data_1MP4
#
_model_server_result.job_id            aFfLcehfmPfSUY9nPxWOEw 
_model_server_result.datetime_utc      '2024-12-22 06:20:28' 
_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          1mp4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":502}' 
#
_entry.id    1MP4 
#
_exptl.entry_id    1MP4 
_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         120 
_cell.entry_id            1MP4 
_cell.length_a            88.958 
_cell.length_b            88.958 
_cell.length_c            329.1 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1MP4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 8_665 x-y+1,-y+1,-z 1 0 0 0 -1 0 0 0 -1 44.479 77.039888 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                     1MP4 
_atom_sites.fract_transf_matrix[1][1]    0.011241 
_atom_sites.fract_transf_matrix[1][2]    0.00649 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01298 
_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]    0.003039 
_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 1 501 501 UPG UPG . 
D 2 UPG B 1 502 502 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 91.979 31.468 7.973 1 42.62 ? N1 UPG 502 B 1 
HETATM 2 C C2 UPG . . . D 2 91.11 30.742 7.136 1 41.56 ? C2 UPG 502 B 1 
HETATM 3 N N3 UPG . . . D 2 91.683 29.703 6.422 1 42.06 ? N3 UPG 502 B 1 
HETATM 4 C C4 UPG . . . D 2 93.047 29.312 6.442 1 40.7 ? C4 UPG 502 B 1 
HETATM 5 C C5 UPG . . . D 2 93.872 30.101 7.317 1 40.46 ? C5 UPG 502 B 1 
HETATM 6 C C6 UPG . . . D 2 93.347 31.111 8.021 1 41.23 ? C6 UPG 502 B 1 
HETATM 7 O O2 UPG . . . D 2 89.932 31.04 7.085 1 40.76 ? O2 UPG 502 B 1 
HETATM 8 O O4 UPG . . . D 2 93.383 28.369 5.742 1 41.1 ? O4 UPG 502 B 1 
HETATM 9 C C1C UPG . . . D 2 91.402 32.61 8.766 1 42.44 ? C1C UPG 502 B 1 
HETATM 10 C C2C UPG . . . D 2 91.572 32.494 10.282 1 45.58 ? C2C UPG 502 B 1 
HETATM 11 O O2C UPG . . . D 2 90.588 31.663 10.921 1 40.61 ? O2C UPG 502 B 1 
HETATM 12 C C3C UPG . . . D 2 91.543 33.97 10.712 1 44.57 ? C3C UPG 502 B 1 
HETATM 13 C C4C UPG . . . D 2 92.336 34.63 9.574 1 46.01 ? C4C UPG 502 B 1 
HETATM 14 O O4C UPG . . . D 2 92.037 33.817 8.393 1 41.36 ? O4C UPG 502 B 1 
HETATM 15 O O3C UPG . . . D 2 90.248 34.493 11.09 1 44.86 ? O3C UPG 502 B 1 
HETATM 16 C C5C UPG . . . D 2 93.879 34.61 9.683 1 46.67 ? C5C UPG 502 B 1 
HETATM 17 O O5C UPG . . . D 2 94.362 34.627 11.038 1 54.26 ? O5C UPG 502 B 1 
HETATM 18 P PA UPG . . . D 2 95.681 33.766 11.507 1 50.02 ? PA UPG 502 B 1 
HETATM 19 O O1A UPG . . . D 2 95.564 32.277 11.307 1 51.66 ? O1A UPG 502 B 1 
HETATM 20 O O2A UPG . . . D 2 96.008 33.911 12.956 1 54.59 ? O2A UPG 502 B 1 
HETATM 21 O O3A UPG . . . D 2 96.865 34.432 10.56 1 51.15 ? O3A UPG 502 B 1 
HETATM 22 P PB UPG . . . D 2 98.263 33.59 10.318 1 49.69 ? PB UPG 502 B 1 
HETATM 23 O O1B UPG . . . D 2 98.952 33.33 11.72 1 50.08 ? O1B UPG 502 B 1 
HETATM 24 O O2B UPG . . . D 2 97.953 32.411 9.539 1 50.08 ? O2B UPG 502 B 1 
HETATM 25 O O3B UPG . . . D 2 99.135 34.574 9.379 1 46.77 ? O3B UPG 502 B 1 
HETATM 26 C C1' UPG . . . D 2 98.686 35.191 8.182 1 42.1 ? C1' UPG 502 B 1 
HETATM 27 C C2' UPG . . . D 2 99.855 35.719 7.279 1 41.42 ? C2' UPG 502 B 1 
HETATM 28 C C3' UPG . . . D 2 100.681 36.821 8.057 1 40.32 ? C3' UPG 502 B 1 
HETATM 29 C C4' UPG . . . D 2 99.771 37.949 8.374 1 40.15 ? C4' UPG 502 B 1 
HETATM 30 C C5' UPG . . . D 2 98.559 37.474 9.258 1 40.2 ? C5' UPG 502 B 1 
HETATM 31 C C6' UPG . . . D 2 97.632 38.618 9.587 1 38.58 ? C6' UPG 502 B 1 
HETATM 32 O O2' UPG . . . D 2 100.776 34.709 6.861 1 38.36 ? O2' UPG 502 B 1 
HETATM 33 O O3' UPG . . . D 2 101.761 37.334 7.275 1 40.68 ? O3' UPG 502 B 1 
HETATM 34 O O4' UPG . . . D 2 100.532 38.934 9.014 1 39.89 ? O4' UPG 502 B 1 
HETATM 35 O O5' UPG . . . D 2 97.819 36.396 8.568 1 39.21 ? O5' UPG 502 B 1 
HETATM 36 O O6' UPG . . . D 2 96.893 38.286 10.76 1 43.78 ? O6' UPG 502 B 1 
#
_model_server_stats.io_time_ms              44 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           36 
#