4 -28.6 1.076 15.68 1 18.73 ? N1 45U 501 A 1 HETATM 11 C C1 45U . . . D 4 -27.631 0.537 14.742 1 14.87 ? C1 45U 501 A 1 HETATM 12 C C7 45U . . . D 4 -26.588 1.607 14.567 1 13.08 ? C7 45U 501 A 1 HETATM 13 O O22 45U . . . D 4 -26.765 2.784 14.801 1 21.69 ? O22 45U 501 A 1 HETATM 14 C C2 45U . . . D 4 -28.442 0.419 13.456 1 19.5 ? C2 45U 501 A 1 HETATM 15 C C3 45U . . . D 4 -29.81 1.051 13.661 1 19.51 ? C3 45U 501 A 1 HETATM 16 C C4 45U . . . D 4 -30.045 1.076 15.16 1 16.89 ? C4 45U 501 A 1 HETATM 17 N N23 45U . . . D 4 -25.448 1.195 14.089 1 11.96 ? N23 45U 501 A 1 HETATM 18 C C24 45U . . . D 4 -24.367 2.032 13.562 1 16.16 ? C24 45U 501 A 1 HETATM 19 C C25 45U . . . D 4 -23.271 1.866 14.635 1 16.01 ? C25 45U 501 A 1 HETATM 20 C C30 45U . . . D 4 -23.358 2.161 15.991 1 11.87 ? C30 45U 501 A 1 HETATM 21 C C29 45U . . . D 4 -22.287 1.978 16.934 1 14.21 ? C29 45U 501 A 1 HETATM 22 C C28 45U . . . D 4 -21.035 1.497 16.672 1 14.39 ? C28 45U 501 A 1 HETATM 23 C C21 45U . . . D 4 -19.877 1.289 17.645 1 14.21 ? C21 45U 501 A 1 HETATM 24 N N47 45U . . . D 4 -19.714 2.05 18.72 1 19.02 ? N47 45U 501 A 1 HETATM 25 N N46 45U . . . D 4 -19.061 0.287 17.318 1 11.19 ? N46 45U 501 A 1 HETATM 26 C C27 45U . . . D 4 -20.968 1.207 15.315 1 20.59 ? C27 45U 501 A 1 HETATM 27 C C26 45U . . . D 4 -22.006 1.378 14.365 1 14.58 ? C26 45U 501 A 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 484 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #