data_4EKE # _model_server_result.job_id 048HhBH46eAEgaUDBTIbzw _model_server_result.datetime_utc '2024-11-21 23:18:15' _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 4eke # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":901}' # _entry.id 4EKE # _exptl.entry_id 4EKE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 368.382 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-(beta-D-glucopyranosyl)-6-pentylfuro[2,3-d]pyrimidin-2(3H)-one _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 4EKE _cell.length_a 128.474 _cell.length_b 128.474 _cell.length_c 116.382 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4EKE _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 116.382 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 covale ? covale1 A C MET 668 A MET 679 1_555 A N LLP 669 A LLP 680 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale2 A C LLP 669 A LLP 680 1_555 A N PHE 670 A PHE 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? # _chem_comp.formula 'C17 H24 N2 O7' _chem_comp.formula_weight 368.382 _chem_comp.id D1I _chem_comp.mon_nstd_flag . _chem_comp.name 3-(beta-D-glucopyranosyl)-6-pentylfuro[2,3-d]pyrimidin-2(3H)-one _chem_comp.type non-polymer _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 O3' C3' D1I sing 83 n n O4' C4' D1I sing 84 n n C3' C4' D1I sing 85 n n C3' C2' D1I sing 86 n n C4' C5' D1I sing 87 n n O2' C2' D1I sing 88 n n C2' C1' D1I sing 89 n n O6' C6' D1I sing 90 n n C5' C6' D1I sing 91 n n C5' O5' D1I sing 92 n n C1' O5' D1I sing 93 n n C1' N1 D1I sing 94 n n C6 N1 D1I sing 95 n n C6 C5 D1I doub 96 n n N1 C2 D1I sing 97 n n C5 C7 D1I sing 98 n n C5 C4 D1I sing 99 n n C2 O2 D1I doub 100 n n C2 N3 D1I sing 101 n n C7 C8 D1I doub 102 n n N3 C4 D1I doub 103 n n C4 O5 D1I sing 104 n n C8 O5 D1I sing 105 n n C8 C9 D1I sing 106 n n C9 C10 D1I sing 107 n n C10 C11 D1I sing 108 n n C11 C12 D1I sing 109 n n C12 C13 D1I sing 110 n n C6 H6 D1I sing 111 n n C7 H7 D1I sing 112 n n C9 H19 D1I sing 113 n n C9 H29 D1I sing 114 n n C1' H1' D1I sing 115 n n C10 H110 D1I sing 116 n n C10 H210 D1I sing 117 n n C11 H111 D1I sing 118 n n C11 H211 D1I sing 119 n n C12 H112 D1I sing 120 n n C12 H212 D1I sing 121 n n C13 H113 D1I sing 122 n n C13 H213 D1I sing 123 n n C13 H313 D1I sing 124 n n C2' H2' D1I sing 125 n n O2' HO2' D1I sing 126 n n C3' H3' D1I sing 127 n n O3' HO3' D1I sing 128 n n C4' H4' D1I sing 129 n n O4' HO4' D1I sing 130 n n C5' H5' D1I sing 131 n n C6' H16' D1I