data_3QEO
#
_model_server_result.job_id            tdf1B9VYVYVGAOspous4RA 
_model_server_result.datetime_utc      '2024-11-20 12:24:11' 
_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          3qeo 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":402}' 
#
_entry.id    3QEO 
#
_exptl.entry_id    3QEO 
_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            3QEO 
_cell.length_a            68.76 
_cell.length_b            68.76 
_cell.length_c            120.597 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3QEO 
_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 390 n n 
N1 C6 UDP sing 391 n n 
N1 C1' UDP sing 392 n n 
C2 N3 UDP sing 393 n n 
C2 O2 UDP doub 394 n n 
N3 C4 UDP sing 395 n n 
N3 HN3 UDP sing 396 n n 
C4 C5 UDP sing 397 n n 
C4 O4 UDP doub 398 n n 
C5 C6 UDP doub 399 n n 
C5 H5 UDP sing 400 n n 
C6 H6 UDP sing 401 n n 
C1' C2' UDP sing 402 n n 
C1' O4' UDP sing 403 n n 
C1' H1' UDP sing 404 n n 
C2' O2' UDP sing 405 n n 
C2' C3' UDP sing 406 n n 
C2' H2' UDP sing 407 n n 
O2' HO2' UDP sing 408 n n 
C3' C4' UDP sing 409 n n 
C3' O3' UDP sing 410 n n 
C3' H3' UDP sing 411 n n 
C4' O4' UDP sing 412 n n 
C4' C5' UDP sing 413 n n 
C4' H4' UDP sing 414 n n 
O3' HO3' UDP sing 415 n n 
C5' O5' UDP sing 416 n n 
C5' "H5'1" UDP sing 417 n n 
C5' "H5'2" UDP sing 418 n n 
O5' PA UDP sing 419 n n 
PA O1A UDP doub 420 n n 
PA O2A UDP sing 421 n n 
PA O3A UDP sing 422 n n 
O2A HOA2 UDP sing 423 n n 
O3A PB UDP sing 424 n n 
PB O1B UDP doub 425 n n 
PB O2B UDP sing 426 n n 
PB O3B UDP sing 427 n n 
O2B HOB2 UDP sing 428 n n 
O3B HOB3 UDP sing 429 n n 
#
_atom_sites.entry_id                     3QEO 
_atom_sites.fract_transf_matrix[1][1]    0.014543 
_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]    0.014543 
_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]    0.008292 
_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 LLT A 1 261 401 LLT LLT . 
E 2 UDP B 1 402 402 UDP UDP . 
F 3 LLT B 1 261 402 LLT LLT . 
G 4 HOH A 1 262 1 HOH HOH . 
G 4 HOH A 2 263 3 HOH HOH . 
G 4 HOH A 3 264 5 HOH HOH . 
G 4 HOH A 4 265 7 HOH HOH . 
G 4 HOH A 5 266 8 HOH HOH . 
G 4 HOH A 6 267 9 HOH HOH . 
G 4 HOH A 7 268 10 HOH HOH . 
G 4 HOH A 8 269 11 HOH HOH . 
G 4 HOH A 9 270 13 HOH HOH . 
G 4 HOH A 10 271 14 HOH HOH . 
G 4 HOH A 11 272 16 HOH HOH . 
G 4 HOH A 12 273 17 HOH HOH . 
G 4 HOH A 13 274 19 HOH HOH . 
G 4 HOH A 14 275 22 HOH HOH . 
G 4 HOH A 15 276 23 HOH HOH . 
G 4 HOH A 16 277 24 HOH HOH . 
G 4 HOH A 17 278 26 HOH HOH . 
G 4 HOH A 18 279 28 HOH HOH . 
G 4 HOH A 19 280 33 HOH HOH . 
G 4 HOH A 20 281 34 HOH HOH . 
G 4 HOH A 21 282 39 HOH HOH . 
G 4 HOH A 22 283 40 HOH HOH . 
G 4 HOH A 23 284 42 HOH HOH . 
G 4 HOH A 24 285 43 HOH HOH . 
G 4 HOH A 25 286 44 HOH HOH . 
G 4 HOH A 26 287 47 HOH HOH . 
G 4 HOH A 27 288 48 HOH HOH . 
G 4 HOH A 28 289 49 HOH HOH . 
G 4 HOH A 29 290 50 HOH HOH . 
G 4 HOH A 30 291 52 HOH HOH . 
G 4 HOH A 31 292 53 HOH HOH . 
G 4 HOH A 32 293 54 HOH HOH . 
G 4 HOH A 33 294 57 HOH HOH . 
G 4 HOH A 34 295 63 HOH HOH . 
G 4 HOH A 35 296 67 HOH HOH . 
G 4 HOH A 36 297 72 HOH HOH . 
G 4 HOH A 37 298 73 HOH HOH . 
G 4 HOH A 38 299 77 HOH HOH . 
G 4 HOH A 39 300 78 HOH HOH . 
G 4 HOH A 40 301 80 HOH HOH . 
G 4 HOH A 41 302 81 HOH HOH . 
G 4 HOH A 42 303 82 HOH HOH . 
G 4 HOH A 43 304 83 HOH HOH . 
G 4 HOH A 44 305 84 HOH HOH . 
G 4 HOH A 45 306 89 HOH HOH . 
G 4 HOH A 46 307 90 HOH HOH . 
G 4 HOH A 47 308 91 HOH HOH . 
G 4 HOH A 48 309 95 HOH HOH . 
G 4 HOH A 49 310 96 HOH HOH . 
G 4 HOH A 50 311 97 HOH HOH . 
G 4 HOH A 51 312 102 HOH HOH . 
G 4 HOH A 52 313 103 HOH HOH . 
G 4 HOH A 53 314 105 HOH HOH . 
G 4 HOH A 54 315 106 HOH HOH . 
G 4 HOH A 55 317 109 HOH HOH . 
G 4 HOH A 56 318 111 HOH HOH . 
G 4 HOH A 57 319 112 HOH HOH . 
G 4 HOH A 58 320 115 HOH HOH . 
G 4 HOH A 59 321 118 HOH HOH . 
G 4 HOH A 60 322 119 HOH HOH . 
G 4 HOH A 61 323 120 HOH HOH . 
G 4 HOH A 62 324 121 HOH HOH . 
G 4 HOH A 63 325 122 HOH HOH . 
G 4 HOH A 64 326 123 HOH HOH . 
G 4 HOH A 65 327 126 HOH HOH . 
G 4 HOH A 66 328 129 HOH HOH . 
G 4 HOH A 67 329 130 HOH HOH . 
G 4 HOH A 68 330 135 HOH HOH . 
G 4 HOH A 69 331 143 HOH HOH . 
G 4 HOH A 70 332 145 HOH HOH . 
G 4 HOH A 71 333 146 HOH HOH . 
G 4 HOH A 72 334 148 HOH HOH . 
G 4 HOH A 73 335 153 HOH HOH . 
G 4 HOH A 74 336 154 HOH HOH . 
G 4 HOH A 75 337 155 HOH HOH . 
G 4 HOH A 76 338 150 HOH HOH . 
H 4 HOH B 1 262 2 HOH HOH . 
H 4 HOH B 2 263 4 HOH HOH . 
H 4 HOH B 3 264 6 HOH HOH . 
H 4 HOH B 4 265 12 HOH HOH . 
H 4 HOH B 5 266 15 HOH HOH . 
H 4 HOH B 6 267 18 HOH HOH . 
H 4 HOH B 7 268 20 HOH HOH . 
H 4 HOH B 8 269 21 HOH HOH . 
H 4 HOH B 9 270 25 HOH HOH . 
H 4 HOH B 10 271 27 HOH HOH . 
H 4 HOH B 11 272 29 HOH HOH . 
H 4 HOH B 12 273 30 HOH HOH . 
H 4 HOH B 13 274 31 HOH HOH . 
H 4 HOH B 14 275 32 HOH HOH . 
H 4 HOH B 15 276 35 HOH HOH . 
H 4 HOH B 16 277 36 HOH HOH . 
H 4 HOH B 17 278 37 HOH HOH . 
H 4 HOH B 18 279 38 HOH HOH . 
H 4 HOH B 19 280 41 HOH HOH . 
H 4 HOH B 20 281 45 HOH HOH . 
H 4 HOH B 21 282 46 HOH HOH . 
H 4 HOH B 22 283 51 HOH HOH . 
H 4 HOH B 23 284 55 HOH HOH . 
H 4 HOH B 24 285 56 HOH HOH . 
H 4 HOH B 25 286 58 HOH HOH . 
H 4 HOH B 26 287 59 HOH HOH . 
H 4 HOH B 27 288 60 HOH HOH . 
H 4 HOH B 28 289 61 HOH HOH . 
H 4 HOH B 29 290 62 HOH HOH . 
H 4 HOH B 30 291 64 HOH HOH . 
H 4 HOH B 31 292 65 HOH HOH . 
H 4 HOH B 32 293 66 HOH HOH . 
H 4 HOH B 33 294 68 HOH HOH . 
H 4 HOH B 34 295 69 HOH HOH . 
H 4 HOH B 35 296 70 HOH HOH . 
H 4 HOH B 36 297 71 HOH HOH . 
H 4 HOH B 37 298 74 HOH HOH . 
H 4 HOH B 38 299 75 HOH HOH . 
H 4 HOH B 39 300 76 HOH HOH . 
H 4 HOH B 40 301 79 HOH HOH . 
H 4 HOH B 41 302 85 HOH HOH . 
H 4 HOH B 42 303 86 HOH HOH . 
H 4 HOH B 43 304 87 HOH HOH . 
H 4 HOH B 44 305 88 HOH HOH . 
H 4 HOH B 45 306 92 HOH HOH . 
H 4 HOH B 46 307 93 HOH HOH . 
H 4 HOH B 47 308 94 HOH HOH . 
H 4 HOH B 48 309 98 HOH HOH . 
H 4 HOH B 49 310 99 HOH HOH . 
H 4 HOH B 50 311 100 HOH HOH . 
H 4 HOH B 51 312 101 HOH HOH . 
H 4 HOH B 52 313 104 HOH HOH . 
H 4 HOH B 53 314 108 HOH HOH . 
H 4 HOH B 54 315 110 HOH HOH . 
H 4 HOH B 55 316 107 HOH HOH . 
H 4 HOH B 56 317 114 HOH HOH . 
H 4 HOH B 57 318 116 HOH HOH . 
H 4 HOH B 58 319 117 HOH HOH . 
H 4 HOH B 59 320 124 HOH HOH . 
H 4 HOH B 60 321 125 HOH HOH . 
H 4 HOH B 61 322 127 HOH HOH . 
H 4 HOH B 62 323 128 HOH HOH . 
H 4 HOH B 63 324 131 HOH HOH . 
H 4 HOH B 64 325 132 HOH HOH . 
H 4 HOH B 65 326 133 HOH HOH . 
H 4 HOH B 66 327 134 HOH HOH . 
H 4 HOH B 67 328 136 HOH HOH . 
H 4 HOH B 68 329 137 HOH HOH . 
H 4 HOH B 69 330 138 HOH HOH . 
H 4 HOH B 70 331 139 HOH HOH . 
H 4 HOH B 71 332 140 HOH HOH . 
H 4 HOH B 72 333 141 HOH HOH . 
H 4 HOH B 73 334 142 HOH HOH . 
H 4 HOH B 74 335 144 HOH HOH . 
H 4 HOH B 75 336 147 HOH HOH . 
H 4 HOH B 76 337 149 HOH HOH . 
H 4 HOH B 77 338 113 HOH HOH . 
H 4 HOH B 78 339 151 HOH HOH . 
H 4 HOH B 79 340 152 HOH HOH . 
H 4 HOH B 80 341 156 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 28.096 25.673 3.57 1 37.92 ? N1 UDP 402 B 1 
HETATM 2 C C2 UDP . . . E 2 29.249 25.659 4.338 1 38.71 ? C2 UDP 402 B 1 
HETATM 3 N N3 UDP . . . E 2 29.356 24.752 5.378 1 38.54 ? N3 UDP 402 B 1 
HETATM 4 C C4 UDP . . . E 2 28.316 23.878 5.655 1 38.65 ? C4 UDP 402 B 1 
HETATM 5 C C5 UDP . . . E 2 27.147 23.909 4.885 1 37.22 ? C5 UDP 402 B 1 
HETATM 6 C C6 UDP . . . E 2 27.139 24.686 3.721 1 38.15 ? C6 UDP 402 B 1 
HETATM 7 O O2 UDP . . . E 2 30.179 26.43 4.08 1 39.68 ? O2 UDP 402 B 1 
HETATM 8 O O4 UDP . . . E 2 28.421 23.087 6.601 1 40.31 ? O4 UDP 402 B 1 
HETATM 9 C C1' UDP . . . E 2 28.023 26.642 2.474 1 36.78 ? C1' UDP 402 B 1 
HETATM 10 C C2' UDP . . . E 2 28.062 25.962 1.111 1 37.27 ? C2' UDP 402 B 1 
HETATM 11 O O2' UDP . . . E 2 29.364 25.663 0.653 1 34.9 ? O2' UDP 402 B 1 
HETATM 12 C C3' UDP . . . E 2 27.349 26.974 0.233 1 36.74 ? C3' UDP 402 B 1 
HETATM 13 C C4' UDP . . . E 2 26.406 27.678 1.206 1 36.19 ? C4' UDP 402 B 1 
HETATM 14 O O4' UDP . . . E 2 26.795 27.34 2.537 1 35.42 ? O4' UDP 402 B 1 
HETATM 15 O O3' UDP . . . E 2 28.253 27.909 -0.339 1 35.46 ? O3' UDP 402 B 1 
HETATM 16 C C5' UDP . . . E 2 24.953 27.295 0.923 1 34.52 ? C5' UDP 402 B 1 
HETATM 17 O O5' UDP . . . E 2 24.728 25.916 1.176 1 32.41 ? O5' UDP 402 B 1 
HETATM 18 P PA UDP . . . E 2 23.795 25.004 0.226 1 32.77 ? PA UDP 402 B 1 
HETATM 19 O O1A UDP . . . E 2 23.944 25.359 -1.201 1 31.87 ? O1A UDP 402 B 1 
HETATM 20 O O2A UDP . . . E 2 24.068 23.559 0.471 1 31.93 ? O2A UDP 402 B 1 
HETATM 21 O O3A UDP . . . E 2 22.368 25.316 0.885 1 27.19 ? O3A UDP 402 B 1 
HETATM 22 P PB UDP . . . E 2 20.947 24.741 0.42 1 25.39 ? PB UDP 402 B 1 
HETATM 23 O O1B UDP . . . E 2 21.024 23.661 -0.607 1 25.06 ? O1B UDP 402 B 1 
HETATM 24 O O2B UDP . . . E 2 20.315 25.954 -0.227 1 25.56 ? O2B UDP 402 B 1 
HETATM 25 O O3B UDP . . . E 2 20.172 24.406 1.619 1 23.95 ? O3B UDP 402 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           229 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#