data_2Y0D
#
_model_server_result.job_id            zIQPf284cS3N5GsVq0xRtw 
_model_server_result.datetime_utc      '2025-06-23 10:17:01' 
_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":"K","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 . . . K 2 -0.297 5.418 23.777 1 8.68 ? C1' UGA 500 C 1 
HETATM 2 C C2' UGA . . . K 2 -1.757 5.512 23.34 1 2.22 ? C2' UGA 500 C 1 
HETATM 3 O O2' UGA . . . K 2 -2.652 5.28 24.422 1 2.5 ? O2' UGA 500 C 1 
HETATM 4 C C3' UGA . . . K 2 -2.147 4.491 22.335 1 0 ? C3' UGA 500 C 1 
HETATM 5 O O3' UGA . . . K 2 -3.452 4.903 21.979 1 0 ? O3' UGA 500 C 1 
HETATM 6 C C4' UGA . . . K 2 -1.192 4.584 21.171 1 15.67 ? C4' UGA 500 C 1 
HETATM 7 O O4' UGA . . . K 2 -1.52 3.59 20.178 1 14.04 ? O4' UGA 500 C 1 
HETATM 8 C C5' UGA . . . K 2 0.215 4.372 21.685 1 10.61 ? C5' UGA 500 C 1 
HETATM 9 O O5' UGA . . . K 2 0.555 5.361 22.64 1 0 ? O5' UGA 500 C 1 
HETATM 10 C C6' UGA . . . K 2 1.137 4.503 20.51 1 16.74 ? C6' UGA 500 C 1 
HETATM 11 O "O'P" UGA . . . K 2 1.84 3.523 20.218 1 19.05 ? "O'P" UGA 500 C 1 
HETATM 12 O "O'Q" UGA . . . K 2 1.189 5.567 19.862 1 13.92 ? "O'Q" UGA 500 C 1 
HETATM 13 P PB UGA . . . K 2 1.009 4.063 25.691 1 16.91 ? PB UGA 500 C 1 
HETATM 14 O O1B UGA . . . K 2 2.307 4.688 25.156 1 18.62 ? O1B UGA 500 C 1 
HETATM 15 O O2B UGA . . . K 2 1.005 2.591 26.017 1 21.35 ? O2B UGA 500 C 1 
HETATM 16 O O3B UGA . . . K 2 -0.164 4.286 24.619 1 11.79 ? O3B UGA 500 C 1 
HETATM 17 O O3A UGA . . . K 2 0.539 4.678 27.104 1 18.51 ? O3A UGA 500 C 1 
HETATM 18 P PA UGA . . . K 2 -0.91 5.226 27.543 1 11.09 ? PA UGA 500 C 1 
HETATM 19 O O1A UGA . . . K 2 -1.765 4.073 28.038 1 2.14 ? O1A UGA 500 C 1 
HETATM 20 O O2A UGA . . . K 2 -1.389 6.114 26.425 1 11.91 ? O2A UGA 500 C 1 
HETATM 21 O O5D UGA . . . K 2 -0.471 6.159 28.784 1 7.3 ? O5D UGA 500 C 1 
HETATM 22 C C5D UGA . . . K 2 0.293 7.337 28.523 1 0 ? C5D UGA 500 C 1 
HETATM 23 C C4D UGA . . . K 2 0.773 7.962 29.814 1 0 ? C4D UGA 500 C 1 
HETATM 24 O O4D UGA . . . K 2 -0.195 8.886 30.293 1 23.77 ? O4D UGA 500 C 1 
HETATM 25 C C3D UGA . . . K 2 0.975 6.967 30.927 1 6.36 ? C3D UGA 500 C 1 
HETATM 26 O O3D UGA . . . K 2 2.136 7.331 31.692 1 13.7 ? O3D UGA 500 C 1 
HETATM 27 C C2D UGA . . . K 2 -0.204 7.16 31.813 1 5.71 ? C2D UGA 500 C 1 
HETATM 28 O O2D UGA . . . K 2 0.186 6.836 33.147 1 10.38 ? O2D UGA 500 C 1 
HETATM 29 C C1D UGA . . . K 2 -0.469 8.651 31.66 1 18.66 ? C1D UGA 500 C 1 
HETATM 30 N N1 UGA . . . K 2 -1.88 8.929 31.905 1 19.49 ? N1 UGA 500 C 1 
HETATM 31 C C6 UGA . . . K 2 -2.792 8.261 31.186 1 4.29 ? C6 UGA 500 C 1 
HETATM 32 C C2 UGA . . . K 2 -2.237 9.794 32.849 1 15.56 ? C2 UGA 500 C 1 
HETATM 33 O O2 UGA . . . K 2 -1.382 10.372 33.534 1 20.35 ? O2 UGA 500 C 1 
HETATM 34 N N3 UGA . . . K 2 -3.526 10.045 33.093 1 18.71 ? N3 UGA 500 C 1 
HETATM 35 C C4 UGA . . . K 2 -4.484 9.401 32.411 1 12.15 ? C4 UGA 500 C 1 
HETATM 36 O O4 UGA . . . K 2 -5.679 9.645 32.658 1 9.38 ? O4 UGA 500 C 1 
HETATM 37 C C5 UGA . . . K 2 -4.134 8.476 31.434 1 7.98 ? C5 UGA 500 C 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           332 
_model_server_stats.encode_time_ms          15 
_model_server_stats.element_count           37 
#