data_3QEN
#
_model_server_result.job_id            opAMNE2DshMaCivECM9O9A 
_model_server_result.datetime_utc      '2024-11-24 13:49:26' 
_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          3qen 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":401}' 
#
_entry.id    3QEN 
#
_exptl.entry_id    3QEN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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            3QEN 
_cell.length_a            69.14 
_cell.length_b            69.14 
_cell.length_c            118.9 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3QEN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41' 
#
_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,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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 E N N 
#
_chem_comp.formula           'C9 H14 N2 O12 P2' 
_chem_comp.formula_weight    404.161 
_chem_comp.id                UDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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 UDP sing 388 n n 
N1 C6 UDP sing 389 n n 
N1 C1' UDP sing 390 n n 
C2 N3 UDP sing 391 n n 
C2 O2 UDP doub 392 n n 
N3 C4 UDP sing 393 n n 
N3 HN3 UDP sing 394 n n 
C4 C5 UDP sing 395 n n 
C4 O4 UDP doub 396 n n 
C5 C6 UDP doub 397 n n 
C5 H5 UDP sing 398 n n 
C6 H6 UDP sing 399 n n 
C1' C2' UDP sing 400 n n 
C1' O4' UDP sing 401 n n 
C1' H1' UDP sing 402 n n 
C2' O2' UDP sing 403 n n 
C2' C3' UDP sing 404 n n 
C2' H2' UDP sing 405 n n 
O2' HO2' UDP sing 406 n n 
C3' C4' UDP sing 407 n n 
C3' O3' UDP sing 408 n n 
C3' H3' UDP sing 409 n n 
C4' O4' UDP sing 410 n n 
C4' C5' UDP sing 411 n n 
C4' H4' UDP sing 412 n n 
O3' HO3' UDP sing 413 n n 
C5' O5' UDP sing 414 n n 
C5' "H5'1" UDP sing 415 n n 
C5' "H5'2" UDP sing 416 n n 
O5' PA UDP sing 417 n n 
PA O1A UDP doub 418 n n 
PA O2A UDP sing 419 n n 
PA O3A UDP sing 420 n n 
O2A HOA2 UDP sing 421 n n 
O3A PB UDP sing 422 n n 
PB O1B UDP doub 423 n n 
PB O2B UDP sing 424 n n 
PB O3B UDP sing 425 n n 
O2B HOB2 UDP sing 426 n n 
O3B HOB3 UDP sing 427 n n 
#
_atom_sites.entry_id                     3QEN 
_atom_sites.fract_transf_matrix[1][1]    0.014463 
_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]    0.014463 
_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]    0.00841 
_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
C 2 UDP A 1 401 401 UDP UDP . 
D 3 5BT A 1 402 402 5BT 5BT . 
E 2 UDP B 1 401 401 UDP UDP . 
F 3 5BT B 1 402 402 5BT 5BT . 
G 4 HOH A 1 261 3 HOH HOH . 
G 4 HOH A 2 262 5 HOH HOH . 
G 4 HOH A 3 263 7 HOH HOH . 
G 4 HOH A 4 264 8 HOH HOH . 
G 4 HOH A 5 265 9 HOH HOH . 
G 4 HOH A 6 266 10 HOH HOH . 
G 4 HOH A 7 267 11 HOH HOH . 
G 4 HOH A 8 268 13 HOH HOH . 
G 4 HOH A 9 269 14 HOH HOH . 
G 4 HOH A 10 270 17 HOH HOH . 
G 4 HOH A 11 271 19 HOH HOH . 
G 4 HOH A 12 272 23 HOH HOH . 
G 4 HOH A 13 273 24 HOH HOH . 
G 4 HOH A 14 274 26 HOH HOH . 
G 4 HOH A 15 275 28 HOH HOH . 
G 4 HOH A 16 276 33 HOH HOH . 
G 4 HOH A 17 277 34 HOH HOH . 
G 4 HOH A 18 278 39 HOH HOH . 
G 4 HOH A 19 279 42 HOH HOH . 
G 4 HOH A 20 280 43 HOH HOH . 
G 4 HOH A 21 281 44 HOH HOH . 
G 4 HOH A 22 282 48 HOH HOH . 
G 4 HOH A 23 283 49 HOH HOH . 
G 4 HOH A 24 284 50 HOH HOH . 
G 4 HOH A 25 285 52 HOH HOH . 
G 4 HOH A 26 286 53 HOH HOH . 
G 4 HOH A 27 287 57 HOH HOH . 
G 4 HOH A 28 288 63 HOH HOH . 
G 4 HOH A 29 289 67 HOH HOH . 
G 4 HOH A 30 290 72 HOH HOH . 
G 4 HOH A 31 291 73 HOH HOH . 
G 4 HOH A 32 292 77 HOH HOH . 
G 4 HOH A 33 293 78 HOH HOH . 
