data_1DUC # _model_server_result.job_id xIq6cKul_PJa88GeJqpElQ _model_server_result.datetime_utc '2024-11-24 03:30:36' _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 1duc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 1DUC # _exptl.entry_id 1DUC _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 90 _cell.entry_id 1DUC _cell.length_a 106.7 _cell.length_b 106.7 _cell.length_c 106.7 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DUC _symmetry.cell_setting ? _symmetry.Int_Tables_number 213 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 3 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 _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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 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 O1A DUD . A DUD 201 1_555 B SR SR . A SR 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? metalc ? metalc2 C O2B DUD . A DUD 201 1_555 B SR SR . A SR 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc3 B SR SR . A SR 202 1_555 D O HOH . A HOH 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? metalc ? metalc4 B SR SR . A SR 202 1_555 D O HOH . A HOH 204 9_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc5 B SR SR . A SR 202 1_555 D O HOH . A HOH 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc6 B SR SR . A SR 202 1_555 D O HOH . A HOH 214 9_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc7 B SR SR . A SR 202 1_555 D O HOH . A HOH 215 9_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc8 B SR SR . A SR 202 1_555 D O HOH . A HOH 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? # _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 1DUC _atom_sites.fract_transf_matrix[1][1] 0.009372 _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] 0.009372 _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] 0.009372 _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 SR A 1 202 202 SR SR . C 3 DUD A 1 201 201 DUD DUD . D 4 HOH A 1 203 1 HOH HOH . D 4 HOH A 2 204 2 HOH HOH . D 4 HOH A 3 205 3 HOH HOH . D 4 HOH A 4 206 4 HOH HOH . D 4 HOH A 5 207 5 HOH HOH . D 4 HOH A 6 208 6 HOH HOH . D 4 HOH A 7 209 7 HOH HOH . D 4 HOH A 8 210 8 HOH HOH . D 4 HOH A 9 211 9 HOH HOH . D 4 HOH A 10 212 10 HOH HOH . D 4 HOH A 11 213 11 HOH HOH . D 4 HOH A 12 214 12 HOH HOH . D 4 HOH A 13 215 13 HOH HOH . D 4 HOH A 14 216 14 HOH HOH . D 4 HOH A 15 217 15 HOH HOH . D 4 HOH A 16 218 16 HOH HOH . D 4 HOH A 17 219 17 HOH HOH . D 4 HOH A 18 220 18 HOH HOH . D 4 HOH A 19 221 19 HOH HOH . D 4 HOH A 20 222 20 HOH HOH . D 4 HOH A 21 223 21 HOH HOH . D 4 HOH A 22 224 22 HOH HOH . D 4 HOH A 23 225 23 HOH HOH . D 4 HOH A 24 226 24 HOH HOH . D 4 HOH A 25 227 25 HOH HOH . D 4 HOH A 26 228 26 HOH HOH . D 4 HOH A 27 229 27 HOH HOH . D 4 HOH A 28 230 28 HOH HOH . D 4 HOH A 29 231 29 HOH HOH . D 4 HOH A 30 232 30 HOH HOH . D 4 HOH A 31 233 31 HOH HOH . D 4 HOH A 32 234 32 HOH HOH . D 4 HOH A 33 235 33 HOH HOH . D 4 HOH A 34 236 34 HOH HOH . D 4 HOH A 35 237 35 HOH HOH . D 4 HOH A 36 238 36 HOH HOH . D 4 HOH A 37 239 37 HOH HOH . D 4 HOH A 38 240 38 HOH HOH . D 4 HOH A 39 241 39 HOH HOH . D 4 HOH A 40 242 40 HOH