data_6JEM
#
_model_server_result.job_id            PH-VehQhe-ukuHaPBzvU5A 
_model_server_result.datetime_utc      '2025-01-25 10:35:17' 
_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          6jem 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":501}' 
#
_entry.id    6JEM 
#
_exptl.entry_id    6JEM 
_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    3 
_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            6JEM 
_cell.length_a            57.374 
_cell.length_b            137.616 
_cell.length_c            208.956 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6JEM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E 1 1 
B,F,G 2 1 
C,H,I 3 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 D N N 
? 2 F N N 
? 2 H 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 386 n n 
C1 C2 U2F sing 387 n n 
C1 O5 U2F sing 388 n n 
C1 H1 U2F sing 389 n n 
O1 PB U2F sing 390 n n 
PB O1B U2F doub 391 n n 
PB O2B U2F sing 392 n n 
PB O3A U2F sing 393 n n 
O3A PA U2F sing 394 n n 
PA O1A U2F doub 395 n n 
PA O2A U2F sing 396 n n 
PA O5' U2F sing 397 n n 
O5' C5' U2F sing 398 n n 
C5' C4' U2F sing 399 n n 
C5' "H5'1" U2F sing 400 n n 
C5' "H5'2" U2F sing 401 n n 
C4' O4' U2F sing 402 n n 
C4' C3' U2F sing 403 n n 
C4' H4' U2F sing 404 n n 
O4' C1' U2F sing 405 n n 
C1' C2' U2F sing 406 n n 
C1' N1 U2F sing 407 n n 
C1' H1' U2F sing 408 n n 
C2' C3' U2F sing 409 n n 
C2' O2' U2F sing 410 n n 
C2' H2' U2F sing 411 n n 
C3' O3' U2F sing 412 n n 
C3' H3' U2F sing 413 n n 
O3' HB U2F sing 414 n n 
O2' HA U2F sing 415 n n 
N1 C6' U2F sing 416 n n 
N1 C9' U2F sing 417 n n 
C6' O6' U2F doub 418 n n 
C6' N3 U2F sing 419 n n 
N3 C7' U2F sing 420 n n 
N3 H3 U2F sing 421 n n 
C7' O7' U2F doub 422 n n 
C7' C8' U2F sing 423 n n 
C8' C9' U2F doub 424 n n 
C8' H8' U2F sing 425 n n 
C9' H9' U2F sing 426 n n 
C2 F1 U2F sing 427 n n 
C2 C3 U2F sing 428 n n 
C2 H2 U2F sing 429 n n 
C3 O3 U2F sing 430 n n 
C3 C4 U2F sing 431 n n 
C3 HC U2F sing 432 n n 
O3 HD U2F sing 433 n n 
C4 O4 U2F sing 434 n n 
C4 C5 U2F sing 435 n n 
C4 H4 U2F sing 436 n n 
O4 HE U2F sing 437 n n 
C5 C6 U2F sing 438 n n 
C5 O5 U2F sing 439 n n 
C5 H5 U2F sing 440 n n 
C6 O6 U2F sing 441 n n 
C6 H6C1 U2F sing 442 n n 
C6 H6C2 U2F sing 443 n n 
O6 H6 U2F sing 444 n n 
HO1 O2A U2F sing 445 n n 
HO2 O2B U2F sing 446 n n 
#
_atom_sites.entry_id                     6JEM 
_atom_sites.fract_transf_matrix[1][1]    0.017429 
_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]    0.007267 
_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]    0.004786 
_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
D 2 U2F A 1 501 1 U2F U2F . 
E 3 STL A 1 502 1 STL STL . 
F 2 U2F B 1 501 2 U2F U2F . 
G 3 STL B 1 502 2 STL STL . 
H 2 U2F C 1 501 3 U2F U2F . 
I 3 STL C 1 502 3 STL STL . 
