data_9J9C
#
_model_server_result.job_id            am4AeJH-ztFjK9NxMFKFBw 
_model_server_result.datetime_utc      '2024-11-08 13:43:19' 
_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          9j9c 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":501}' 
#
_entry.id    9J9C 
#
_exptl.entry_id    9J9C 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              568.293 
_entity.id                          2 
_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    7 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          93.39 
_cell.angle_gamma         90 
_cell.entry_id            9J9C 
_cell.length_a            87.13 
_cell.length_b            170.39 
_cell.length_c            152.13 
_cell.Z_PDB               14 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9J9C 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
? monomeric 1 author_defined_assembly 5 
? monomeric 1 author_defined_assembly 6 
? monomeric 1 author_defined_assembly 7 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,H,I 1 1 
B,J,K 2 1 
C,L,M 3 1 
D,N,O 4 1 
E,P 5 1 
F,Q,R 6 1 
G,S 7 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 H N N 
? 2 J N N 
? 2 L N N 
? 2 N N N 
? 2 P N N 
? 2 Q N N 
? 2 S 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                     9J9C 
_atom_sites.fract_transf_matrix[1][1]    0.011477 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00068 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.005869 
_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]    0.006585 
_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
H 2 U2F A 1 501 501 U2F U2F . 
I 3 T83 A 1 502 502 T83 UNL . 
J 2 U2F B 1 501 501 U2F U2F . 
K 3 T83 B 1 502 502 T83 UNL . 
L 2 U2F C 1 501 501 U2F U2F . 
M 3 T83 C 1 502 502 T83 UNL . 
N 2 U2F D 1 501 501 U2F U2F . 
O 3 T83 D 1 502 502 T83 UNL . 
P 2 U2F E 1 501 501 U2F U2F . 
Q 2 U2F F 1 501 501 U2F U2F . 
R 3 T83 F 1 502 502 T83 UNL . 
S 2 U2F G 1 501 501 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 . . . Q 2 35.934 49.364 -11.536 1 85.37 ? C1 U2F 501 F 1 
HETATM 2 O O1 U2F . . . Q 2 35.471 48.452 -10.557 1 90.77 ? O1 U2F 501 F 1 
HETATM 3 P PB U2F . . . Q 2 34.14 48.839 -9.707 1 87.81 ? PB U2F 501 F 1 
HETATM 4 O O1B U2F . . . Q 2 33.201 49.515 -10.651 1 104.73 ? O1B U2F 501 F 1 
HETATM 5 O O2B U2F . . . Q 2 33.699 47.648 -8.911 1 83.92 ? O2B U2F 501 F 1 
HETATM 6 O O3A U2F . . . Q 2 34.527 50.095 -8.776 1 72.35 ? O3A U2F 501 F 1 
HETATM 7 P PA U2F . . . Q 2 35.842 50.521 -7.96 1 70.98 ? PA U2F 501 F 1 
HETATM 8 O O1A U2F . . . Q 2 37.027 50.645 -8.842 1 92.01 ? O1A U2F 501 F 1 
HETATM 9 O O2A U2F . . . Q 2 35.933 49.533 -6.857 1 77.07 ? O2A U2F 501 F 1 
HETATM 10 O O5' U2F . . . Q 2 35.49 51.974 -7.4 1 78.81 ? O5' U2F 501 F 1 
HETATM 11 C C5' U2F . . . Q 2 34.529 51.996 -6.322 1 79.96 ? C5' U2F 501 F 1 
HETATM 12 C C4' U2F . . . Q 2 33.753 53.285 -6.391 1 65.01 ? C4' U2F 501 F 1 
HETATM 13 O O4' U2F . . . Q 2 32.436 53.102 -5.815 1 57.56 ? O4' U2F 501 F 1 
HETATM 14 C C1' U2F . . . Q 2 32.344 53.775 -4.576 1 55.72 ? C1' U2F 501 F 1 
HETATM 15 C C2' U2F . . . Q 2 33.739 54.249 -4.201 1 53.41 ? C2' U2F 501 F 1 
HETATM 16 C C3' U2F . . . Q 2 34.368 54.439 -5.597 1 64.79 ? C3' U2F 501 F 1 
HETATM 17 O O3' U2F . . . Q 2 34.212 55.628 -6.372 1 61.76 ? O3' U2F 501 F 1 
HETATM 18 O O2' U2F . . . Q 2 33.515 55.449 -3.503 1 58.35 ? O2' U2F 501 F 1 
HETATM 19 N N1 U2F . . . Q 2 31.679 52.901 -3.588 1 60.64 ? N1 U2F 501 F 1 
HETATM 20 C C6' U2F . . . Q 2 31.698 51.529 -3.821 1 69.52 ? C6' U2F 501 F 1 
HETATM 21 O O6' U2F . . . Q 2 32.299 51.006 -4.749 1 85.2 ? O6' U2F 501 F 1 
HETATM 22 N N3 U2F . . . Q 2 30.983 50.774 -2.923 1 51.49 ? N3 U2F 501 F 1 
HETATM 23 C C7' U2F . . . Q 2 30.255 51.247 -1.855 1 49.69 ? C7' U2F 501 F 1 
HETATM 24 O O7' U2F . . . Q 2 29.683 50.439 -1.13 1 49.26 ? O7' U2F 501 F 1 
HETATM 25 C C8' U2F . . . Q 2 30.258 52.674 -1.694 1 54.46 ? C8' U2F 501 F 1 
HETATM 26 C C9' U2F . . . Q 2 30.948 53.44 -2.553 1 54 ? C9' U2F 501 F 1 
HETATM 27 C C2 U2F . . . Q 2 37.338 49.06 -12.055 1 76.22 ? C2 U2F 501 F 1 
HETATM 28 F F1 U2F . . . Q 2 37.904 47.921 -11.45 1 64.06 ? F1 U2F 501 F 1 
HETATM 29 C C3 U2F . . . Q 2 38.264 50.246 -11.828 1 77.35 ? C3 U2F 501 F 1 
HETATM 30 O O3 U2F . . . Q 2 39.55 49.974 -12.379 1 61.39 ? O3 U2F 501 F 1 
HETATM 31 C C4 U2F . . . Q 2 37.602 51.517 -12.38 1 94.34 ? C4 U2F 501 F 1 
HETATM 32 O O4 U2F . . . Q 2 38.477 52.656 -12.241 1 92.73 ? O4 U2F 501 F 1 
HETATM 33 C C5 U2F . . . Q 2 36.263 51.777 -11.601 1 89.11 ? C5 U2F 501 F 1 
HETATM 34 C C6 U2F . . . Q 2 35.014 52.145 -12.38 1 82.62 ? C6 U2F 501 F 1 
HETATM 35 O O6 U2F . . . Q 2 33.878 52.056 -11.505 1 82.47 ? O6 U2F 501 F 1 
HETATM 36 O O5 U2F . . . Q 2 35.899 50.609 -10.854 1 90.84 ? O5 U2F 501 F 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    172 
_model_server_stats.query_time_ms           491 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           36 
#