G 4 HOH A 34 294 84 HOH HOH . 
G 4 HOH A 35 295 89 HOH HOH . 
G 4 HOH A 36 296 90 HOH HOH . 
G 4 HOH A 37 297 91 HOH HOH . 
G 4 HOH A 38 298 95 HOH HOH . 
G 4 HOH A 39 299 96 HOH HOH . 
G 4 HOH A 40 300 97 HOH HOH . 
G 4 HOH A 41 301 102 HOH HOH . 
G 4 HOH A 42 302 103 HOH HOH . 
G 4 HOH A 43 303 107 HOH HOH . 
G 4 HOH A 44 304 109 HOH HOH . 
G 4 HOH A 45 305 111 HOH HOH . 
G 4 HOH A 46 306 112 HOH HOH . 
G 4 HOH A 47 307 115 HOH HOH . 
G 4 HOH A 48 308 118 HOH HOH . 
G 4 HOH A 49 309 119 HOH HOH . 
G 4 HOH A 50 310 121 HOH HOH . 
G 4 HOH A 51 311 122 HOH HOH . 
G 4 HOH A 52 312 123 HOH HOH . 
G 4 HOH A 53 313 126 HOH HOH . 
G 4 HOH A 54 314 129 HOH HOH . 
G 4 HOH A 55 315 130 HOH HOH . 
G 4 HOH A 56 316 135 HOH HOH . 
G 4 HOH A 57 317 143 HOH HOH . 
G 4 HOH A 58 318 145 HOH HOH . 
G 4 HOH A 59 319 146 HOH HOH . 
G 4 HOH A 60 320 148 HOH HOH . 
G 4 HOH A 61 321 153 HOH HOH . 
G 4 HOH A 62 322 154 HOH HOH . 
G 4 HOH A 63 323 155 HOH HOH . 
G 4 HOH A 64 324 160 HOH HOH . 
G 4 HOH A 65 325 161 HOH HOH . 
G 4 HOH A 66 326 162 HOH HOH . 
G 4 HOH A 67 327 163 HOH HOH . 
G 4 HOH A 68 328 164 HOH HOH . 
G 4 HOH A 69 329 165 HOH HOH . 
G 4 HOH A 70 330 64 HOH HOH . 
H 4 HOH B 1 261 1 HOH HOH . 
H 4 HOH B 2 262 2 HOH HOH . 
H 4 HOH B 3 263 4 HOH HOH . 
H 4 HOH B 4 264 6 HOH HOH . 
H 4 HOH B 5 265 12 HOH HOH . 
H 4 HOH B 6 266 15 HOH HOH . 
H 4 HOH B 7 267 18 HOH HOH . 
H 4 HOH B 8 268 20 HOH HOH . 
H 4 HOH B 9 269 21 HOH HOH . 
H 4 HOH B 10 270 25 HOH HOH . 
H 4 HOH B 11 271 27 HOH HOH . 
H 4 HOH B 12 272 29 HOH HOH . 
H 4 HOH B 13 273 31 HOH HOH . 
H 4 HOH B 14 274 32 HOH HOH . 
H 4 HOH B 15 275 35 HOH HOH . 
H 4 HOH B 16 276 36 HOH HOH . 
H 4 HOH B 17 277 37 HOH HOH . 
H 4 HOH B 18 278 45 HOH HOH . 
H 4 HOH B 19 279 46 HOH HOH . 
H 4 HOH B 20 280 47 HOH HOH . 
H 4 HOH B 21 281 51 HOH HOH . 
H 4 HOH B 22 282 55 HOH HOH . 
H 4 HOH B 23 283 58 HOH HOH . 
H 4 HOH B 24 284 59 HOH HOH . 
H 4 HOH B 25 285 60 HOH HOH . 
H 4 HOH B 26 286 61 HOH HOH . 
H 4 HOH B 27 287 62 HOH HOH . 
H 4 HOH B 28 289 65 HOH HOH . 
H 4 HOH B 29 290 66 HOH HOH . 
H 4 HOH B 30 291 68 HOH HOH . 
H 4 HOH B 31 292 70 HOH HOH . 
H 4 HOH B 32 293 71 HOH HOH . 
H 4 HOH B 33 294 74 HOH HOH . 
H 4 HOH B 34 295 75 HOH HOH . 
H 4 HOH B 35 296 76 HOH HOH . 
H 4 HOH B 36 297 79 HOH HOH . 
H 4 HOH B 37 298 86 HOH HOH . 
H 4 HOH B 38 299 87 HOH HOH . 
H 4 HOH B 39 300 88 HOH HOH . 
H 4 HOH B 40 301 92 HOH HOH . 
H 4 HOH B 41 302 93 HOH HOH . 
H 4 HOH B 42 303 94 HOH HOH . 
H 4 HOH B 43 304 98 HOH HOH . 
H 4 HOH B 44 305 99 HOH HOH . 