sing 132 n n C6' H26' D1I sing 133 n n O6' HO6' D1I sing 134 n n # _atom_sites.entry_id 4EKE _atom_sites.fract_transf_matrix[1][1] 0.007784 _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] 0.007784 _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] 0.008592 _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 D1I A 1 901 1 D1I D1I . C 3 HOH A 1 1001 1 HOH HOH . C 3 HOH A 2 1002 2 HOH HOH . C 3 HOH A 3 1003 3 HOH HOH . C 3 HOH A 4 1004 4 HOH HOH . C 3 HOH A 5 1005 5 HOH HOH . C 3 HOH A 6 1006 6 HOH HOH . C 3 HOH A 7 1007 7 HOH HOH . C 3 HOH A 8 1008 8 HOH HOH . C 3 HOH A 9 1009 9 HOH HOH . C 3 HOH A 10 1010 10 HOH HOH . C 3 HOH A 11 1011 11 HOH HOH . C 3 HOH A 12 1012 12 HOH HOH . C 3 HOH A 13 1013 13 HOH HOH . C 3 HOH A 14 1014 14 HOH HOH . C 3 HOH A 15 1015 15 HOH HOH . C 3 HOH A 16 1016 16 HOH HOH . C 3 HOH A 17 1017 17 HOH HOH . C 3 HOH A 18 1018 18 HOH HOH . C 3 HOH A 19 1019 19 HOH HOH . C 3 HOH A 20 1020 20 HOH HOH . C 3 HOH A 21 1021 21 HOH HOH . C 3 HOH A 22 1022 22 HOH HOH . C 3 HOH A 23 1023 23 HOH HOH . C 3 HOH A 24 1024 24 HOH HOH . C 3 HOH A 25 1025 25 HOH HOH . C 3 HOH A 26 1026 26 HOH HOH . C 3 HOH A 27 1027 27 HOH HOH . C 3 HOH A 28 1028 28 HOH HOH . C 3 HOH A 29 1029 29 HOH HOH . C 3 HOH A 30 1030 30 HOH HOH . C 3 HOH A 31 1031 31 HOH HOH . C 3 HOH A 32 1032 32 HOH HOH . C 3 HOH A 33 1033 33 HOH HOH . C 3 HOH A 34 1034 34 HOH HOH . C 3 HOH A 35 1035 35 HOH HOH . C 3 HOH A 36 1036 36 HOH HOH . C 3 HOH A 37 1037 37 HOH HOH . C 3 HOH A 38 1038 38 HOH HOH . C 3 HOH A 39 1039 39 HOH HOH . C 3 HOH A 40 1040 40 HOH HOH . C 3 HOH A 41 1041 41 HOH HOH . C 3 HOH A 42 1042 42 HOH HOH . C 3 HOH A 43 1043 43 HOH HOH . C 3 HOH A 44 1044 44 HOH HOH . C 3 HOH A 45 1045 45 HOH HOH . C 3 HOH A 46 1046 46 HOH HOH . C 3 HOH A 47 1047 47 HOH HOH . C 3 HOH A 48 1048 48 HOH HOH . C 3 HOH A 49 1049 49 HOH HOH . C 3 HOH A 50 1050 50 HOH HOH . C 3 HOH A 51 1051 51 HOH HOH . C 3 HOH A 52 1052 52 HOH HOH . C 3 HOH A 53 1053 53 HOH HOH . C 3 HOH A 54 1054 54 HOH HOH . C 3 HOH A 55 1055 55 HOH HOH . C 3 HOH A 56 1056 56 HOH HOH . C 3 HOH A 57 1057 57 HOH HOH . C 3 HOH A 58 1058 58 HOH HOH . C 3 HOH A 59 1059 59 HOH HOH . C 3 HOH A 60 1060 60 HOH HOH . C 3 HOH A 61 1061 61 HOH HOH . C 3 HOH A 62 1062 62 HOH HOH . C 3 HOH A 63 1063 63 HOH HOH . C 3 HOH A 64 1064 64 HOH HOH . C 3 HOH A 65 1065 65 HOH HOH . C 3 HOH A 66 1066 66 HOH HOH . C 3 HOH A 67 1067 67 HOH HOH . C 3 HOH A 68 1068 68 HOH HOH . C 3 HOH A 69 1069 69 