data_1BGU
#
_model_server_result.job_id            FlikdGD12cQt44pT6nsXHg 
_model_server_result.datetime_utc      '2025-02-05 05:51:31' 
_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          1bgu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":353}' 
#
_entry.id    1BGU 
#
_exptl.entry_id    1BGU 
_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    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            1BGU 
_cell.length_a            151.92 
_cell.length_b            52.26 
_cell.length_c            52.74 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1BGU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_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 
_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                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 343 n n 
N1 C6 UDP sing 344 n n 
N1 C1' UDP sing 345 n n 
C2 N3 UDP sing 346 n n 
C2 O2 UDP doub 347 n n 
N3 C4 UDP sing 348 n n 
N3 HN3 UDP sing 349 n n 
C4 C5 UDP sing 350 n n 
C4 O4 UDP doub 351 n n 
C5 C6 UDP doub 352 n n 
C5 H5 UDP sing 353 n n 
C6 H6 UDP sing 354 n n 
C1' C2' UDP sing 355 n n 
C1' O4' UDP sing 356 n n 
C1' H1' UDP sing 357 n n 
C2' O2' UDP sing 358 n n 
C2' C3' UDP sing 359 n n 
C2' H2' UDP sing 360 n n 
O2' HO2' UDP sing 361 n n 
C3' C4' UDP sing 362 n n 
C3' O3' UDP sing 363 n n 
C3' H3' UDP sing 364 n n 
C4' O4' UDP sing 365 n n 
C4' C5' UDP sing 366 n n 
C4' H4' UDP sing 367 n n 
O3' HO3' UDP sing 368 n n 
C5' O5' UDP sing 369 n n 
C5' "H5'1" UDP sing 370 n n 
C5' "H5'2" UDP sing 371 n n 
O5' PA UDP sing 372 n n 
PA O1A UDP doub 373 n n 
PA O2A UDP sing 374 n n 
PA O3A UDP sing 375 n n 
O2A HOA2 UDP sing 376 n n 
O3A PB UDP sing 377 n n 
PB O1B UDP doub 378 n n 
PB O2B UDP sing 379 n n 
PB O3B UDP sing 380 n n 
O2B HOB2 UDP sing 381 n n 
O3B HOB3 UDP sing 382 n n 
#
_atom_sites.entry_id                     1BGU 
_atom_sites.fract_transf_matrix[1][1]    0.006582 
_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]    0.019135 
_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]    0.018961 
_atom_sites.fract_transf_vector[1]       -0.25 
_atom_sites.fract_transf_vector[2]       -0.25 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          B 
_pdbx_nonpoly_scheme.entity_id        2 
_pdbx_nonpoly_scheme.mon_id           UDP 
_pdbx_nonpoly_scheme.pdb_strand_id    A 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      353 
_pdbx_nonpoly_scheme.auth_seq_num     353 
_pdbx_nonpoly_scheme.pdb_mon_id       UDP 
_pdbx_nonpoly_scheme.auth_mon_id      UDP 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 . . . B 2 53.589 3.867 16.708 1 16.74 ? N1 UDP 353 A 1 
HETATM 2 C C2 UDP . . . B 2 52.309 4.22 17.054 1 17.25 ? C2 UDP 353 A 1 
HETATM 3 N N3 UDP . . . B 2 51.815 3.785 18.251 1 17.83 ? N3 UDP 353 A 1 
HETATM 4 C C4 UDP . . . B 2 52.531 3.01 19.119 1 17.84 ? C4 UDP 353 A 1 
HETATM 5 C C5 UDP . . . B 2 53.98 2.701 18.907 1 17.3 ? C5 UDP 353 A 1 
HETATM 6 C C6 UDP . . . B 2 54.442 3.079 17.691 1 17.21 ? C6 UDP 353 A 1 
HETATM 7 O O2 UDP . . . B 2 51.615 4.928 16.329 1 17.27 ? O2 UDP 353 A 1 
HETATM 8 O O4 UDP . . . B 2 51.988 2.5 20.096 1 18.48 ? O4 UDP 353 A 1 
HETATM 9 C C1' UDP . . . B 2 54.116 4.214 15.37 1 15.8 ? C1' UDP 353 A 1 
HETATM 10 C C2' UDP . . . B 2 54.939 5.421 15.521 1 15.59 ? C2' UDP 353 A 1 
HETATM 11 O O2' UDP . . . B 2 54.677 6.386 14.502 1 15.55 ? O2' UDP 353 A 1 
HETATM 12 C C3' UDP . . . B 2 56.347 4.889 15.578 1 15.42 ? C3' UDP 353 A 1 
HETATM 13 C C4' UDP . . . B 2 56.278 3.787 14.663 1 15.34 ? C4' UDP 353 A 1 
HETATM 14 O O4' UDP . . . B 2 55.037 3.175 15.022 1 15.66 ? O4' UDP 353 A 1 
HETATM 15 O O3' UDP . . . B 2 57.319 5.836 15.158 1 16.08 ? O3' UDP 353 A 1 
HETATM 16 C C5' UDP . . . B 2 57.402 2.857 14.892 1 15.54 ? C5' UDP 353 A 1 
HETATM 17 O O5' UDP . . . B 2 57.229 1.693 14.024 1 15.36 ? O5' UDP 353 A 1 
HETATM 18 P PA UDP . . . B 2 58.275 0.48 14.125 1 15.45 ? PA UDP 353 A 1 
HETATM 19 O O1A UDP . . . B 2 58.086 -0.181 15.378 1 15.26 ? O1A UDP 353 A 1 
HETATM 20 O O2A UDP . . . B 2 57.889 -0.442 13.054 1 15.61 ? O2A UDP 353 A 1 
HETATM 21 O O3A UDP . . . B 2 59.775 0.951 13.952 1 15.39 ? O3A UDP 353 A 1 
HETATM 22 P PB UDP . . . B 2 60.687 1.928 13.093 1 15.37 ? PB UDP 353 A 1 
HETATM 23 O O1B UDP . . . B 2 59.942 2.979 12.601 1 15.61 ? O1B UDP 353 A 1 
HETATM 24 O O2B UDP . . . B 2 61.188 1.123 11.964 1 15.64 ? O2B UDP 353 A 1 
HETATM 25 O O3B UDP . . . B 2 61.693 2.586 13.976 1 15.68 ? O3B UDP 353 A 1 
#
_model_server_stats.io_time_ms              4 
_model_server_stats.parse_time_ms           4 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#