data_1DUC
#
_model_server_result.job_id            0sJ3MfHsnsYKecCtFeCHgg 
_model_server_result.datetime_utc      '2024-11-12 21:46:28' 
_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              6 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           24 
#