data_3BIV # _model_server_result.job_id ps0xnbAzepuRkOq-CwZm6w _model_server_result.datetime_utc '2024-10-19 09:25:43' _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 3biv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":999}' # _entry.id 3BIV # _exptl.entry_id 3BIV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 385.503 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclohexylamino)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 100.9 _cell.angle_gamma 90 _cell.entry_id 3BIV _cell.length_a 70.7 _cell.length_b 71.5 _cell.length_c 72.8 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BIV _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 PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 5 _struct_asym.id E _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 4 L CYS 1 1_555 B SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? disulf ? disulf2 B SG CYS 28 H CYS 42 1_555 B SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf3 B SG CYS 173 H CYS 168 1_555 B SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? disulf ? disulf4 B SG CYS 201 H CYS 191 1_555 B SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? covale ? covale1 D C1 NAG . H NAG 1 1_555 B ND2 ASN 53 H ASN 60 1_555 ? ? ? G ? ? ? ? ? ? ? ? 1.781 ? covale ? covale2 C C GLU 10 I GLU 62 1_555 C N TYS 11 I TYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 C C TYS 11 I TYS 63 1_555 C N LEU 12 I LEU 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? # _chem_comp.formula 'C21 H31 N5 O2' _chem_comp.formula_weight 385.503 _chem_comp.id 11U _chem_comp.mon_nstd_flag . _chem_comp.name (S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclohexylamino)ethanoyl)pyrrolidine-2-carboxamide _chem_comp.type peptide-like _chem_comp.pdbx_synonyms (2S)-1-[cyclohexylamino)acetyl-N-{4-[amino(imino)methyl]benzyl}pyrrolidine-2-carboxamide # 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 N1 C14 11U sing 1 n n N1 C5 11U sing 2 n n N1 C2 11U sing 3 n n C14 O32 11U doub 4 n n C14 C15 11U sing 5 n n C5 C4 11U sing 6 n n C4 C3 11U sing 7 n n C3 C2 11U sing 8 n n C2 C7 11U sing 9 n n C7 N23 11U sing 10 n n C7 O22 11U doub 11 n n N23 C24 11U sing 12 n n C24 C25 11U sing 13 n n C25 C30 11U doub 14 n y C25 C26 11U sing 15 n y C30 C29 11U sing 16 n y C29 C28 11U doub 17 n y C28 C31 11U sing 18 n n C28 C27 11U sing 19 n y C31 N49 11U doub 20 n n C31 N48 11U sing 21 n n C27 C26 11U doub 22 n y C15 N5 11U sing 23 n n N5 C16 11U sing 24 n n C16 C17 11U sing 25 n n C16 C21 11U sing 26 n n C17 C18 11U sing 27 n n C18 C19 11U