data_2Y0D
#
_model_server_result.job_id            RyZI1A0jVirSYZTAjnTFQg 
_model_server_result.datetime_utc      '2025-06-24 02:17:11' 
_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          2y0d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":500}' 
#
_entry.id    2Y0D 
#
_exptl.entry_id    2Y0D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              580.285 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID" 
_entity.pdbx_number_of_molecules    4 
_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            2Y0D 
_cell.length_a            101.622 
_cell.length_b            109.25 
_cell.length_c            183.439 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2Y0D 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 I N N 
? 2 K N N 
? 2 O N N 
#
_chem_comp.formula           'C15 H22 N2 O18 P2' 
_chem_comp.formula_weight    580.285 
_chem_comp.id                UGA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'UDP-GLUCURONIC ACID' 
#
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' C2' UGA sing 360 n n 
C1' O5' UGA sing 361 n n 
C1' O3B UGA sing 362 n n 
C1' "H1'1" UGA sing 363 n n 
C2' O2' UGA sing 364 n n 
C2' C3' UGA sing 365 n n 
C2' "H2'1" UGA sing 366 n n 
O2' "HO'2" UGA sing 367 n n 
C3' O3' UGA sing 368 n n 
C3' C4' UGA sing 369 n n 
C3' "H3'1" UGA sing 370 n n 
O3' "HO'3" UGA sing 371 n n 
C4' O4' UGA sing 372 n n 
C4' C5' UGA sing 373 n n 
C4' "H4'1" UGA sing 374 n n 
O4' "HO'4" UGA sing 375 n n 
C5' O5' UGA sing 376 n n 
C5' C6' UGA sing 377 n n 
C5' "H5'1" UGA sing 378 n n 
C6' "O'P" UGA doub 379 n n 
C6' "O'Q" UGA sing 380 n n 
"O'Q" "HO'6" UGA sing 381 n n 
PB O1B UGA doub 382 n n 
PB O2B UGA sing 383 n n 
PB O3B UGA sing 384 n n 
PB O3A UGA sing 385 n n 
O2B HOB2 UGA sing 386 n n 
O3A PA UGA sing 387 n n 
PA O1A UGA doub 388 n n 
PA O2A UGA sing 389 n n 
PA O5D UGA sing 390 n n 
O2A HOA2 UGA sing 391 n n 
O5D C5D UGA sing 392 n n 
C5D C4D UGA sing 393 n n 
C5D H5A1 UGA sing 394 n n 
C5D "H5'2" UGA sing 395 n n 
C4D O4D UGA sing 396 n n 
C4D C3D UGA sing 397 n n 
C4D H4A1 UGA sing 398 n n 
O4D C1D UGA sing 399 n n 
C3D O3D UGA sing 400 n n 
C3D C2D UGA sing 401 n n 
C3D H3A1 UGA sing 402 n n 
O3D HOA3 UGA sing 403 n n 
C2D O2D UGA sing 404 n n 
C2D C1D UGA sing 405 n n 
C2D H2A1 UGA sing 406 n n 
O2D HOC2 UGA sing 407 n n 
C1D N1 UGA sing 408 n n 
C1D H1A1 UGA sing 409 n n 
N1 C6 UGA sing 410 n y 
N1 C2 UGA sing 411 n y 
C6 C5 UGA doub 412 n y 
C6 H61 UGA sing 413 n n 
C2 O2 UGA doub 414 n n 
C2 N3 UGA sing 415 n y 
N3 C4 UGA sing 416 n y 
N3 HN3 UGA sing 417 n n 
C4 O4 UGA doub 418 n n 
C4 C5 UGA sing 419 n y 
C5 H51 UGA sing 420 n n 
#
_atom_sites.entry_id                     2Y0D 
_atom_sites.fract_transf_matrix[1][1]    0.00984 
_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]    0.009153 
_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]    0.005451 
_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
E 2 UGA A 1 500 500 UGA UGA . 
F 3 SO4 A 1 1457 1457 SO4 SO4 . 
G 3 SO4 A 1 1458 1458 SO4 SO4 . 
H 3 SO4 A 1 1459 1459 SO4 SO4 . 
I 2 UGA B 1 500 500 UGA UGA . 
J 3 SO4 B 1 1454 1454 SO4 SO4 . 
K 2 UGA C 1 500 500 UGA UGA . 
L 3 SO4 C 1 1454 1454 SO4 SO4 . 
M 3 SO4 C 1 1455 1455 SO4 SO4 . 
N 3 SO4 C 1 1456 1456 SO4 SO4 . 
O 2 UGA D 1 500 500 UGA UGA . 
P 3 SO4 D 1 1456 1456 SO4 SO4 . 
