data_1SS9
#
_model_server_result.job_id            BIGapifpGGVpbGZJSqbwKg 
_model_server_result.datetime_utc      '2025-06-24 22:20:49' 
_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          1ss9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    1SS9 
#
_exptl.entry_id    1SS9 
_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-FLUOROGALACTOSE" 
_entity.pdbx_number_of_molecules    1 
_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            1SS9 
_cell.length_a            39.85 
_cell.length_b            75.934 
_cell.length_c            86.905 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1SS9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 A OD1 ASP 103 A ASP 103 1_555 B MN MN . A MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc2 A OD2 ASP 105 A ASP 105 1_555 B MN MN . A MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? 
metalc ? metalc3 A OD1 ASP 105 A ASP 105 1_555 B MN MN . A MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? 
metalc ? metalc4 A NE2 HIS 244 A HIS 244 1_555 B MN MN . A MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? 
metalc ? metalc5 B MN MN . A MN 400 1_555 C O1A UPF . A UPF 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc6 B MN MN . A MN 400 1_555 C O1B UPF . A UPF 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
#
_chem_comp.formula           'C15 H23 F N2 O16 P2' 
_chem_comp.formula_weight    568.293 
_chem_comp.id                UPF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUOROGALACTOSE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "URIDINE-5'-MONOPHOSPHATE 2-DEOXY-2-FLUORO-GALACTOPYRANOSYL-MONOPHOSPHATE ESTER" 
#
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 UPF sing 358 n n 
N1 C6 UPF sing 359 n n 
N1 C1D UPF sing 360 n n 
C2 N3 UPF sing 361 n n 
C2 O2 UPF doub 362 n n 
N3 C4 UPF sing 363 n n 
N3 HN3 UPF sing 364 n n 
C4 C5 UPF sing 365 n n 
C4 O4 UPF doub 366 n n 
C5 C6 UPF doub 367 n n 
C5 H5 UPF sing 368 n n 
C6 H6 UPF sing 369 n n 
C1D C2D UPF sing 370 n n 
C1D O4D UPF sing 371 n n 
C1D H1D UPF sing 372 n n 
C2D O2' UPF sing 373 n n 
C2D C3D UPF sing 374 n n 
C2D H2D UPF sing 375 n n 
O2' HO2' UPF sing 376 n n 
C3D C4D UPF sing 377 n n 
C3D O3D UPF sing 378 n n 
C3D H3D UPF sing 379 n n 
C4D O4D UPF sing 380 n n 
C4D C5D UPF sing 381 n n 
C4D H4D UPF sing 382 n n 
O3D HO3' UPF sing 383 n n 
C5D O5D UPF sing 384 n n 
C5D "H5'1" UPF sing 385 n n 
C5D "H5'2" UPF sing 386 n n 
O5D PA UPF sing 387 n n 
PA O1A UPF doub 388 n n 
PA O2A UPF sing 389 n n 
PA O3A UPF sing 390 n n 
O2A HOA2 UPF sing 391 n n 
O3A PB UPF sing 392 n n 
PB O1B UPF doub 393 n n 
PB O2B UPF sing 394 n n 
PB O3B UPF sing 395 n n 
O2B HOB2 UPF sing 396 n n 
O3B C1' UPF sing 397 n n 
C1' C2' UPF sing 398 n n 
C1' O5' UPF sing 399 n n 
C1' H1' UPF sing 400 n n 
C2' C3' UPF sing 401 n n 
C2' F2' UPF sing 402 n n 
C2' H2' UPF sing 403 n n 
C3' C4' UPF sing 404 n n 
C3' O3' UPF sing 405 n n 
C3' H3' UPF sing 406 n n 
C4' C5' UPF sing 407 n n 
C4' O4' UPF sing 408 n n 
C4' H4' UPF sing 409 n n 
C5' C6' UPF sing 410 n n 
C5' O5' UPF sing 411 n n 
C5' H5' UPF sing 412 n n 
C6' O6' UPF sing 413 n n 
C6' "H6'1" UPF sing 414 n n 
C6' "H6'2" UPF sing 415 n n 
O3' HO3A UPF sing 416 n n 
O4' HO4' UPF sing 417 n n 
O6' HO6' UPF sing 418 n n 
#
_atom_sites.entry_id                     1SS9 
_atom_sites.fract_transf_matrix[1][1]    0.025094 
_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]    0.013169 
_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]    0.011507 
_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
B 2 MN A 1 400 400 MN MN . 
C 3 UPF A 1 401 300 UPF UPF . 
D 4 HOH A 1 402 1 HOH WAT . 
D 4 HOH A 2 403 2 HOH WAT . 
D 4 HOH A 3 404 3 HOH WAT . 
D 4 HOH A 4 405 4 HOH WAT . 
D 4 HOH A 5 406 5 HOH WAT . 
D 4 HOH A 6 407 6 HOH WAT . 
D 4 HOH A 7 408 7 HOH WAT . 
D 4 HOH A 8 409 8 HOH WAT . 
D 4 HOH A 9 410 9 HOH WAT . 
D 4 HOH A 10 411 10 HOH WAT . 
D 4 HOH A 11 412 11 HOH WAT . 
D 4 HOH A 12 413 12 HOH WAT . 
D 4 HOH A 13 414 13 HOH WAT . 
D 4 HOH A 14 415 14 HOH WAT . 
D 4 HOH A 15 416 15 HOH WAT . 
D 4 HOH A 16 417 16 HOH WAT . 
