data_6K8D
#
_model_server_result.job_id            6OElrTDSrfEUTIb4mvX9MA 
_model_server_result.datetime_utc      '2025-07-08 07:06:23' 
_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          6k8d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":301}' 
#
_entry.id    6K8D 
#
_exptl.entry_id    6K8D 
_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    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            6K8D 
_cell.length_a            110.525 
_cell.length_b            114.382 
_cell.length_c            114.374 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6K8D 
_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,Q,R,S,T 
_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 M N N 
? 2 O 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                     6K8D 
_atom_sites.fract_transf_matrix[1][1]    0.009048 
_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]    0.008743 
_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]    0.008743 
_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 UPG A 1 301 1 UPG UPG . 
F 3 SO4 A 1 302 2 SO4 SO4 . 
G 3 SO4 A 1 303 6 SO4 SO4 . 
H 4 EDO A 1 304 2 EDO EDO . 
I 2 UPG B 1 301 2 UPG UPG . 
J 3 SO4 B 1 302 1 SO4 SO4 . 
K 3 SO4 B 1 303 3 SO4 SO4 . 
L 5 GOL B 1 304 1 GOL GOL . 
M 2 UPG C 1 301 3 UPG UPG . 
N 3 SO4 C 1 302 4 SO4 SO4 . 
O 2 UPG D 1 301 4 UPG UPG . 
P 3 SO4 D 1 302 5 SO4 SO4 . 
Q 3 SO4 D 1 303 7 SO4 SO4 . 
R 6 HOH B 1 401 13 HOH HOH . 
R 6 HOH B 2 402 6 HOH HOH . 
S 6 HOH C 1 401 1 HOH HOH . 
S 6 HOH C 2 402 16 HOH HOH . 
T 6 HOH D 1 401 12 HOH HOH . 
T 6 HOH D 2 402 17 HOH HOH . 
#
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 . . . M 2 -7.562 43.785 -50.773 1 54.58 ? N1 UPG 301 C 1 
HETATM 2 C C2 UPG . . . M 2 -7.367 42.783 -51.696 1 51.66 ? C2 UPG 301 C 1 
HETATM 3 N N3 UPG . . . M 2 -6.061 42.533 -52.018 1 49.55 ? N3 UPG 301 C 1 
HETATM 4 C C4 UPG . . . M 2 -4.943 43.149 -51.493 1 52 ? C4 UPG 301 C 1 
HETATM 5 C C5 UPG . . . M 2 -5.228 44.16 -50.521 1 56.11 ? C5 UPG 301 C 1 
HETATM 6 C C6 UPG . . . M 2 -6.501 44.426 -50.191 1 57.3 ? C6 UPG 301 C 1 
HETATM 7 O O2 UPG . . . M 2 -8.294 42.184 -52.212 1 58.73 ? O2 UPG 301 C 1 
HETATM 8 O O4 UPG . . . M 2 -3.82 42.811 -51.871 1 48.97 ? O4 UPG 301 C 1 
HETATM 9 C C1C UPG . . . M 2 -8.946 44.071 -50.364 1 56.66 ? C1C UPG 301 C 1 
HETATM 10 C C2C UPG . . . M 2 -9.183 43.625 -48.926 1 58.41 ? C2C UPG 301 C 1 
HETATM 11 O O2C UPG . . . M 2 -9.633 42.288 -48.913 1 65.51 ? O2C UPG 301 C 1 
HETATM 12 C C3C UPG . . . M 2 -10.281 44.58 -48.448 1 61.46 ? C3C UPG 301 C 1 
HETATM 13 C C4C UPG . . . M 2 -10.201 45.783 -49.407 1 60.14 ? C4C UPG 301 C 1 
HETATM 14 O O4C UPG . . . M 2 -9.189 45.458 -50.398 1 55.68 ? O4C UPG 301 C 1 
HETATM 15 O O3C UPG . . . M 2 -11.542 43.923 -48.471 1 64.15 ? O3C UPG 301 C 1 
HETATM 16 C C5C UPG . . . M 2 -9.861 47.095 -48.748 1 61.13 ? C5C UPG 301 C 1 
HETATM 17 O O5C UPG . . . M 2 -8.46 47.087 -48.368 1 67.72 ? O5C UPG 301 C 1 
HETATM 18 P PA UPG . . . M 2 -7.966 46.888 -46.852 1 68.1 ? PA UPG 301 C 1 
HETATM 19 O O1A UPG . . . M 2 -8.873 45.951 -46.114 1 65.81 ? O1A UPG 301 C 1 
HETATM 20 O O2A UPG . . . M 2 -6.49 46.633 -46.9 1 60.93 ? O2A UPG 301 C 1 
HETATM 21 O O3A UPG . . . M 2 -8.242 48.335 -46.235 1 63.45 ? O3A UPG 301 C 1 
HETATM 22 P PB UPG . . . M 2 -7.111 49.455 -46.246 1 67.32 ? PB UPG 301 C 1 
HETATM 23 O O1B UPG . . . M 2 -6.25 49.238 -47.453 1 64.28 ? O1B UPG 301 C 1 
HETATM 24 O O2B UPG . . . M 2 -6.462 49.468 -44.903 1 74.63 ? O2B UPG 301 C 1 
HETATM 25 O O3B UPG . . . M 2 -7.989 50.773 -46.42 1 60.96 ? O3B UPG 301 C 1 
HETATM 26 C C1' UPG . . . M 2 -8.829 50.872 -47.521 1 57.95 ? C1' UPG 301 C 1 
HETATM 27 C C2' UPG . . . M 2 -8.33 51.958 -48.479 1 57.32 ? C2' UPG 301 C 1 
HETATM 28 C C3' UPG . . . M 2 -8.406 53.305 -47.827 1 56 ? C3' UPG 301 C 1 
HETATM 29 C C4' UPG . . . M 2 -9.794 53.547 -47.281 1 55.28 ? C4' UPG 301 C 1 
HETATM 30 C C5' UPG . . . M 2 -10.185 52.409 -46.319 1 56.83 ? C5' UPG 301 C 1 
HETATM 31 C C6' UPG . . . M 2 -11.602 52.468 -45.799 1 60.93 ? C6' UPG 301 C 1 
HETATM 32 O O2' UPG . . . M 2 -6.988 51.722 -48.906 1 60.41 ? O2' UPG 301 C 1 
HETATM 33 O O3' UPG . . . M 2 -8.064 54.281 -48.807 1 61.35 ? O3' UPG 301 C 1 
HETATM 34 O O4' UPG . . . M 2 -9.801 54.808 -46.633 1 51.2 ? O4' UPG 301 C 1 
HETATM 35 O O5' UPG . . . M 2 -10.113 51.172 -47.017 1 54.66 ? O5' UPG 301 C 1 
HETATM 36 O O6' UPG . . . M 2 -11.841 51.354 -44.926 1 64.16 ? O6' UPG 301 C 1 
#
_model_server_stats.io_time_ms              49 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           398 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           36 
#