HOH . D 4 HOH A 41 243 41 HOH HOH . D 4 HOH A 42 244 42 HOH HOH . D 4 HOH A 43 245 43 HOH HOH . D 4 HOH A 44 246 44 HOH HOH . D 4 HOH A 45 247 45 HOH HOH . D 4 HOH A 46 248 46 HOH HOH . D 4 HOH A 47 249 47 HOH HOH . D 4 HOH A 48 250 48 HOH HOH . D 4 HOH A 49 251 49 HOH HOH . D 4 HOH A 50 252 50 HOH HOH . D 4 HOH A 51 253 51 HOH HOH . D 4 HOH A 52 254 52 HOH HOH . D 4 HOH A 53 255 53 HOH HOH . D 4 HOH A 54 256 54 HOH HOH . D 4 HOH A 55 257 55 HOH HOH . D 4 HOH A 56 258 56 HOH HOH . D 4 HOH A 57 259 57 HOH HOH . D 4 HOH A 58 260 58 HOH HOH . D 4 HOH A 59 261 59 HOH HOH . D 4 HOH A 60 262 60 HOH HOH . D 4 HOH A 61 263 61 HOH HOH . D 4 HOH A 62 264 62 HOH HOH . D 4 HOH A 63 265 63 HOH HOH . D 4 HOH A 64 266 64 HOH HOH . D 4 HOH A 65 267 65 HOH HOH . D 4 HOH A 66 268 66 HOH HOH . D 4 HOH A 67 269 67 HOH HOH . D 4 HOH A 68 270 68 HOH HOH . D 4 HOH A 69 271 69 HOH HOH . D 4 HOH A 70 272 70 HOH HOH . D 4 HOH A 71 273 71 HOH HOH . D 4 HOH A 72 274 72 HOH HOH . D 4 HOH A 73 275 73 HOH HOH . D 4 HOH A 74 276 74 HOH HOH . D 4 HOH A 75 277 75 HOH HOH . D 4 HOH A 76 278 76 HOH HOH . D 4 HOH A 77 279 77 HOH HOH . D 4 HOH A 78 280 78 HOH HOH . D 4 HOH A 79 281 79 HOH HOH . D 4 HOH A 80 282 80 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 15.971 34.869 31.016 1 15.7 ? N1 DUD 201 A 1 HETATM 2 C C2 DUD . . . C 3 15.469 33.803 31.734 1 21.26 ? C2 DUD 201 A 1 HETATM 3 N N3 DUD . . . C 3 15.844 32.533 31.335 1 15.64 ? N3 DUD 201 A 1 HETATM 4 C C4 DUD . . . C 3 16.696 32.335 30.245 1 20.89 ? C4 DUD 201 A 1 HETATM 5 C C5 DUD . . . C 3 17.212 33.481 29.541 1 14.7 ? C5 DUD 201 A 1 HETATM 6 C C6 DUD . . . C 3 16.81 34.74 29.928 1 18.15 ? C6 DUD 201 A 1 HETATM 7 O O2 DUD . . . C 3 14.745 33.97 32.698 1 18.94 ? O2 DUD 201 A 1 HETATM 8 O O4 DUD . . . C 3 17 31.184 29.97 1 21.52 ? O4 DUD 201 A 1 HETATM 9 C C1' DUD . . . C 3 15.524 36.224 31.504 1 12.72 ? C1' DUD 201 A 1 HETATM 10 C C2' DUD . . . C 3 16.715 36.952 32.187 1 13.54 ? C2' DUD 201 A 1 HETATM 11 C C3' DUD . . . C 3 17.232 37.889 31.085 1 15.92 ? C3' DUD 201 A 1 HETATM 12 C C4' DUD . . . C 3 15.949 38.265 30.363 1 17.22 ? C4' DUD 201 A 1 HETATM 13 O O4' DUD . . . C 3 15.202 36.991 30.338 1 14.99 ? O4' DUD 201 A 1 HETATM 14 O O3' DUD . . . C 3 17.846 39.084 31.564 1 17.69 ? O3' DUD 201 A 1 HETATM 15 C C5' DUD . . . C 3 16.185 38.742 28.927 1 17.47 ? C5' DUD 201 A 1 HETATM 16 O O5' DUD . . . C 3 14.904 38.942 28.3 1 20.89 ? O5' DUD 201 A 1 HETATM 17 P PA DUD . . . C 3 14.863 39.921 27.025 1 19.68 ? PA DUD 201 A 1 HETATM 18 O O1A DUD . . . C 3 15.838 41.027 27.182 1 15.61 ? O1A DUD 201 A 1 HETATM 19 O O2A DUD . . . C 3 13.467 40.373 26.847 1 21.9 ? O2A DUD 201 A 1 HETATM 20 O O3A DUD . . . C 3 15.202 38.979 25.752 1 19.18 ? O3A DUD 201 A 1 HETATM 21 P PB DUD . . . C 3 16.433 38.746 24.791 1 19.25 ? PB DUD 201 A 1 HETATM 22 O O1B DUD . . . C 3 17.387 37.873 25.575 1 18.33 ? O1B DUD 201 A 1 HETATM 23 O O2B DUD . . . C 3 17.074 40.02 24.393 1 15.97 ? O2B DUD 201 A 1 HETATM 24 O O3B DUD . . . C 3 15.787 37.949 23.639 1 18.43 ? O3B DUD 201 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 934 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 24 #