D 4 HOH A 17 418 17 HOH WAT . 
D 4 HOH A 18 419 18 HOH WAT . 
D 4 HOH A 19 420 19 HOH WAT . 
D 4 HOH A 20 421 20 HOH WAT . 
D 4 HOH A 21 422 21 HOH WAT . 
D 4 HOH A 22 423 22 HOH WAT . 
D 4 HOH A 23 424 23 HOH WAT . 
D 4 HOH A 24 425 24 HOH WAT . 
D 4 HOH A 25 426 25 HOH WAT . 
#
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 UPF . . . C 3 12.882 31.468 14.088 1 11.17 ? N1 UPF 401 A 1 
HETATM 2 C C2 UPF . . . C 3 12.405 31.977 12.844 1 12.38 ? C2 UPF 401 A 1 
HETATM 3 N N3 UPF . . . C 3 13.276 31.719 11.754 1 14.43 ? N3 UPF 401 A 1 
HETATM 4 C C4 UPF . . . C 3 14.558 31.007 11.792 1 15.57 ? C4 UPF 401 A 1 
HETATM 5 C C5 UPF . . . C 3 15.004 30.493 13.092 1 16.72 ? C5 UPF 401 A 1 
HETATM 6 C C6 UPF . . . C 3 14.197 30.721 14.173 1 14.55 ? C6 UPF 401 A 1 
HETATM 7 O O2 UPF . . . C 3 11.372 32.569 12.745 1 18.14 ? O2 UPF 401 A 1 
HETATM 8 O O4 UPF . . . C 3 15.18 30.878 10.753 1 18.6 ? O4 UPF 401 A 1 
HETATM 9 C C1D UPF . . . C 3 12.163 31.593 15.481 1 8.04 ? C1D UPF 401 A 1 
HETATM 10 C C2D UPF . . . C 3 10.82 30.908 15.49 1 5.44 ? C2D UPF 401 A 1 
HETATM 11 O O2' UPF . . . C 3 9.912 31.703 16.193 1 6.8 ? O2' UPF 401 A 1 
HETATM 12 C C3D UPF . . . C 3 11.072 29.577 16.123 1 6.34 ? C3D UPF 401 A 1 
HETATM 13 C C4D UPF . . . C 3 11.826 30.079 17.308 1 9.37 ? C4D UPF 401 A 1 
HETATM 14 O O4D UPF . . . C 3 12.757 31.032 16.649 1 7.07 ? O4D UPF 401 A 1 
HETATM 15 O O3D UPF . . . C 3 9.902 28.931 16.615 1 13.9 ? O3D UPF 401 A 1 
HETATM 16 C C5D UPF . . . C 3 13.069 29.619 17.993 1 14.48 ? C5D UPF 401 A 1 
HETATM 17 O O5D UPF . . . C 3 13.709 28.336 17.673 1 19.34 ? O5D UPF 401 A 1 
HETATM 18 P PA UPF . . . C 3 13.328 26.863 17.333 1 13.1 ? PA UPF 401 A 1 
HETATM 19 O O1A UPF . . . C 3 11.894 26.542 17.285 1 18.36 ? O1A UPF 401 A 1 
HETATM 20 O O2A UPF . . . C 3 14.01 26.572 16.034 1 22.8 ? O2A UPF 401 A 1 
HETATM 21 O O3A UPF . . . C 3 14.045 26.61 18.719 1 20.53 ? O3A UPF 401 A 1 
HETATM 22 P PB UPF . . . C 3 14.268 25.316 19.543 1 18.99 ? PB UPF 401 A 1 
HETATM 23 O O1B UPF . . . C 3 12.904 24.874 19.803 1 20.59 ? O1B UPF 401 A 1 
HETATM 24 O O2B UPF . . . C 3 15.005 24.437 18.661 1 19.55 ? O2B UPF 401 A 1 
HETATM 25 O O3B UPF . . . C 3 14.988 25.348 20.946 1 27.91 ? O3B UPF 401 A 1 
HETATM 26 C C1' UPF . . . C 3 15.023 25.728 22.369 1 35.63 ? C1' UPF 401 A 1 
HETATM 27 C C2' UPF . . . C 3 13.581 25.794 22.9 1 37.5 ? C2' UPF 401 A 1 
HETATM 28 C C3' UPF . . . C 3 12.785 26.919 22.174 1 39.78 ? C3' UPF 401 A 1 
HETATM 29 C C4' UPF . . . C 3 13.445 28.316 22.43 1 39.21 ? C4' UPF 401 A 1 
HETATM 30 C C5' UPF . . . C 3 14.91 28.17 21.893 1 39.28 ? C5' UPF 401 A 1 
HETATM 31 C C6' UPF . . . C 3 15.67 29.462 22.147 1 42.43 ? C6' UPF 401 A 1 
HETATM 32 F F2' UPF . . . C 3 13.012 24.504 22.702 1 36.38 ? F2' UPF 401 A 1 
HETATM 33 O O3' UPF . . . C 3 11.443 26.97 22.658 1 38.15 ? O3' UPF 401 A 1 
HETATM 34 O O4' UPF . . . C 3 13.421 28.591 23.889 1 41.66 ? O4' UPF 401 A 1 
HETATM 35 O O5' UPF . . . C 3 15.663 27.076 22.579 1 37.89 ? O5' UPF 401 A 1 
HETATM 36 O O6' UPF . . . C 3 17.016 29.689 21.8 1 41.44 ? O6' UPF 401 A 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           29 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           1399 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           36 
#