#
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 . . . H 2 38.014 64.566 23.051 1 60.77 ? C1 U2F 501 C 1 
HETATM 2 O O1 U2F . . . H 2 38.482 65.187 24.219 1 65.07 ? O1 U2F 501 C 1 
HETATM 3 P PB U2F . . . H 2 39.747 64.635 25.036 1 67.33 ? PB U2F 501 C 1 
HETATM 4 O O1B U2F . . . H 2 39.447 63.258 25.527 1 71.35 ? O1B U2F 501 C 1 
HETATM 5 O O2B U2F . . . H 2 40.98 64.83 24.217 1 86.7 ? O2B U2F 501 C 1 
HETATM 6 O O3A U2F . . . H 2 39.783 65.641 26.285 1 72.95 ? O3A U2F 501 C 1 
HETATM 7 P PA U2F . . . H 2 38.949 65.702 27.654 1 74.51 ? PA U2F 501 C 1 
HETATM 8 O O1A U2F . . . H 2 37.668 64.959 27.468 1 67.52 ? O1A U2F 501 C 1 
HETATM 9 O O2A U2F . . . H 2 38.883 67.122 28.111 1 83.47 ? O2A U2F 501 C 1 
HETATM 10 O O5' U2F . . . H 2 39.909 64.872 28.635 1 80.15 ? O5' U2F 501 C 1 
HETATM 11 C C5' U2F . . . H 2 41.322 65.197 28.664 1 73.39 ? C5' U2F 501 C 1 
HETATM 12 C C4' U2F . . . H 2 42.039 64.223 29.566 1 70.16 ? C4' U2F 501 C 1 
HETATM 13 O O4' U2F . . . H 2 43.408 64.665 29.772 1 72.44 ? O4' U2F 501 C 1 
HETATM 14 C C1' U2F . . . H 2 43.61 65.002 31.129 1 75.66 ? C1' U2F 501 C 1 
HETATM 15 C C2' U2F . . . H 2 42.226 65.123 31.765 1 73.7 ? C2' U2F 501 C 1 
HETATM 16 C C3' U2F . . . H 2 41.457 64.058 30.977 1 70.66 ? C3' U2F 501 C 1 
HETATM 17 O O3' U2F . . . H 2 41.693 62.75 31.483 1 72.12 ? O3' U2F 501 C 1 
HETATM 18 O O2' U2F . . . H 2 42.312 64.832 33.144 1 73.47 ? O2' U2F 501 C 1 
HETATM 19 N N1 U2F . . . H 2 44.384 66.257 31.196 1 88 ? N1 U2F 501 C 1 
HETATM 20 C C6' U2F . . . H 2 45.255 66.404 32.26 1 92.6 ? C6' U2F 501 C 1 
HETATM 21 O O6' U2F . . . H 2 45.398 65.549 33.123 1 82.26 ? O6' U2F 501 C 1 
HETATM 22 N N3 U2F . . . H 2 45.949 67.587 32.277 1 85.69 ? N3 U2F 501 C 1 
HETATM 23 C C7' U2F . . . H 2 45.864 68.615 31.358 1 85.25 ? C7' U2F 501 C 1 
HETATM 24 O O7' U2F . . . H 2 46.558 69.621 31.511 1 87.19 ? O7' U2F 501 C 1 
HETATM 25 C C8' U2F . . . H 2 44.94 68.386 30.285 1 85.88 ? C8' U2F 501 C 1 
HETATM 26 C C9' U2F . . . H 2 44.246 67.238 30.243 1 89.92 ? C9' U2F 501 C 1 
HETATM 27 C C2 U2F . . . H 2 36.979 65.47 22.418 1 65.64 ? C2 U2F 501 C 1 
HETATM 28 F F1 U2F . . . H 2 37.533 66.754 22.267 1 79.96 ? F1 U2F 501 C 1 
HETATM 29 C C3 U2F . . . H 2 35.732 65.581 23.274 1 65.64 ? C3 U2F 501 C 1 
HETATM 30 O O3 U2F . . . H 2 34.736 66.301 22.553 1 60.19 ? O3 U2F 501 C 1 
HETATM 31 C C4 U2F . . . H 2 35.228 64.181 23.607 1 64.08 ? C4 U2F 501 C 1 
HETATM 32 O O4 U2F . . . H 2 34.126 64.259 24.506 1 64.79 ? O4 U2F 501 C 1 
HETATM 33 C C5 U2F . . . H 2 36.341 63.366 24.254 1 65.59 ? C5 U2F 501 C 1 
HETATM 34 C C6 U2F . . . H 2 35.93 61.943 24.555 1 64.15 ? C6 U2F 501 C 1 
HETATM 35 O O6 U2F . . . H 2 34.878 61.514 23.693 1 73.88 ? O6 U2F 501 C 1 
HETATM 36 O O5 U2F . . . H 2 37.461 63.296 23.354 1 68.04 ? O5 U2F 501 C 1 
#
_model_server_stats.io_time_ms              38 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           460 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           36 
#