data_7VA8
#
_model_server_result.job_id            -B9PgUzrH05yWlCnTe8vUg 
_model_server_result.datetime_utc      '2024-11-15 02:48:26' 
_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          7va8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    7VA8 
#
_exptl.entry_id    7VA8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              566.302 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE-GLUCOSE" 
_entity.pdbx_number_of_molecules    2 
_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            7VA8 
_cell.length_a            92.39 
_cell.length_b            104.68 
_cell.length_c            109.73 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7VA8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    'P 2 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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 C N N 
? 2 D N N 
#
_chem_comp.formula           'C15 H24 N2 O17 P2' 
_chem_comp.formula_weight    566.302 
_chem_comp.id                UPG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE-GLUCOSE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" 
#
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 UPG sing 356 n n 
N1 C6 UPG sing 357 n n 
N1 C1C UPG sing 358 n n 
C2 N3 UPG sing 359 n n 
C2 O2 UPG doub 360 n n 
N3 C4 UPG sing 361 n n 
N3 HN3 UPG sing 362 n n 
C4 C5 UPG sing 363 n n 
C4 O4 UPG doub 364 n n 
C5 C6 UPG doub 365 n n 
C5 H5 UPG sing 366 n n 
C6 H6 UPG sing 367 n n 
C1C C2C UPG sing 368 n n 
C1C O4C UPG sing 369 n n 
C1C H1C UPG sing 370 n n 
C2C O2C UPG sing 371 n n 
C2C C3C UPG sing 372 n n 
C2C H2C UPG sing 373 n n 
O2C HO2C UPG sing 374 n n 
C3C C4C UPG sing 375 n n 
C3C O3C UPG sing 376 n n 
C3C H3C UPG sing 377 n n 
C4C O4C UPG sing 378 n n 
C4C C5C UPG sing 379 n n 
C4C H4C UPG sing 380 n n 
O3C HO3C UPG sing 381 n n 
C5C O5C UPG sing 382 n n 
C5C H5C1 UPG sing 383 n n 
C5C H5C2 UPG sing 384 n n 
O5C PA UPG sing 385 n n 
PA O1A UPG doub 386 n n 
PA O2A UPG sing 387 n n 
PA O3A UPG sing 388 n n 
O2A HOA2 UPG sing 389 n n 
O3A PB UPG sing 390 n n 
PB O1B UPG doub 391 n n 
PB O2B UPG sing 392 n n 
PB O3B UPG sing 393 n n 
O2B HOB2 UPG sing 394 n n 
O3B C1' UPG sing 395 n n 
C1' C2' UPG sing 396 n n 
C1' O5' UPG sing 397 n n 
C1' H1' UPG sing 398 n n 
C2' C3' UPG sing 399 n n 
C2' O2' UPG sing 400 n n 
C2' H2' UPG sing 401 n n 
C3' C4' UPG sing 402 n n 
C3' O3' UPG sing 403 n n 
C3' H3' UPG sing 404 n n 
C4' C5' UPG sing 405 n n 
C4' O4' UPG sing 406 n n 
C4' H4' UPG sing 407 n n 
C5' C6' UPG sing 408 n n 
C5' O5' UPG sing 409 n n 
C5' H5' UPG sing 410 n n 
C6' O6' UPG sing 411 n n 
C6' "H6'1" UPG sing 412 n n 
C6' "H6'2" UPG sing 413 n n 
O2' HO2' UPG sing 414 n n 
O3' HO3' UPG sing 415 n n 
O4' HO4' UPG sing 416 n n 
O6' HO6' UPG sing 417 n n 
#
_atom_sites.entry_id                     7VA8 
_atom_sites.fract_transf_matrix[1][1]    0.010824 
_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]    0.009553 
_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]    0.009113 
_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
C 2 UPG A 1 501 1 UPG UPG . 
D 2 UPG B 1 501 2 UPG UPG . 