#
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' UGA . . . E 2 -24.886 -17.339 29.451 1 8.3 ? C1' UGA 500 A 1 
HETATM 2 C C2' UGA . . . E 2 -24.979 -15.851 29.181 1 0 ? C2' UGA 500 A 1 
HETATM 3 O O2' UGA . . . E 2 -24.231 -15.618 27.998 1 3.96 ? O2' UGA 500 A 1 
HETATM 4 C C3' UGA . . . E 2 -24.454 -14.983 30.334 1 17.17 ? C3' UGA 500 A 1 
HETATM 5 O O3' UGA . . . E 2 -24.592 -13.554 30.104 1 0 ? O3' UGA 500 A 1 
HETATM 6 C C4' UGA . . . E 2 -25.169 -15.412 31.615 1 7.81 ? C4' UGA 500 A 1 
HETATM 7 O O4' UGA . . . E 2 -24.613 -14.762 32.744 1 12.8 ? O4' UGA 500 A 1 
HETATM 8 C C5' UGA . . . E 2 -24.857 -16.867 31.833 1 11.22 ? C5' UGA 500 A 1 
HETATM 9 O O5' UGA . . . E 2 -25.399 -17.62 30.755 1 13.25 ? O5' UGA 500 A 1 
HETATM 10 C C6' UGA . . . E 2 -25.458 -17.305 33.131 1 16.32 ? C6' UGA 500 A 1 
HETATM 11 O "O'P" UGA . . . E 2 -26.695 -17.22 33.301 1 11.27 ? "O'P" UGA 500 A 1 
HETATM 12 O "O'Q" UGA . . . E 2 -24.66 -17.737 33.992 1 26.65 ? "O'Q" UGA 500 A 1 
HETATM 13 P PB UGA . . . E 2 -22.943 -19.199 28.796 1 12.77 ? PB UGA 500 A 1 
HETATM 14 O O1B UGA . . . E 2 -24.034 -20.218 28.785 1 20.13 ? O1B UGA 500 A 1 
HETATM 15 O O2B UGA . . . E 2 -21.682 -19.516 29.578 1 29.53 ? O2B UGA 500 A 1 
HETATM 16 O O3B UGA . . . E 2 -23.538 -17.78 29.308 1 11.12 ? O3B UGA 500 A 1 
HETATM 17 O O3A UGA . . . E 2 -22.294 -18.846 27.351 1 7.61 ? O3A UGA 500 A 1 
HETATM 18 P PA UGA . . . E 2 -23.021 -18.191 26.068 1 14.62 ? PA UGA 500 A 1 
HETATM 19 O O1A UGA . . . E 2 -21.928 -17.348 25.469 1 12.22 ? O1A UGA 500 A 1 
HETATM 20 O O2A UGA . . . E 2 -24.394 -17.632 26.379 1 10.66 ? O2A UGA 500 A 1 
HETATM 21 O O5D UGA . . . E 2 -23.301 -19.459 25.12 1 21.41 ? O5D UGA 500 A 1 
HETATM 22 C C5D UGA . . . E 2 -24.629 -19.973 24.966 1 18.38 ? C5D UGA 500 A 1 
HETATM 23 C C4D UGA . . . E 2 -24.787 -20.965 23.804 1 9.54 ? C4D UGA 500 A 1 
HETATM 24 O O4D UGA . . . E 2 -25.395 -20.341 22.671 1 13.77 ? O4D UGA 500 A 1 
HETATM 25 C C3D UGA . . . E 2 -23.464 -21.52 23.308 1 4.42 ? C3D UGA 500 A 1 
HETATM 26 O O3D UGA . . . E 2 -23.703 -22.914 23.116 1 6.34 ? O3D UGA 500 A 1 
HETATM 27 C C2D UGA . . . E 2 -23.241 -20.791 21.996 1 7.62 ? C2D UGA 500 A 1 
HETATM 28 O O2D UGA . . . E 2 -22.517 -21.58 21.07 1 12.21 ? O2D UGA 500 A 1 
HETATM 29 C C1D UGA . . . E 2 -24.644 -20.597 21.483 1 9.73 ? C1D UGA 500 A 1 
HETATM 30 N N1 UGA . . . E 2 -24.728 -19.439 20.612 1 14.99 ? N1 UGA 500 A 1 
HETATM 31 C C6 UGA . . . E 2 -24.347 -18.269 21.132 1 10.33 ? C6 UGA 500 A 1 
HETATM 32 C C2 UGA . . . E 2 -25.208 -19.537 19.335 1 25.44 ? C2 UGA 500 A 1 
HETATM 33 O O2 UGA . . . E 2 -25.571 -20.675 18.921 1 19.43 ? O2 UGA 500 A 1 
HETATM 34 N N3 UGA . . . E 2 -25.316 -18.443 18.504 1 0 ? N3 UGA 500 A 1 
HETATM 35 C C4 UGA . . . E 2 -24.937 -17.209 18.983 1 17.25 ? C4 UGA 500 A 1 
HETATM 36 O O4 UGA . . . E 2 -24.999 -16.119 18.296 1 7.59 ? O4 UGA 500 A 1 
HETATM 37 C C5 UGA . . . E 2 -24.457 -17.137 20.306 1 12.72 ? C5 UGA 500 A 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           231 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           37 
#