sing 28 n n C19 C20 11U sing 29 n n C20 C21 11U sing 30 n n C15 H15 11U sing 31 n n C15 H15A 11U sing 32 n n C5 H5 11U sing 33 n n C5 H5A 11U sing 34 n n C4 H4 11U sing 35 n n C4 H4A 11U sing 36 n n C3 H3 11U sing 37 n n C3 H3A 11U sing 38 n n C2 H2 11U sing 39 n n N23 HN23 11U sing 40 n n C24 H24 11U sing 41 n n C24 H24A 11U sing 42 n n C30 H30 11U sing 43 n n C29 H29 11U sing 44 n n N49 HN49 11U sing 45 n n N48 HN48 11U sing 46 n n N48 HN4A 11U sing 47 n n C27 H27 11U sing 48 n n C26 H26 11U sing 49 n n N5 H20 11U sing 50 n n C16 H21 11U sing 51 n n C17 H22 11U sing 52 n n C17 H23 11U sing 53 n n C18 H241 11U sing 54 n n C18 H25 11U sing 55 n n C19 H261 11U sing 56 n n C19 H271 11U sing 57 n n C20 H28 11U sing 58 n n C20 H291 11U sing 59 n n C21 H301 11U sing 60 n n C21 H31 11U sing 61 n n # _atom_sites.entry_id 3BIV _atom_sites.fract_transf_matrix[1][1] 0.014144 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002724 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013986 _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] 0.013989 _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 NAG H 1 1 1 NAG NAG . E 5 11U H 1 999 999 11U 11U . F 6 HOH L 1 1004 1004 HOH HOH . F 6 HOH L 2 1007 1007 HOH HOH . F 6 HOH L 3 1023 1023 HOH HOH . F 6 HOH L 4 1029 1029 HOH HOH . F 6 HOH L 5 1031 1031 HOH HOH . F 6 HOH L 6 1033 1033 HOH HOH . F 6 HOH L 7 1034 1034 HOH HOH . F 6 HOH L 8 1042 1042 HOH HOH . F 6 HOH L 9 1048 1048 HOH HOH . F 6 HOH L 10 1049 1049 HOH HOH . F 6 HOH L 11 1060 1060 HOH HOH . F 6 HOH L 12 1068 1068 HOH HOH . F 6 HOH L 13 1070 1070 HOH HOH . F 6 HOH L 14 1076 1076 HOH HOH . F 6 HOH L 15 1083 1083 HOH HOH . F 6 HOH L 16 1088 1088 HOH HOH . F 6 HOH L 17 1089 1089 HOH HOH . F 6 HOH L 18 1104 1104 HOH HOH . F 6 HOH L 19 1127 1127 HOH HOH . F 6 HOH L 20 1129 1129 HOH HOH . F 6 HOH L 21 1135 1135 HOH HOH . F 6 HOH L 22 1140 1140 HOH HOH . G 6 HOH H 1 1001 1001 HOH HOH . G 6 HOH H 2 1002 1002 HOH HOH . G 6 HOH H 3 1003 1003 HOH HOH . G 6 HOH H 4 1005 1005 HOH HOH . G 6 HOH H 5 1006 1006 HOH HOH . G 6 HOH H 6 1008 1008 HOH HOH . G 6 HOH H 7 1009 1009 HOH HOH . G 6 HOH H 8 1010 1010 HOH HOH . G 6 HOH H 9 1011 1011 HOH HOH . G 6 HOH H 10 1012 1012 HOH HOH . G 6 HOH H 11 1013 1013 HOH HOH . G 6 HOH H 12 1014 1014 HOH HOH . G 6 HOH H 13 1015 1015 HOH HOH . G 6 HOH H 14 1016 1016 HOH HOH . G 6 HOH H 15 1017 1017 HOH HOH . G 6 HOH H 16 1018 1018 HOH HOH . G 6 HOH H 17 1019 1019 HOH HOH . G 6 HOH H 18 1020 1020 HOH HOH . G 6 HOH H 19 1021 1021 HOH HOH . G 6 HOH H 20 1022 1022 HOH HOH . G 6 HOH H 21 1024 1024 