HOH HOH . C 3 HOH A 70 1070 70 HOH HOH . C 3 HOH A 71 1071 71 HOH HOH . C 3 HOH A 72 1072 72 HOH HOH . C 3 HOH A 73 1073 73 HOH HOH . C 3 HOH A 74 1074 74 HOH HOH . C 3 HOH A 75 1075 75 HOH HOH . C 3 HOH A 76 1076 76 HOH HOH . C 3 HOH A 77 1077 77 HOH HOH . C 3 HOH A 78 1078 78 HOH HOH . C 3 HOH A 79 1079 79 HOH HOH . C 3 HOH A 80 1080 80 HOH HOH . C 3 HOH A 81 1081 81 HOH HOH . C 3 HOH A 82 1082 82 HOH HOH . C 3 HOH A 83 1083 83 HOH HOH . C 3 HOH A 84 1084 84 HOH HOH . C 3 HOH A 85 1085 85 HOH HOH . C 3 HOH A 86 1086 86 HOH HOH . C 3 HOH A 87 1087 87 HOH HOH . C 3 HOH A 88 1088 88 HOH HOH . C 3 HOH A 89 1089 89 HOH HOH . C 3 HOH A 90 1090 90 HOH HOH . C 3 HOH A 91 1091 91 HOH HOH . C 3 HOH A 92 1092 92 HOH HOH . C 3 HOH A 93 1093 93 HOH HOH . C 3 HOH A 94 1094 94 HOH HOH . C 3 HOH A 95 1095 95 HOH HOH . C 3 HOH A 96 1096 96 HOH HOH . C 3 HOH A 97 1097 97 HOH HOH . C 3 HOH A 98 1098 98 HOH HOH . C 3 HOH A 99 1099 99 HOH HOH . C 3 HOH A 100 1100 100 HOH HOH . C 3 HOH A 101 1101 101 HOH HOH . C 3 HOH A 102 1102 102 HOH HOH . C 3 HOH A 103 1103 103 HOH HOH . C 3 HOH A 104 1104 104 HOH HOH . C 3 HOH A 105 1105 105 HOH HOH . C 3 HOH A 106 1106 106 HOH HOH . C 3 HOH A 107 1107 107 HOH HOH . C 3 HOH A 108 1108 108 HOH HOH . C 3 HOH A 109 1109 109 HOH HOH . C 3 HOH A 110 1110 110 HOH HOH . C 3 HOH A 111 1111 111 HOH HOH . C 3 HOH A 112 1112 112 HOH HOH . C 3 HOH A 113 1113 113 HOH HOH . C 3 HOH A 114 1114 114 HOH HOH . C 3 HOH A 115 1115 115 HOH HOH . C 3 HOH A 116 1116 116 HOH HOH . C 3 HOH A 117 1117 117 HOH HOH . C 3 HOH A 118 1118 118 HOH HOH . C 3 HOH A 119 1119 119 HOH HOH . C 3 HOH A 120 1120 120 HOH HOH . C 3 HOH A 121 1121 121 HOH HOH . C 3 HOH A 122 1122 122 HOH HOH . C 3 HOH A 123 1123 123 HOH HOH . C 3 HOH A 124 1124 124 HOH HOH . C 3 HOH A 125 1125 125 HOH HOH . C 3 HOH A 126 1126 126 HOH HOH . C 3 HOH A 127 1127 127 HOH HOH . C 3 HOH A 128 1128 128 HOH HOH . C 3 HOH A 129 1129 129 HOH HOH . C 3 HOH A 130 1130 130 HOH HOH . C 3 HOH A 131 1131 131 HOH HOH . C 3 HOH A 132 1132 132 HOH HOH . C 3 HOH A 133 1133 133 HOH HOH . C 3 HOH A 134 1134 134 HOH HOH . C 3 HOH A 135 1135 135 HOH HOH . C 3 HOH A 136 1136 136 HOH HOH . C 3 HOH A 137 1137 137 HOH HOH . C 3 HOH A 138 1138 138 HOH HOH . C 3 HOH A 139 1139 139 HOH HOH . C 3 HOH A 140 1140 140 HOH HOH . C 3 HOH A 141 1141 141 HOH HOH . C 3 HOH A 142 1142 142 HOH HOH . C 3 HOH A 143 1143 143 HOH HOH . C 3 HOH A 144 1144 144 HOH HOH . C 3 HOH A 145 1145 145 HOH HOH . C 3 HOH