data_7XX4
#
_model_server_result.job_id            1KOFWHsxfmIanFyS7tydng 
_model_server_result.datetime_utc      '2024-12-27 11:14:42' 
_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          7xx4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    7XX4 
#
_exptl.entry_id    7XX4 
_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            7XX4 
_cell.length_a            65.716 
_cell.length_b            92.285 
_cell.length_c            191.438 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7XX4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 2 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 358 n n 
N1 C6 UPG sing 359 n n 
N1 C1C UPG sing 360 n n 
C2 N3 UPG sing 361 n n 
C2 O2 UPG doub 362 n n 
N3 C4 UPG sing 363 n n 
N3 HN3 UPG sing 364 n n 
C4 C5 UPG sing 365 n n 
C4 O4 UPG doub 366 n n 
C5 C6 UPG doub 367 n n 
C5 H5 UPG sing 368 n n 
C6 H6 UPG sing 369 n n 
C1C C2C UPG sing 370 n n 
C1C O4C UPG sing 371 n n 
C1C H1C UPG sing 372 n n 
C2C O2C UPG sing 373 n n 
C2C C3C UPG sing 374 n n 
C2C H2C UPG sing 375 n n 
O2C HO2C UPG sing 376 n n 
C3C C4C UPG sing 377 n n 
C3C O3C UPG sing 378 n n 
C3C H3C UPG sing 379 n n 
C4C O4C UPG sing 380 n n 
C4C C5C UPG sing 381 n n 
C4C H4C UPG sing 382 n n 
O3C HO3C UPG sing 383 n n 
C5C O5C UPG sing 384 n n 
C5C H5C1 UPG sing 385 n n 
C5C H5C2 UPG sing 386 n n 
O5C PA UPG sing 387 n n 
PA O1A UPG doub 388 n n 
PA O2A UPG sing 389 n n 
PA O3A UPG sing 390 n n 
O2A HOA2 UPG sing 391 n n 
O3A PB UPG sing 392 n n 
PB O1B UPG doub 393 n n 
PB O2B UPG sing 394 n n 
PB O3B UPG sing 395 n n 
O2B HOB2 UPG sing 396 n n 
O3B C1' UPG sing 397 n n 
C1' C2' UPG sing 398 n n 
C1' O5' UPG sing 399 n n 
C1' H1' UPG sing 400 n n 
C2' C3' UPG sing 401 n n 
C2' O2' UPG sing 402 n n 
C2' H2' UPG sing 403 n n 
C3' C4' UPG sing 404 n n 
C3' O3' UPG sing 405 n n 
C3' H3' UPG sing 406 n n 
C4' C5' UPG sing 407 n n 
C4' O4' UPG sing 408 n n 
C4' H4' UPG sing 409 n n 
C5' C6' UPG sing 410 n n 
C5' O5' UPG sing 411 n n 
C5' H5' UPG sing 412 n n 
C6' O6' UPG sing 413 n n 
C6' "H6'1" UPG sing 414 n n 
C6' "H6'2" UPG sing 415 n n 
O2' HO2' UPG sing 416 n n 
O3' HO3' UPG sing 417 n n 
O4' HO4' UPG sing 418 n n 
O6' HO6' UPG sing 419 n n 
#
_atom_sites.entry_id                     7XX4 
_atom_sites.fract_transf_matrix[1][1]    0.015217 
_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]    0.010836 
_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]    0.005224 
_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 LIG . 
D 2 UPG B 1 501 2 UPG LIG . 
E 3 HOH A 1 601 2 HOH HOH . 
E 3 HOH A 2 602 4 HOH HOH . 
E 3 HOH A 3 603 14 HOH HOH . 
E 3 HOH A 4 604 16 HOH HOH . 
E 3 HOH A 5 605 5 HOH HOH . 
E 3 HOH A 6 606 6 HOH HOH . 
E 3 HOH A 7 607 9 HOH HOH . 
E 3 HOH A 8 608 3 HOH HOH . 
E 3 HOH A 9 609 18 HOH HOH . 
E 3 HOH A 10 610 17 HOH HOH . 
E 3 HOH A 11 611 15 HOH HOH . 
E 3 HOH A 12 612 19 HOH HOH . 
F 3 HOH B 1 601 11 HOH HOH . 
F 3 HOH B 2 602 1 HOH HOH . 
F 3 HOH B 3 603 13 HOH HOH . 
F 3 HOH B 4 604 12 HOH HOH . 
F 3 HOH B 5 605 7 HOH HOH . 
F 3 HOH B 6 606 8 HOH HOH . 