HOH HOH . G 6 HOH H 22 1025 1025 HOH HOH . G 6 HOH H 23 1026 1026 HOH HOH . G 6 HOH H 24 1027 1027 HOH HOH . G 6 HOH H 25 1028 1028 HOH HOH . G 6 HOH H 26 1030 1030 HOH HOH . G 6 HOH H 27 1032 1032 HOH HOH . G 6 HOH H 28 1035 1035 HOH HOH . G 6 HOH H 29 1036 1036 HOH HOH . G 6 HOH H 30 1037 1037 HOH HOH . G 6 HOH H 31 1038 1038 HOH HOH . G 6 HOH H 32 1039 1039 HOH HOH . G 6 HOH H 33 1041 1041 HOH HOH . G 6 HOH H 34 1043 1043 HOH HOH . G 6 HOH H 35 1044 1044 HOH HOH . G 6 HOH H 36 1045 1045 HOH HOH . G 6 HOH H 37 1046 1046 HOH HOH . G 6 HOH H 38 1047 1047 HOH HOH . G 6 HOH H 39 1050 1050 HOH HOH . G 6 HOH H 40 1051 1051 HOH HOH . G 6 HOH H 41 1052 1052 HOH HOH . G 6 HOH H 42 1053 1053 HOH HOH . G 6 HOH H 43 1054 1054 HOH HOH . G 6 HOH H 44 1055 1055 HOH HOH . G 6 HOH H 45 1056 1056 HOH HOH . G 6 HOH H 46 1057 1057 HOH HOH . G 6 HOH H 47 1058 1058 HOH HOH . G 6 HOH H 48 1059 1059 HOH HOH . G 6 HOH H 49 1061 1061 HOH HOH . G 6 HOH H 50 1062 1062 HOH HOH . G 6 HOH H 51 1063 1063 HOH HOH . G 6 HOH H 52 1064 1064 HOH HOH . G 6 HOH H 53 1065 1065 HOH HOH . G 6 HOH H 54 1066 1066 HOH HOH . G 6 HOH H 55 1067 1067 HOH HOH . G 6 HOH H 56 1069 1069 HOH HOH . G 6 HOH H 57 1071 1071 HOH HOH . G 6 HOH H 58 1072 1072 HOH HOH . G 6 HOH H 59 1073 1073 HOH HOH . G 6 HOH H 60 1074 1074 HOH HOH . G 6 HOH H 61 1075 1075 HOH HOH . G 6 HOH H 62 1077 1077 HOH HOH . G 6 HOH H 63 1078 1078 HOH HOH . G 6 HOH H 64 1079 1079 HOH HOH . G 6 HOH H 65 1080 1080 HOH HOH . G 6 HOH H 66 1081 1081 HOH HOH . G 6 HOH H 67 1082 1082 HOH HOH . G 6 HOH H 68 1084 1084 HOH HOH . G 6 HOH H 69 1085 1085 HOH HOH . G 6 HOH H 70 1086 1086 HOH HOH . G 6 HOH H 71 1087 1087 HOH HOH . G 6 HOH H 72 1090 1090 HOH HOH . G 6 HOH H 73 1091 1091 HOH HOH . G 6 HOH H 74 1092 1092 HOH HOH . G 6 HOH H 75 1093 1093 HOH HOH . G 6 HOH H 76 1094 1094 HOH HOH . G 6 HOH H 77 1095 1095 HOH HOH . G 6 HOH H 78 1096 1096 HOH HOH . G 6 HOH H 79 1097 1097 HOH HOH . G 6 HOH H 80 1098 1098 HOH HOH . G 6 HOH H 81 1099 1099 HOH HOH . G 6 HOH H 82 1100 1100 HOH HOH . G 6 HOH H 83 1101 1101 HOH HOH . G 6 HOH H 84 1102 1102 HOH HOH . G 6 HOH H 85 1103 1103 HOH HOH . G 6 HOH H 86 1105 1105 HOH HOH . G 6 HOH H 87 1107 1107 HOH HOH . G 6 HOH H 88 1108 1108 HOH HOH . G 6 HOH H 89 1109 1109 HOH HOH . G 6 HOH H 90 1110 1110 HOH HOH . G 6 HOH H 91 1111 1111 HOH HOH . G 6 HOH H 92 1112 1112 HOH HOH . G 6 HOH H 93 1113 1113 HOH HOH . G 6 HOH H 94 1114 1114 HOH HOH . G 6 HOH H 95 1115 1115 HOH HOH . G 6 HOH H 96 1116 1116 HOH HOH . G 6 HOH H 97 1117 1117 HOH HOH . G 6 HOH H 98 1118 1118 HOH HOH . G 6 HOH