data_2Y0D
#
_model_server_result.job_id            pJ-Q7YFfAr-8yB9xxSMQpg 
_model_server_result.datetime_utc      '2024-11-30 17:17:50' 
_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":"O","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 . . . O 2 -22.67 25.986 26.689 1 14.14 ? C1' UGA 500 D 1 
HETATM 2 C C2' UGA . . . O 2 -22.478 24.532 27.094 1 11.82 ? C2' UGA 500 D 1 
HETATM 3 O O2' UGA . . . O 2 -22.613 23.695 25.962 1 6.03 ? O2' UGA 500 D 1 
HETATM 4 C C3' UGA . . . O 2 -23.509 24.019 28.067 1 12.4 ? C3' UGA 500 D 1 
HETATM 5 O O3' UGA . . . O 2 -22.927 22.859 28.66 1 3.31 ? O3' UGA 500 D 1 
HETATM 6 C C4' UGA . . . O 2 -23.686 24.976 29.214 1 15.59 ? C4' UGA 500 D 1 
HETATM 7 O O4' UGA . . . O 2 -24.825 24.544 29.943 1 11.56 ? O4' UGA 500 D 1 
HETATM 8 C C5' UGA . . . O 2 -23.882 26.413 28.768 1 20.72 ? C5' UGA 500 D 1 
HETATM 9 O O5' UGA . . . O 2 -22.87 26.823 27.846 1 15.04 ? O5' UGA 500 D 1 
HETATM 10 C C6' UGA . . . O 2 -23.849 27.284 30.002 1 27.55 ? C6' UGA 500 D 1 
HETATM 11 O "O'P" UGA . . . O 2 -22.853 27.282 30.755 1 24.19 ? "O'P" UGA 500 D 1 
HETATM 12 O "O'Q" UGA . . . O 2 -24.852 27.986 30.251 1 38.83 ? "O'Q" UGA 500 D 1 
HETATM 13 P PB UGA . . . O 2 -23.929 27.3 24.685 1 20.12 ? PB UGA 500 D 1 
HETATM 14 O O1B UGA . . . O 2 -23.391 28.576 25.3 1 17.81 ? O1B UGA 500 D 1 
HETATM 15 O O2B UGA . . . O 2 -25.412 27.289 24.332 1 12.93 ? O2B UGA 500 D 1 
HETATM 16 O O3B UGA . . . O 2 -23.722 26.056 25.729 1 7.25 ? O3B UGA 500 D 1 
HETATM 17 O O3A UGA . . . O 2 -23.204 26.975 23.249 1 13.16 ? O3A UGA 500 D 1 
HETATM 18 P PA UGA . . . O 2 -22.661 25.554 22.646 1 19.08 ? PA UGA 500 D 1 
HETATM 19 O O1A UGA . . . O 2 -23.681 24.836 21.803 1 24.89 ? O1A UGA 500 D 1 
HETATM 20 O O2A UGA . . . O 2 -21.989 24.831 23.781 1 2.17 ? O2A UGA 500 D 1 
HETATM 21 O O5D UGA . . . O 2 -21.556 26.031 21.579 1 12.31 ? O5D UGA 500 D 1 
HETATM 22 C C5D UGA . . . O 2 -20.886 27.259 21.896 1 11.96 ? C5D UGA 500 D 1 
HETATM 23 C C4D UGA . . . O 2 -20.007 27.78 20.777 1 8.97 ? C4D UGA 500 D 1 
HETATM 24 O O4D UGA . . . O 2 -19.112 26.753 20.38 1 14.49 ? O4D UGA 500 D 1 
HETATM 25 C C3D UGA . . . O 2 -20.787 28.128 19.527 1 17.21 ? C3D UGA 500 D 1 
HETATM 26 O O3D UGA . . . O 2 -20.084 29.251 18.965 1 13.89 ? O3D UGA 500 D 1 
HETATM 27 C C2D UGA . . . O 2 -20.626 26.895 18.656 1 14.59 ? C2D UGA 500 D 1 
HETATM 28 O O2D UGA . . . O 2 -20.723 27.167 17.265 1 20.76 ? O2D UGA 500 D 1 
HETATM 29 C C1D UGA . . . O 2 -19.199 26.571 18.968 1 12.29 ? C1D UGA 500 D 1 
HETATM 30 N N1 UGA . . . O 2 -18.757 25.231 18.602 1 22.08 ? N1 UGA 500 D 1 
HETATM 31 C C6 UGA . . . O 2 -19.237 24.15 19.228 1 15.14 ? C6 UGA 500 D 1 
HETATM 32 C C2 UGA . . . O 2 -17.802 25.102 17.679 1 0 ? C2 UGA 500 D 1 
HETATM 33 O O2 UGA . . . O 2 -17.33 26.091 17.138 1 24.73 ? O2 UGA 500 D 1 
HETATM 34 N N3 UGA . . . O 2 -17.312 23.904 17.323 1 21.9 ? N3 UGA 500 D 1 
HETATM 35 C C4 UGA . . . O 2 -17.765 22.768 17.898 1 12.07 ? C4 UGA 500 D 1 
HETATM 36 O O4 UGA . . . O 2 -17.298 21.653 17.531 1 10.74 ? O4 UGA 500 D 1 
HETATM 37 C C5 UGA . . . O 2 -18.755 22.881 18.878 1 3.58 ? C5 UGA 500 D 1 
#
_model_server_stats.io_time_ms              73 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           37 
#