data_2HR6 # _model_server_result.job_id NhxhEBJrtiSJp30jaSIBjw _model_server_result.datetime_utc '2024-11-05 04:38:30' _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 2hr6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":777}' # _entry.id 2HR6 # _exptl.entry_id 2HR6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 388.162 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "DEOXYURIDINE-5'-DIPHOSPHATE" _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 2HR6 _cell.length_a 75.049 _cell.length_b 75.049 _cell.length_c 99.936 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2HR6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 37.5245 64.994341 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -37.5245 64.994341 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 metalc ? metalc1 C O1B DUD . A DUD 777 1_555 B MN MN . A MN 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc2 C O1A DUD . A DUD 777 1_555 B MN MN . A MN 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc3 B MN MN . A MN 997 1_555 E O HOH . A HOH 1021 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc4 B MN MN . A MN 997 1_555 E O HOH . A HOH 1025 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc5 B MN MN . A MN 997 1_555 E O HOH . A HOH 1044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc6 B MN MN . A MN 997 1_555 E O HOH . A HOH 1133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? # _chem_comp.formula 'C9 H14 N2 O11 P2' _chem_comp.formula_weight 388.162 _chem_comp.id DUD _chem_comp.mon_nstd_flag . _chem_comp.name "DEOXYURIDINE-5'-DIPHOSPHATE" _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 N1 C2 DUD sing 83 n n N1 C6 DUD sing 84 n n N1 C1' DUD sing 85 n n C2 N3 DUD sing 86 n n C2 O2 DUD doub 87 n n N3 C4 DUD sing 88 n n N3 HN3 DUD sing 89 n n C4 C5 DUD sing 90 n n C4 O4 DUD doub 91 n n C5 C6 DUD doub 92 n n C5 H5 DUD sing 93 n n C6 H6 DUD sing 94 n n C1' C2' DUD sing 95 n n C1' O4' DUD sing 96 n n C1' H1' DUD sing 97 n n C2' C3' DUD sing 98 n n C2' "H2'1" DUD sing 99 n n C2' "H2'2" DUD sing 100 n n C3' C4' DUD sing 101 n n C3' O3' DUD sing 102 n n C3' H3' DUD sing 103 n n C4' O4' DUD sing 104 n n C4' C5' DUD sing 105 n n C4' H4' DUD sing 106 n n O3' HO3' DUD sing 107 n n C5' O5' DUD sing 108 n n C5' "H5'1" DUD sing 109 n n C5' "H5'2" DUD sing 110 n n O5' PA DUD sing 111 n n PA O1A DUD doub 112 n n PA O2A DUD sing 113 n n PA O3A DUD sing 114 n n O2A HOA2 DUD sing 115 n n O3A PB DUD sing 116 n