data_8GJH
#
_model_server_result.job_id            FZJ5R1wnLrVrzhghSh4b8g 
_model_server_result.datetime_utc      '2024-12-01 12:04:50' 
_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          8gjh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":1100}' 
#
_entry.id    8GJH 
#
_exptl.entry_id    8GJH 
_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    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         62.99 
_cell.angle_beta          71.66 
_cell.angle_gamma         77.76 
_cell.entry_id            8GJH 
_cell.length_a            90.826 
_cell.length_b            129.439 
_cell.length_c            140.188 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8GJH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    'P 1' 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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 
_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 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L 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 356 n n 
C1' O5' UGA sing 357 n n 
C1' O3B UGA sing 358 n n 
C1' "H1'1" UGA sing 359 n n 
C2' O2' UGA sing 360 n n 
C2' C3' UGA sing 361 n n 
C2' "H2'1" UGA sing 362 n n 
O2' "HO'2" UGA sing 363 n n 
C3' O3' UGA sing 364 n n 
C3' C4' UGA sing 365 n n 
C3' "H3'1" UGA sing 366 n n 
O3' "HO'3" UGA sing 367 n n 
C4' O4' UGA sing 368 n n 
C4' C5' UGA sing 369 n n 
C4' "H4'1" UGA sing 370 n n 
O4' "HO'4" UGA sing 371 n n 
C5' O5' UGA sing 372 n n 
C5' C6' UGA sing 373 n n 
C5' "H5'1" UGA sing 374 n n 
C6' "O'P" UGA doub 375 n n 
C6' "O'Q" UGA sing 376 n n 
"O'Q" "HO'6" UGA sing 377 n n 
PB O1B UGA doub 378 n n 
PB O2B UGA sing 379 n n 
PB O3B UGA sing 380 n n 
PB O3A UGA sing 381 n n 
O2B HOB2 UGA sing 382 n n 
O3A PA UGA sing 383 n n 
PA O1A UGA doub 384 n n 
PA O2A UGA sing 385 n n 
PA O5D UGA sing 386 n n 
O2A HOA2 UGA sing 387 n n 
O5D C5D UGA sing 388 n n 
C5D C4D UGA sing 389 n n 
C5D H5A1 UGA sing 390 n n 
C5D "H5'2" UGA sing 391 n n 
C4D O4D UGA sing 392 n n 
C4D C3D UGA sing 393 n n 
C4D H4A1 UGA sing 394 n n 
O4D C1D UGA sing 395 n n 
C3D O3D UGA sing 396 n n 
C3D C2D UGA sing 397 n n 
C3D H3A1 UGA sing 398 n n 
O3D HOA3 UGA sing 399 n n 
C2D O2D UGA sing 400 n n 
C2D C1D UGA sing 401 n n 
C2D H2A1 UGA sing 402 n n 
O2D HOC2 UGA sing 403 n n 
C1D N1 UGA sing 404 n n 
C1D H1A1 UGA sing 405 n n 
N1 C6 UGA sing 406 n y 
N1 C2 UGA sing 407 n y 
C6 C5 UGA doub 408 n y 
C6 H61 UGA sing 409 n n 
C2 O2 UGA doub 410 n n 
C2 N3 UGA sing 411 n y 
N3 C4 UGA sing 412 n y 
N3 HN3 UGA sing 413 n n 
C4 O4 UGA doub 414 n n 
C4 C5 UGA sing 415 n y 
C5 H51 UGA sing 416 n n 
#
_atom_sites.entry_id                     8GJH 
_atom_sites.fract_transf_matrix[1][1]    0.01101 
_atom_sites.fract_transf_matrix[1][2]    -0.002389 
_atom_sites.fract_transf_matrix[1][3]    -0.002919 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007905 
_atom_sites.fract_transf_matrix[2][3]    -0.003634 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.008271 
_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
G 2 UGA A 1 1100 1100 UGA UGA . 
H 2 UGA B 1 1100 1100 UGA UGA . 
I 2 UGA C 1 1100 1100 UGA UGA . 
J 2 UGA D 1 1100 1100 UGA UGA . 
K 2 UGA E 1 1100 1100 UGA UGA . 
L 2 UGA F 1 1100 1100 UGA UGA . 