H 4 HOH B 45 306 100 HOH HOH . 
H 4 HOH B 46 307 101 HOH HOH . 
H 4 HOH B 47 308 104 HOH HOH . 
H 4 HOH B 48 309 108 HOH HOH . 
H 4 HOH B 49 310 116 HOH HOH . 
H 4 HOH B 50 311 125 HOH HOH . 
H 4 HOH B 51 312 128 HOH HOH . 
H 4 HOH B 52 313 131 HOH HOH . 
H 4 HOH B 53 314 132 HOH HOH . 
H 4 HOH B 54 315 133 HOH HOH . 
H 4 HOH B 55 316 134 HOH HOH . 
H 4 HOH B 56 317 136 HOH HOH . 
H 4 HOH B 57 318 137 HOH HOH . 
H 4 HOH B 58 319 138 HOH HOH . 
H 4 HOH B 59 320 141 HOH HOH . 
H 4 HOH B 60 321 142 HOH HOH . 
H 4 HOH B 61 322 144 HOH HOH . 
H 4 HOH B 62 323 147 HOH HOH . 
H 4 HOH B 63 324 149 HOH HOH . 
H 4 HOH B 64 325 152 HOH HOH . 
H 4 HOH B 65 326 156 HOH HOH . 
H 4 HOH B 66 327 157 HOH HOH . 
H 4 HOH B 67 328 159 HOH HOH . 
H 4 HOH B 68 329 166 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 UDP . . . E 2 29.852 25.059 1.383 1 35.06 ? N1 UDP 401 B 1 
HETATM 2 C C2 UDP . . . E 2 30.975 25.188 2.192 1 35.64 ? C2 UDP 401 B 1 
HETATM 3 N N3 UDP . . . E 2 31.211 24.314 3.239 1 36.87 ? N3 UDP 401 B 1 
HETATM 4 C C4 UDP . . . E 2 30.318 23.301 3.494 1 38.5 ? C4 UDP 401 B 1 
HETATM 5 C C5 UDP . . . E 2 29.177 23.174 2.705 1 37.06 ? C5 UDP 401 B 1 
HETATM 6 C C6 UDP . . . E 2 28.903 24.121 1.714 1 36.36 ? C6 UDP 401 B 1 
HETATM 7 O O2 UDP . . . E 2 31.798 26.07 2 1 35.25 ? O2 UDP 401 B 1 
HETATM 8 O O4 UDP . . . E 2 30.532 22.54 4.434 1 40.21 ? O4 UDP 401 B 1 
HETATM 9 C C1' UDP . . . E 2 29.65 26.007 0.251 1 36.89 ? C1' UDP 401 B 1 
HETATM 10 C C2' UDP . . . E 2 29.469 25.36 -1.124 1 37.91 ? C2' UDP 401 B 1 
HETATM 11 O O2' UDP . . . E 2 30.666 25.131 -1.832 1 36.26 ? O2' UDP 401 B 1 
HETATM 12 C C3' UDP . . . E 2 28.638 26.395 -1.873 1 39.48 ? C3' UDP 401 B 1 
HETATM 13 C C4' UDP . . . E 2 27.825 27.062 -0.771 1 36.05 ? C4' UDP 401 B 1 
HETATM 14 O O4' UDP . . . E 2 28.495 26.816 0.451 1 37.87 ? O4' UDP 401 B 1 
HETATM 15 O O3' UDP . . . E 2 29.475 27.339 -2.527 1 37.7 ? O3' UDP 401 B 1 
HETATM 16 C C5' UDP . . . E 2 26.426 26.451 -0.642 1 36.8 ? C5' UDP 401 B 1 
HETATM 17 O O5' UDP . . . E 2 26.47 25.034 -0.702 1 35.54 ? O5' UDP 401 B 1 
HETATM 18 P PA UDP . . . E 2 25.388 24.169 -1.507 1 37.2 ? PA UDP 401 B 1 
HETATM 19 O O1A UDP . . . E 2 25.281 24.694 -2.896 1 36.06 ? O1A UDP 401 B 1 
HETATM 20 O O2A UDP . . . E 2 25.75 22.73 -1.568 1 34.51 ? O2A UDP 401 B 1 
HETATM 21 O O3A UDP . . . E 2 24.024 24.348 -0.715 1 34.29 ? O3A UDP 401 B 1 
HETATM 22 P PB UDP . . . E 2 22.574 23.87 -1.245 1 32.11 ? PB UDP 401 B 1 
HETATM 23 O O1B UDP . . . E 2 22.636 22.792 -2.251 1 29.76 ? O1B UDP 401 B 1 
HETATM 24 O O2B UDP . . . E 2 21.977 25.049 -1.916 1 34.79 ? O2B UDP 401 B 1 
HETATM 25 O O3B UDP . . . E 2 21.799 23.544 -0.054 1 26.65 ? O3B UDP 401 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#