n PB O1B DUD doub 117 n n PB O2B DUD sing 118 n n PB O3B DUD sing 119 n n O2B HOB2 DUD sing 120 n n O3B HOB3 DUD sing 121 n n # _atom_sites.entry_id 2HR6 _atom_sites.fract_transf_matrix[1][1] 0.013325 _atom_sites.fract_transf_matrix[1][2] 0.007693 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015386 _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] 0.010006 _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 MN A 1 997 997 MN MN . C 3 DUD A 1 777 777 DUD DUD . D 4 EDO A 1 301 1 EDO EDO . E 5 HOH A 1 998 1 HOH HOH . E 5 HOH A 2 999 2 HOH HOH . E 5 HOH A 3 1000 3 HOH HOH . E 5 HOH A 4 1001 4 HOH HOH . E 5 HOH A 5 1002 5 HOH HOH . E 5 HOH A 6 1003 6 HOH HOH . E 5 HOH A 7 1004 7 HOH HOH . E 5 HOH A 8 1005 8 HOH HOH . E 5 HOH A 9 1006 9 HOH HOH . E 5 HOH A 10 1007 10 HOH HOH . E 5 HOH A 11 1008 11 HOH HOH . E 5 HOH A 12 1009 12 HOH HOH . E 5 HOH A 13 1010 13 HOH HOH . E 5 HOH A 14 1011 14 HOH HOH . E 5 HOH A 15 1012 15 HOH HOH . E 5 HOH A 16 1013 16 HOH HOH . E 5 HOH A 17 1014 18 HOH HOH . E 5 HOH A 18 1015 19 HOH HOH . E 5 HOH A 19 1016 20 HOH HOH . E 5 HOH A 20 1017 21 HOH HOH . E 5 HOH A 21 1018 22 HOH HOH . E 5 HOH A 22 1019 23 HOH HOH . E 5 HOH A 23 1020 24 HOH HOH . E 5 HOH A 24 1021 25 HOH HOH . E 5 HOH A 25 1022 26 HOH HOH . E 5 HOH A 26 1023 27 HOH HOH . E 5 HOH A 27 1024 28 HOH HOH . E 5 HOH A 28 1025 29 HOH HOH . E 5 HOH A 29 1026 30 HOH HOH . E 5 HOH A 30 1027 31 HOH HOH . E 5 HOH A 31 1028 32 HOH HOH . E 5 HOH A 32 1029 33 HOH HOH . E 5 HOH A 33 1030 34 HOH HOH . E 5 HOH A 34 1031 35 HOH HOH . E 5 HOH A 35 1032 36 HOH HOH . E 5 HOH A 36 1033 37 HOH HOH . E 5 HOH A 37 1034 38 HOH HOH . E 5 HOH A 38 1035 39 HOH HOH . E 5 HOH A 39 1036 40 HOH HOH . E 5 HOH A 40 1037 41 HOH HOH . E 5 HOH A 41 1038 42 HOH HOH . E 5 HOH A 42 1039 43 HOH HOH . E 5 HOH A 43 1040 44 HOH HOH . E 5 HOH A 44 1041 45 HOH HOH . E 5 HOH A 45 1042 46 HOH HOH . E 5 HOH A 46 1043 47 HOH HOH . E 5 HOH A 47 1044 48 HOH HOH . E 5 HOH A 48 1045 49 HOH HOH . E 5 HOH A 49 1046 50 HOH HOH . E 5 HOH A 50 1047 52 HOH HOH . E 5 HOH A 51 1048 53 HOH HOH . E 5 HOH A 52 1049 54 HOH HOH . E 5 HOH A 53 1050 55 HOH HOH . E 5 HOH A 54 1051 56 HOH HOH . E 5 HOH A 55 1052 57 HOH HOH . E 5 HOH A 56 1053 58 HOH HOH . E 5 HOH A 57 1054 59 HOH HOH . E 5 HOH A 58 1055 60 HOH HOH . E 5 HOH A 59 1056 61 HOH HOH . E 5 HOH A 60 1057 62 HOH HOH . E 5 HOH A 61 1058 63 HOH HOH . E 5 HOH A 62 1059 64 HOH HOH . E 5 HOH A 63 1060 65 HOH HOH . E 5 HOH A 64 1061 66 HOH HOH . E 5 HOH A 65 1062 68 HOH HOH . E 5 HOH A 66 1063 69 HOH HOH . E 5 HOH A 67 1064 70 HOH HOH . E 5 HOH A 68 1065 72 HOH HOH . E 5 HOH A 69 1066 75 HOH HOH . E 5 HOH A 70 1067 76 HOH HOH . E 5 HOH A 71 1068 77 HOH HOH . E 5 HOH A 72 1069 78 HOH HOH . E 5 HOH A 73 1070 79 HOH HOH . E 5 HOH A 74 1071 80 HOH HOH . E 5 HOH A 75 1072 81 HOH HOH . E 5 HOH A 76 1073 82 HOH HOH . E 5 HOH A 77 1074 83 HOH HOH . E 5 HOH A 78 1075 85 HOH HOH . E 5 HOH A 79 1076 86 HOH HOH . E 5 HOH A 80 1077 87 HOH HOH . E 5 HOH A 81 1078 88 HOH HOH . E 5 HOH A 82 1079 89 HOH HOH . E 5 HOH A 83 1080 90 HOH HOH . E 5 HOH A 84 1081 91 HOH HOH . E 5 HOH A 85 1082 93 HOH HOH . E 5 HOH A 86 1083 94 HOH HOH . E 5 HOH A 87 1084 95 HOH HOH . E 5 HOH A 88 1085 96 HOH HOH . E 5 HOH A 89 1086 97 HOH HOH . E 5 HOH A 90 1087 99 HOH HOH . E 5 HOH A 91 1088 101 HOH HOH . E 5 HOH A 92 1089 102 HOH HOH . E 5 HOH A 93 1090 103 HOH HOH . E 5 HOH A 94 1091 104 HOH HOH . E 5 HOH A 95 1092 106 HOH HOH . E 5 HOH A 96 1093 107 HOH HOH . E 5 HOH A 97 1094 109 HOH HOH . E 5 HOH A 98 1095 110 HOH HOH . E 5 HOH A 99 1096 111 HOH HOH . E 5 HOH A 100 1097 112 HOH HOH . E 5 HOH A 101 1098 113 HOH HOH . E 5 HOH A 102 1099 114 HOH HOH . E 5 HOH A 103 1100 115 HOH HOH . E 5 HOH A 104 1101 117 HOH HOH . E 5 HOH A 105 1102 118 HOH HOH . E 5 HOH A 106 1103 119 HOH HOH . E 5 HOH A 107 1104 123 HOH HOH . E 5 HOH A 108 1105 125 HOH HOH . E 5 HOH A 109 1106 127 HOH HOH . E 5 HOH A 110 1107 128 HOH HOH . E 5 HOH A 111 1108 130 HOH HOH . E 5 HOH A 112 1109 132 HOH HOH . E 5 HOH A 113 1110 134 HOH HOH . E 5 HOH A 114 1111 137 HOH HOH . E 5 HOH A 115 1112 138 HOH HOH . E 5 HOH A 116 1113 139 HOH HOH . E 5 HOH A 117 1114 141 HOH HOH . E 5 HOH A 118 1115 146 HOH HOH . E 5 HOH A 119 1116 147 HOH HOH . E 5 HOH A 120 1117 149 HOH HOH . E 5 HOH A 121 1118 150 HOH HOH . E 5 HOH A 122 1119 151 HOH HOH . E 5 HOH A 123 1120 154 HOH HOH . E 5 HOH A 124 1121 155 HOH HOH . E 5 HOH A 125 1122 156 HOH HOH . E 5 HOH A 126 1123 159 HOH HOH . E 5 HOH A 127 1124 160 HOH HOH . E 5 HOH A 128 1125 161 HOH HOH . E 5 HOH A 129 1126 162 HOH HOH . E 5 HOH A 130 1127 163 HOH HOH . E 5 HOH A 131 1128 167 HOH HOH . E 5 HOH A 132 1129 170 HOH HOH . E 5 HOH A 133 1130 172 HOH HOH . E 5 HOH A 134 1131 175 HOH HOH . E 5 HOH A 135 1132 176 HOH HOH . E 5 HOH A 136 1133 177 HOH HOH . E 5 HOH A 137 1134 178 HOH HOH . E 5 HOH A 138 1135 179 HOH HOH . E 5 HOH A 139 1136 180 HOH HOH . E 5 HOH A 140 1137 183 HOH HOH . E 5 HOH A 141 1138 187 HOH HOH . E 5 HOH A 142 1139 188 HOH HOH . E 5 HOH A 143 1140 189 HOH HOH . E 5 HOH A 144 1141 191 HOH HOH . E 5 HOH A 145 1142 193 HOH HOH . E 5 HOH A 146 1143 197 HOH HOH . E 5 HOH A 147 1144 198 HOH HOH . E 5 HOH A 148 1145 199 HOH HOH . E 5 HOH A 149 1146 200 HOH HOH . E 5 HOH A 150 1147 202 HOH HOH . E 5 HOH A 151 1148 203 HOH HOH . E 5 HOH A 152 1149 205 HOH HOH . E 5 HOH A 153 1150 206 HOH HOH . E 5 HOH A 154 1151 207 HOH HOH . E 5 HOH A 155 1152 208 HOH HOH . E 5 HOH A 156 1153 209 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 DUD . . . C 3 -7.58 31.432 4.614 1 20.14 ? N1 DUD 777 A 1 HETATM 2 C C2 DUD . . . C 3 -6.568 30.659 4.138 1 25.56 ? C2 DUD 777 A 1 HETATM 3 N N3 DUD . . . C 3 -5.567 31.279 3.409 1 22.2 ? N3 DUD 777 A 1 HETATM 4 C C4 DUD . . . C 3 -5.525 32.63 3.113 1 24.64 ? C4 DUD 777 A 1 HETATM 5 C C5 DUD . . . C 3 -6.549 33.452 3.618 1 23.56 ? C5 DUD 777 A 1 HETATM 6 C C6 DUD . . . C 3 -7.566 32.826 4.343 1 20.98 ? C6 DUD 777 A 1 HETATM 7 O O2 DUD . . . C 3 -6.524 29.442 4.327 1 23.04 ? O2 DUD 777 A 1 HETATM 8 O O4 DUD . . . C 3 -4.558 33.055 2.461 1 22.98 ? O4 DUD 777 A 1 HETATM 9 C C1' DUD . . . C 3 -8.664 30.865 5.415 1 23.64 ? C1' DUD 777 A 1 HETATM 10 C C2' DUD . . . C 3 -8.521 31.308 6.878 1 20.98 ? C2' DUD 777 A 1 HETATM 11 C C3' DUD . . . C 3 -9.606 32.365 7.055 1 21.77 ? C3' DUD 777 A 1 HETATM 12 C C4' DUD . . . C 3 -10.637 31.957 6 1 23.27 ? C4' DUD 777 A 1 HETATM 13 O O4' DUD . . . C 3 -9.877 31.379 4.917 1 22.68 ? O4' DUD 777 A 1 HETATM 14 O O3' DUD . . . C 3 -10.079 32.356 8.389 1 24.33 ? O3' DUD 777 A 1 HETATM 15 C C5' DUD . . . C 3 -11.491 33.107 5.488 1 25.21 ? C5' DUD 777 A 1 HETATM 16 O O5' DUD . . . C 3 -10.67 34.155 4.976 1 27.24 ? O5' DUD 777 A 1 HETATM 17 P PA DUD . . . C 3 -11.359 35.557 4.544 1 29.14 ? PA DUD 777 A 1 HETATM 18 O O1A DUD . . . C 3 -12.39 35.957 5.587 1 24.54 ? O1A DUD 777 A 1 HETATM 19 O O2A DUD . . . C 3 -10.242 36.574 4.278 1 29.89 ? O2A DUD 777 A 1 HETATM 20 O O3A DUD . . . C 3 -12.024 35.308 3.129 1 31.84 ? O3A DUD 777 A 1 HETATM 21 P PB DUD . . . C 3 -13.48 35.496 2.525 1 33.15 ? PB DUD 777 A 1 HETATM 22 O O1B DUD . . . C 3 -14.491 36.272 3.335 1 26.82 ? O1B DUD 777 A 1 HETATM 23 O O2B DUD . . . C 3 -13.44 35.602 1.039 1 25.51 ? O2B DUD 777 A 1 HETATM 24 O O3B DUD . . . C 3 -13.969 33.968 2.635 1 45.6 ? O3B DUD 777 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 238 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 24 #