H 99 1119 1119 HOH HOH . G 6 HOH H 100 1120 1120 HOH HOH . G 6 HOH H 101 1121 1121 HOH HOH . G 6 HOH H 102 1122 1122 HOH HOH . G 6 HOH H 103 1123 1123 HOH HOH . G 6 HOH H 104 1124 1124 HOH HOH . G 6 HOH H 105 1125 1125 HOH HOH . G 6 HOH H 106 1126 1126 HOH HOH . G 6 HOH H 107 1128 1128 HOH HOH . G 6 HOH H 108 1130 1130 HOH HOH . G 6 HOH H 109 1131 1131 HOH HOH . G 6 HOH H 110 1132 1132 HOH HOH . G 6 HOH H 111 1133 1133 HOH HOH . G 6 HOH H 112 1134 1134 HOH HOH . G 6 HOH H 113 1136 1136 HOH HOH . G 6 HOH H 114 1137 1137 HOH HOH . G 6 HOH H 115 1138 1138 HOH HOH . G 6 HOH H 116 1139 1139 HOH HOH . G 6 HOH H 117 1141 1141 HOH HOH . G 6 HOH H 118 1142 1142 HOH HOH . G 6 HOH H 119 1143 1143 HOH HOH . G 6 HOH H 120 1145 1145 HOH HOH . G 6 HOH H 121 1146 1146 HOH HOH . H 6 HOH I 1 1040 1040 HOH HOH . H 6 HOH I 2 1106 1106 HOH HOH . H 6 HOH I 3 1144 1144 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 C14 11U . . . E 5 18.358 -14.065 22.383 1 27.05 ? C14 11U 999 H 1 HETATM 2 O O32 11U . . . E 5 17.42 -13.658 23.059 1 39.68 ? O32 11U 999 H 1 HETATM 3 C C15 11U . . . E 5 19.134 -15.239 22.968 1 49.33 ? C15 11U 999 H 1 HETATM 4 N N1 11U . . . E 5 18.996 -13.218 21.54 1 31.11 ? N1 11U 999 H 1 HETATM 5 C C2 11U . . . E 5 18.501 -11.896 21.147 1 26.83 ? C2 11U 999 H 1 HETATM 6 C C7 11U . . . E 5 17.094 -12.032 20.59 1 25.97 ? C7 11U 999 H 1 HETATM 7 O O22 11U . . . E 5 16.877 -12.943 19.805 1 25.52 ? O22 11U 999 H 1 HETATM 8 C C3 11U . . . E 5 19.442 -11.356 20.052 1 30.65 ? C3 11U 999 H 1 HETATM 9 C C4 11U . . . E 5 20.214 -12.61 19.57 1 39.24 ? C4 11U 999 H 1 HETATM 10 C C5 11U . . . E 5 20.283 -13.453 20.869 1 39.3 ? C5 11U 999 H 1 HETATM 11 N N23 11U . . . E 5 16.32 -10.924 20.561 1 15.71 ? N23 11U 999 H 1 HETATM 12 C C24 11U . . . E 5 15.028 -10.963 19.886 1 17.22 ? C24 11U 999 H 1 HETATM 13 C C25 11U . . . E 5 13.98 -10.888 20.965 1 18.08 ? C25 11U 999 H 1 HETATM 14 C C26 11U . . . E 5 13.498 -9.668 21.393 1 18.54 ? C26 11U 999 H 1 HETATM 15 C C27 11U . . . E 5 12.513 -9.619 22.36 1 18.44 ? C27 11U 999 H 1 HETATM 16 C C28 11U . . . E 5 12.01 -10.799 22.899 1 15.08 ? C28 11U 999 H 1 HETATM 17 C C31 11U . . . E 5 10.956 -10.787 23.938 1 21.82 ? C31 11U 999 H 1 HETATM 18 N N49 11U . . . E 5 10.314 -11.854 24.332 1 16.29 ? N49 11U 999 H 1 HETATM 19 N N48 11U . . . E 5 10.562 -9.513 24.609 1 19.75 ? N48 11U 999 H 1 HETATM 20 C C29 11U . . . E 5 12.506 -12.028 22.461 1 17.39 ? C29 11U 999 H 1 HETATM 21 C C30 11U . . . E 5 13.486 -12.064 21.496 1 17.97 ? C30 11U 999 H 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #