data_9J9K
#
_model_server_result.job_id            Ece1wMaX1StADmYNEOf5ow 
_model_server_result.datetime_utc      '2024-11-08 06:05:24' 
_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          9j9k 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":502}' 
#
_entry.id    9J9K 
#
_exptl.entry_id    9J9K 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              568.293 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE" 
_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          103.12 
_cell.angle_gamma         90 
_cell.entry_id            9J9K 
_cell.length_a            101.607 
_cell.length_b            114.919 
_cell.length_c            104.249 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9J9K 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_and_software_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D 1 1 
B,E,F 2 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
? 3 D N N 
? 3 F N N 
#
_chem_comp.formula           'C15 H23 F N2 O16 P2' 
_chem_comp.formula_weight    568.293 
_chem_comp.id                U2F 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE" 
_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
C1 O1 U2F sing 379 n n 
C1 C2 U2F sing 380 n n 
C1 O5 U2F sing 381 n n 
C1 H1 U2F sing 382 n n 
O1 PB U2F sing 383 n n 
PB O1B U2F doub 384 n n 
PB O2B U2F sing 385 n n 
PB O3A U2F sing 386 n n 
O3A PA U2F sing 387 n n 
PA O1A U2F doub 388 n n 
PA O2A U2F sing 389 n n 
PA O5' U2F sing 390 n n 
O5' C5' U2F sing 391 n n 
C5' C4' U2F sing 392 n n 
C5' "H5'1" U2F sing 393 n n 
C5' "H5'2" U2F sing 394 n n 
C4' O4' U2F sing 395 n n 
C4' C3' U2F sing 396 n n 
C4' H4' U2F sing 397 n n 
O4' C1' U2F sing 398 n n 
C1' C2' U2F sing 399 n n 
C1' N1 U2F sing 400 n n 
C1' H1' U2F sing 401 n n 
C2' C3' U2F sing 402 n n 
C2' O2' U2F sing 403 n n 
C2' H2' U2F sing 404 n n 
C3' O3' U2F sing 405 n n 
C3' H3' U2F sing 406 n n 
O3' HB U2F sing 407 n n 
O2' HA U2F sing 408 n n 
N1 C6' U2F sing 409 n n 
N1 C9' U2F sing 410 n n 
C6' O6' U2F doub 411 n n 
C6' N3 U2F sing 412 n n 
N3 C7' U2F sing 413 n n 
N3 H3 U2F sing 414 n n 
C7' O7' U2F doub 415 n n 
C7' C8' U2F sing 416 n n 
C8' C9' U2F doub 417 n n 
C8' H8' U2F sing 418 n n 
C9' H9' U2F sing 419 n n 
C2 F1 U2F sing 420 n n 
C2 C3 U2F sing 421 n n 
C2 H2 U2F sing 422 n n 
C3 O3 U2F sing 423 n n 
C3 C4 U2F sing 424 n n 
C3 HC U2F sing 425 n n 
O3 HD U2F sing 426 n n 
C4 O4 U2F sing 427 n n 
C4 C5 U2F sing 428 n n 
C4 H4 U2F sing 429 n n 
O4 HE U2F sing 430 n n 
C5 C6 U2F sing 431 n n 
C5 O5 U2F sing 432 n n 
C5 H5 U2F sing 433 n n 
C6 O6 U2F sing 434 n n 
C6 H6C1 U2F sing 435 n n 
C6 H6C2 U2F sing 436 n n 
O6 H6 U2F sing 437 n n 
HO1 O2A U2F sing 438 n n 
HO2 O2B U2F sing 439 n n 
#
_atom_sites.entry_id                     9J9K 
_atom_sites.fract_transf_matrix[1][1]    0.009842 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002294 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008702 
_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]    0.00985 
_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 T83 A 1 501 501 T83 T83 . 
D 3 U2F A 1 502 502 U2F U2F . 
E 2 T83 B 1 501 501 T83 T83 . 
F 3 U2F B 1 502 502 U2F U2F . 
#
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 C C1 U2F . . . F 3 -24.94 -30.434 21.824 1 146.35 ? C1 U2F 502 B 1 
HETATM 2 O O1 U2F . . . F 3 -25.18 -31.801 21.972 1 103.06 ? O1 U2F 502 B 1 
HETATM 3 P PB U2F . . . F 3 -26.289 -32.516 21.078 1 79.53 ? PB U2F 502 B 1 
HETATM 4 O O1B U2F . . . F 3 -26.526 -33.886 21.612 1 79.68 ? O1B U2F 502 B 1 
HETATM 5 O O2B U2F . . . F 3 -27.449 -31.59 20.961 1 75.37 ? O2B U2F 502 B 1 
HETATM 6 O O3A U2F . . . F 3 -25.56 -32.615 19.657 1 80.41 ? O3A U2F 502 B 1 
HETATM 7 P PA U2F . . . F 3 -24.052 -32.851 19.173 1 66.46 ? PA U2F 502 B 1 
HETATM 8 O O1A U2F . . . F 3 -23.158 -33.03 20.351 1 57.97 ? O1A U2F 502 B 1 
HETATM 9 O O2A U2F . . . F 3 -23.71 -31.8 18.18 1 68.84 ? O2A U2F 502 B 1 
HETATM 10 O O5' U2F . . . F 3 -24.194 -34.243 18.407 1 63.42 ? O5' U2F 502 B 1 
HETATM 11 C C5' U2F . . . F 3 -25.345 -35.079 18.653 1 59.81 ? C5' U2F 502 B 1 
HETATM 12 C C4' U2F . . . F 3 -25.313 -36.201 17.652 1 58.14 ? C4' U2F 502 B 1 
HETATM 13 O O4' U2F . . . F 3 -26.633 -36.766 17.481 1 56.27 ? O4' U2F 502 B 1 
HETATM 14 C C1' U2F . . . F 3 -26.718 -37.346 16.196 1 56.07 ? C1' U2F 502 B 1 
HETATM 15 C C2' U2F . . . F 3 -25.431 -37.001 15.442 1 52.26 ? C2' U2F 502 B 1 
HETATM 16 C C3' U2F . . . F 3 -24.934 -35.79 16.23 1 63.83 ? C3' U2F 502 B 1 
HETATM 17 O O3' U2F . . . F 3 -23.533 -35.597 16.12 1 86.07 ? O3' U2F 502 B 1 
HETATM 18 O O2' U2F . . . F 3 -24.524 -38.078 15.513 1 46.16 ? O2' U2F 502 B 1 
HETATM 19 N N1 U2F . . . F 3 -27.918 -36.82 15.527 1 55.97 ? N1 U2F 502 B 1 
HETATM 20 C C6' U2F . . . F 3 -28.456 -37.588 14.515 1 63.81 ? C6' U2F 502 B 1 
HETATM 21 O O6' U2F . . . F 3 -27.982 -38.661 14.17 1 59.92 ? O6' U2F 502 B 1 
HETATM 22 N N3 U2F . . . F 3 -29.571 -37.056 13.926 1 70.07 ? N3 U2F 502 B 1 
HETATM 23 C C7' U2F . . . F 3 -30.187 -35.862 14.231 1 70.28 ? C7' U2F 502 B 1 
HETATM 24 O O7' U2F . . . F 3 -31.187 -35.525 13.601 1 80.38 ? O7' U2F 502 B 1 
HETATM 25 C C8' U2F . . . F 3 -29.567 -35.121 15.29 1 59.96 ? C8' U2F 502 B 1 
HETATM 26 C C9' U2F . . . F 3 -28.476 -35.618 15.889 1 55.77 ? C9' U2F 502 B 1 
HETATM 27 C C2 U2F . . . F 3 -23.469 -30.197 22.077 1 151.88 ? C2 U2F 502 B 1 
HETATM 28 F F1 U2F . . . F 3 -22.736 -31.087 21.27 1 119.32 ? F1 U2F 502 B 1 
HETATM 29 C C3 U2F . . . F 3 -23.085 -30.444 23.52 1 182.84 ? C3 U2F 502 B 1 
HETATM 30 O O3 U2F . . . F 3 -21.76 -29.962 23.717 1 183.95 ? O3 U2F 502 B 1 
HETATM 31 C C4 U2F . . . F 3 -24.056 -29.711 24.437 1 202.77 ? C4 U2F 502 B 1 
HETATM 32 O O4 U2F . . . F 3 -23.79 -30.043 25.795 1 219.86 ? O4 U2F 502 B 1 
HETATM 33 C C5 U2F . . . F 3 -25.482 -30.112 24.09 1 195.48 ? C5 U2F 502 B 1 
HETATM 34 C C6 U2F . . . F 3 -26.528 -29.444 24.949 1 198.96 ? C6 U2F 502 B 1 
HETATM 35 O O6 U2F . . . F 3 -27.841 -29.835 24.553 1 190.44 ? O6 U2F 502 B 1 
HETATM 36 O O5 U2F . . . F 3 -25.738 -29.713 22.74 1 170.81 ? O5 U2F 502 B 1 
#
_model_server_stats.io_time_ms              25 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           232 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           36 
#