#
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 UPG . . . D 2 -43.008 31.725 -35.366 1 66.01 ? N1 UPG 501 B 1 
HETATM 2 C C2 UPG . . . D 2 -42.806 32.436 -34.096 1 63.31 ? C2 UPG 501 B 1 
HETATM 3 N N3 UPG . . . D 2 -43.661 33.615 -33.759 1 70.81 ? N3 UPG 501 B 1 
HETATM 4 C C4 UPG . . . D 2 -44.668 34.045 -34.671 1 74.07 ? C4 UPG 501 B 1 
HETATM 5 C C5 UPG . . . D 2 -44.857 33.328 -35.932 1 72.02 ? C5 UPG 501 B 1 
HETATM 6 C C6 UPG . . . D 2 -44.013 32.165 -36.264 1 68.23 ? C6 UPG 501 B 1 
HETATM 7 O O2 UPG . . . D 2 -41.968 32.076 -33.343 1 59.84 ? O2 UPG 501 B 1 
HETATM 8 O O4 UPG . . . D 2 -45.368 35.008 -34.401 1 73.57 ? O4 UPG 501 B 1 
HETATM 9 C C1C UPG . . . D 2 -42.25 30.684 -35.669 1 65.75 ? C1C UPG 501 B 1 
HETATM 10 C C2C UPG . . . D 2 -42.842 29.393 -35.159 1 68.53 ? C2C UPG 501 B 1 
HETATM 11 O O2C UPG . . . D 2 -42.296 29.072 -33.8 1 58.45 ? O2C UPG 501 B 1 
HETATM 12 C C3C UPG . . . D 2 -42.466 28.459 -36.045 1 67.23 ? C3C UPG 501 B 1 
HETATM 13 C C4C UPG . . . D 2 -41.811 29.227 -37.317 1 69.1 ? C4C UPG 501 B 1 
HETATM 14 O O4C UPG . . . D 2 -42.188 30.455 -37.229 1 65.06 ? O4C UPG 501 B 1 
HETATM 15 O O3C UPG . . . D 2 -41.495 27.593 -35.449 1 69.92 ? O3C UPG 501 B 1 
HETATM 16 C C5C UPG . . . D 2 -42.224 28.604 -38.647 1 69.27 ? C5C UPG 501 B 1 
HETATM 17 O O5C UPG . . . D 2 -43.646 28.69 -38.885 1 70.45 ? O5C UPG 501 B 1 
HETATM 18 P PA UPG . . . D 2 -44.34 27.473 -39.629 1 61.4 ? PA UPG 501 B 1 
HETATM 19 O O1A UPG . . . D 2 -43.283 26.588 -40.207 1 60.3 ? O1A UPG 501 B 1 
HETATM 20 O O2A UPG . . . D 2 -45.147 26.689 -38.647 1 67.45 ? O2A UPG 501 B 1 
HETATM 21 O O3A UPG . . . D 2 -45.292 27.972 -40.792 1 58.69 ? O3A UPG 501 B 1 
HETATM 22 P PB UPG . . . D 2 -44.859 28.973 -41.946 1 69.1 ? PB UPG 501 B 1 
HETATM 23 O O1B UPG . . . D 2 -45.548 30.297 -41.707 1 73.02 ? O1B UPG 501 B 1 
HETATM 24 O O2B UPG . . . D 2 -43.363 29.208 -41.876 1 67.09 ? O2B UPG 501 B 1 
HETATM 25 O O3B UPG . . . D 2 -45.338 28.436 -43.401 1 71.16 ? O3B UPG 501 B 1 
HETATM 26 C C1' UPG . . . D 2 -44.588 27.619 -44.223 1 57.85 ? C1' UPG 501 B 1 
HETATM 27 C C2' UPG . . . D 2 -45.44 26.406 -44.527 1 51.7 ? C2' UPG 501 B 1 
HETATM 28 C C3' UPG . . . D 2 -45.288 25.445 -43.446 1 61.85 ? C3' UPG 501 B 1 
HETATM 29 C C4' UPG . . . D 2 -43.927 24.853 -43.449 1 68.81 ? C4' UPG 501 B 1 
HETATM 30 C C5' UPG . . . D 2 -42.813 25.897 -43.629 1 59.63 ? C5' UPG 501 B 1 
HETATM 31 C C6' UPG . . . D 2 -42.054 25.621 -44.891 1 66.9 ? C6' UPG 501 B 1 
HETATM 32 O O2' UPG . . . D 2 -46.822 26.811 -44.61 1 61.34 ? O2' UPG 501 B 1 
HETATM 33 O O3' UPG . . . D 2 -46.307 24.374 -43.597 1 64.63 ? O3' UPG 501 B 1 
HETATM 34 O O4' UPG . . . D 2 -43.72 24.182 -42.208 1 83.39 ? O4' UPG 501 B 1 
HETATM 35 O O5' UPG . . . D 2 -43.253 27.285 -43.617 1 56.33 ? O5' UPG 501 B 1 
HETATM 36 O O6' UPG . . . D 2 -41.843 24.23 -45.015 1 68.51 ? O6' UPG 501 B 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           254 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           36 
#