#
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 . . . J 2 -3.792 38.607 129.118 1 127.16 ? C1' UGA 1100 D 1 
HETATM 2 C C2' UGA . . . J 2 -5.084 39.258 129.548 1 113.64 ? C2' UGA 1100 D 1 
HETATM 3 O O2' UGA . . . J 2 -5.906 38.295 130.108 1 107.5 ? O2' UGA 1100 D 1 
HETATM 4 C C3' UGA . . . J 2 -5.79 39.898 128.405 1 107.03 ? C3' UGA 1100 D 1 
HETATM 5 O O3' UGA . . . J 2 -6.746 40.762 128.921 1 115.15 ? O3' UGA 1100 D 1 
HETATM 6 C C4' UGA . . . J 2 -4.901 40.705 127.536 1 105.75 ? C4' UGA 1100 D 1 
HETATM 7 O O4' UGA . . . J 2 -5.535 40.889 126.315 1 104.36 ? O4' UGA 1100 D 1 
HETATM 8 C C5' UGA . . . J 2 -3.595 40.035 127.276 1 116.59 ? C5' UGA 1100 D 1 
HETATM 9 O O5' UGA . . . J 2 -3.014 39.524 128.417 1 138.67 ? O5' UGA 1100 D 1 
HETATM 10 C C6' UGA . . . J 2 -2.672 41.065 126.711 1 122.33 ? C6' UGA 1100 D 1 
HETATM 11 O "O'P" UGA . . . J 2 -1.969 41.548 127.637 1 120.82 ? "O'P" UGA 1100 D 1 
HETATM 12 O "O'Q" UGA . . . J 2 -2.859 41.161 125.47 1 114.87 ? "O'Q" UGA 1100 D 1 
HETATM 13 P PB UGA . . . J 2 -2.879 36.421 128.179 1 130.29 ? PB UGA 1100 D 1 
HETATM 14 O O1B UGA . . . J 2 -1.872 37.006 127.217 1 119.37 ? O1B UGA 1100 D 1 
HETATM 15 O O2B UGA . . . J 2 -3.431 35.13 127.627 1 107.26 ? O2B UGA 1100 D 1 
HETATM 16 O O3B UGA . . . J 2 -4.058 37.45 128.377 1 120.76 ? O3B UGA 1100 D 1 
HETATM 17 O O3A UGA . . . J 2 -2.231 36.178 129.599 1 129.48 ? O3A UGA 1100 D 1 
HETATM 18 P PA UGA . . . J 2 -0.685 36.258 129.893 1 108.4 ? PA UGA 1100 D 1 
HETATM 19 O O1A UGA . . . J 2 -0.526 36.339 131.397 1 109.43 ? O1A UGA 1100 D 1 
HETATM 20 O O2A UGA . . . J 2 -0.062 37.482 129.258 1 110.02 ? O2A UGA 1100 D 1 
HETATM 21 O O5D UGA . . . J 2 0.025 34.941 129.404 1 114.53 ? O5D UGA 1100 D 1 
HETATM 22 C C5D UGA . . . J 2 0.208 34.694 128.046 1 114.42 ? C5D UGA 1100 D 1 
HETATM 23 C C4D UGA . . . J 2 -0.201 33.264 127.796 1 112.88 ? C4D UGA 1100 D 1 
HETATM 24 O O4D UGA . . . J 2 0.858 32.4 128.087 1 98.99 ? O4D UGA 1100 D 1 
HETATM 25 C C3D UGA . . . J 2 -1.366 32.898 128.653 1 120.47 ? C3D UGA 1100 D 1 
HETATM 26 O O3D UGA . . . J 2 -2.51 32.75 127.913 1 129.18 ? O3D UGA 1100 D 1 
HETATM 27 C C2D UGA . . . J 2 -0.994 31.637 129.308 1 117.16 ? C2D UGA 1100 D 1 
HETATM 28 O O2D UGA . . . J 2 -1.785 30.598 128.859 1 111.92 ? O2D UGA 1100 D 1 
HETATM 29 C C1D UGA . . . J 2 0.439 31.408 128.976 1 104.75 ? C1D UGA 1100 D 1 
HETATM 30 N N1 UGA . . . J 2 1.309 31.354 130.145 1 105.62 ? N1 UGA 1100 D 1 
HETATM 31 C C6 UGA . . . J 2 2.37 32.209 130.221 1 99.89 ? C6 UGA 1100 D 1 
HETATM 32 C C2 UGA . . . J 2 1.088 30.465 131.155 1 109.85 ? C2 UGA 1100 D 1 
HETATM 33 O O2 UGA . . . J 2 0.15 29.692 131.113 1 113.81 ? O2 UGA 1100 D 1 
HETATM 34 N N3 UGA . . . J 2 1.905 30.425 132.232 1 102.27 ? N3 UGA 1100 D 1 
HETATM 35 C C4 UGA . . . J 2 2.948 31.251 132.329 1 103.84 ? C4 UGA 1100 D 1 
HETATM 36 O O4 UGA . . . J 2 3.67 31.192 133.314 1 105.64 ? O4 UGA 1100 D 1 
HETATM 37 C C5 UGA . . . J 2 3.205 32.159 131.333 1 104.29 ? C5 UGA 1100 D 1 
#
_model_server_stats.io_time_ms              46 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           289 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           37 
#