F 3 HOH B 7 607 10 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 . . . D 2 -21.519 -74.41 35.437 1 59.06 ? N1 UPG 501 B 1 
HETATM 2 C C2 UPG . . . D 2 -20.734 -75.489 34.949 1 58.86 ? C2 UPG 501 B 1 
HETATM 3 N N3 UPG . . . D 2 -21.381 -76.681 34.444 1 65.03 ? N3 UPG 501 B 1 
HETATM 4 C C4 UPG . . . D 2 -22.792 -76.8 34.437 1 68.65 ? C4 UPG 501 B 1 
HETATM 5 C C5 UPG . . . D 2 -23.564 -75.655 34.964 1 63.71 ? C5 UPG 501 B 1 
HETATM 6 C C6 UPG . . . D 2 -22.919 -74.541 35.431 1 59.98 ? C6 UPG 501 B 1 
HETATM 7 O O2 UPG . . . D 2 -19.509 -75.407 34.956 1 59.32 ? O2 UPG 501 B 1 
HETATM 8 O O4 UPG . . . D 2 -23.298 -77.849 33.993 1 65.89 ? O4 UPG 501 B 1 
HETATM 9 C C1C UPG . . . D 2 -20.764 -73.131 35.982 1 59.31 ? C1C UPG 501 B 1 
HETATM 10 C C2C UPG . . . D 2 -20.866 -71.865 35.073 1 62.75 ? C2C UPG 501 B 1 
HETATM 11 O O2C UPG . . . D 2 -19.742 -71.799 34.237 1 71.14 ? O2C UPG 501 B 1 
HETATM 12 C C3C UPG . . . D 2 -20.828 -70.687 36.102 1 65.89 ? C3C UPG 501 B 1 
HETATM 13 C C4C UPG . . . D 2 -21.479 -71.319 37.311 1 67.99 ? C4C UPG 501 B 1 
HETATM 14 O O4C UPG . . . D 2 -21.371 -72.749 37.176 1 70.24 ? O4C UPG 501 B 1 
HETATM 15 O O3C UPG . . . D 2 -19.571 -70.27 36.525 1 66.96 ? O3C UPG 501 B 1 
HETATM 16 C C5C UPG . . . D 2 -22.968 -70.862 37.388 1 64.72 ? C5C UPG 501 B 1 
HETATM 17 O O5C UPG . . . D 2 -23.05 -69.751 38.14 1 64.27 ? O5C UPG 501 B 1 
HETATM 18 P PA UPG . . . D 2 -24.166 -68.409 37.691 1 74.35 ? PA UPG 501 B 1 
HETATM 19 O O1A UPG . . . D 2 -23.926 -68.405 36.227 1 81.34 ? O1A UPG 501 B 1 
HETATM 20 O O2A UPG . . . D 2 -23.789 -67.237 38.516 1 85.49 ? O2A UPG 501 B 1 
HETATM 21 O O3A UPG . . . D 2 -25.674 -68.934 37.978 1 83.26 ? O3A UPG 501 B 1 
HETATM 22 P PB UPG . . . D 2 -26.171 -69.821 39.275 1 75.07 ? PB UPG 501 B 1 
HETATM 23 O O1B UPG . . . D 2 -25.474 -71.115 39.402 1 74.62 ? O1B UPG 501 B 1 
HETATM 24 O O2B UPG . . . D 2 -27.66 -69.802 39.221 1 79.42 ? O2B UPG 501 B 1 
HETATM 25 O O3B UPG . . . D 2 -25.78 -68.944 40.898 1 102.6 ? O3B UPG 501 B 1 
HETATM 26 C C1' UPG . . . D 2 -26.237 -69.186 42.184 1 112.89 ? C1' UPG 501 B 1 
HETATM 27 C C2' UPG . . . D 2 -27.825 -69.381 42.277 1 110.83 ? C2' UPG 501 B 1 
HETATM 28 C C3' UPG . . . D 2 -28.112 -69.517 43.796 1 108.07 ? C3' UPG 501 B 1 
HETATM 29 C C4' UPG . . . D 2 -28.043 -68.118 44.462 1 104.64 ? C4' UPG 501 B 1 
HETATM 30 C C5' UPG . . . D 2 -26.707 -67.394 43.99 1 105.26 ? C5' UPG 501 B 1 
HETATM 31 C C6' UPG . . . D 2 -26.087 -66.688 45.263 1 93.62 ? C6' UPG 501 B 1 
HETATM 32 O O2' UPG . . . D 2 -28.519 -68.295 41.744 1 111.85 ? O2' UPG 501 B 1 
HETATM 33 O O3' UPG . . . D 2 -27.087 -70.314 44.316 1 112.19 ? O3' UPG 501 B 1 
HETATM 34 O O4' UPG . . . D 2 -29.174 -67.364 44.124 1 100.18 ? O4' UPG 501 B 1 
HETATM 35 O O5' UPG . . . D 2 -25.804 -68.194 43.212 1 110.88 ? O5' UPG 501 B 1 
HETATM 36 O O6' UPG . . . D 2 -26.382 -65.296 45.31 1 92.26 ? O6' UPG 501 B 1 
#
_model_server_stats.io_time_ms              119 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           36 
#