A 146 1146 146 HOH HOH . C 3 HOH A 147 1147 147 HOH HOH . C 3 HOH A 148 1148 148 HOH HOH . C 3 HOH A 149 1149 149 HOH HOH . C 3 HOH A 150 1150 150 HOH HOH . C 3 HOH A 151 1151 151 HOH HOH . C 3 HOH A 152 1152 152 HOH HOH . C 3 HOH A 153 1153 153 HOH HOH . C 3 HOH A 154 1154 154 HOH HOH . C 3 HOH A 155 1155 155 HOH HOH . C 3 HOH A 156 1156 156 HOH HOH . C 3 HOH A 157 1157 157 HOH HOH . C 3 HOH A 158 1158 158 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 N N1 D1I . . . B 2 34.02 23.67 28.735 1 25.72 ? N1 D1I 901 A 1 HETATM 2 C C2 D1I . . . B 2 33.291 24.198 29.745 1 26.95 ? C2 D1I 901 A 1 HETATM 3 O O2 D1I . . . B 2 32.063 24.148 29.799 1 25.63 ? O2 D1I 901 A 1 HETATM 4 N N3 D1I . . . B 2 33.899 24.95 30.717 1 31.09 ? N3 D1I 901 A 1 HETATM 5 C C4 D1I . . . B 2 35.331 24.825 30.792 1 33.01 ? C4 D1I 901 A 1 HETATM 6 C C5 D1I . . . B 2 36.044 24.457 29.661 1 33.82 ? C5 D1I 901 A 1 HETATM 7 O O5 D1I . . . B 2 36.038 25.722 31.579 1 35.84 ? O5 D1I 901 A 1 HETATM 8 C C6 D1I . . . B 2 35.438 23.752 28.704 1 29.4 ? C6 D1I 901 A 1 HETATM 9 C C7 D1I . . . B 2 37.309 24.7 30.011 1 38.21 ? C7 D1I 901 A 1 HETATM 10 C C8 D1I . . . B 2 37.312 25.449 31.154 1 41.79 ? C8 D1I 901 A 1 HETATM 11 C C9 D1I . . . B 2 38.627 25.982 31.818 1 45.52 ? C9 D1I 901 A 1 HETATM 12 C C1' D1I . . . B 2 33.275 22.882 27.756 1 22.7 ? C1' D1I 901 A 1 HETATM 13 C C10 D1I . . . B 2 38.529 27.506 32.24 1 47.71 ? C10 D1I 901 A 1 HETATM 14 C C11 D1I . . . B 2 38.675 27.741 33.775 1 48.11 ? C11 D1I 901 A 1 HETATM 15 C C12 D1I . . . B 2 39.698 26.796 34.458 1 47.31 ? C12 D1I 901 A 1 HETATM 16 C C13 D1I . . . B 2 40.08 27.338 35.849 1 50.22 ? C13 D1I 901 A 1 HETATM 17 C C2' D1I . . . B 2 33.69 23.039 26.312 1 21.82 ? C2' D1I 901 A 1 HETATM 18 O O2' D1I . . . B 2 33.922 24.418 25.997 1 22.03 ? O2' D1I 901 A 1 HETATM 19 C C3' D1I . . . B 2 32.559 22.42 25.465 1 18.69 ? C3' D1I 901 A 1 HETATM 20 O O3' D1I . . . B 2 32.911 22.373 24.109 1 15.27 ? O3' D1I 901 A 1 HETATM 21 C C4' D1I . . . B 2 32.322 20.994 25.917 1 19.99 ? C4' D1I 901 A 1 HETATM 22 O O4' D1I . . . B 2 31.198 20.46 25.205 1 25.61 ? O4' D1I 901 A 1 HETATM 23 C C5' D1I . . . B 2 32.125 20.866 27.444 1 18.46 ? C5' D1I 901 A 1 HETATM 24 O O5' D1I . . . B 2 33.219 21.464 28.143 1 19.77 ? O5' D1I 901 A 1 HETATM 25 C C6' D1I . . . B 2 32.158 19.405 27.875 1 15.51 ? C6' D1I 901 A 1 HETATM 26 O O6' D1I . . . B 2 33.2 18.687 27.247 1 15.45 ? O6' D1I 901 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #