data_1MP4 # _model_server_result.job_id 4ohDFJ4ttAwOahYEoplAAw _model_server_result.datetime_utc '2025-03-11 11:23:01' _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":"C","auth_seq_id":501}' # _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 . . . C 2 60.067 38.976 24.556 1 35.59 ? N1 UPG 501 A 1 HETATM 2 C C2 UPG . . . C 2 59.8 37.675 24.09 1 33.96 ? C2 UPG 501 A 1 HETATM 3 N N3 UPG . . . C 2 58.469 37.406 23.828 1 34.29 ? N3 UPG 501 A 1 HETATM 4 C C4 UPG . . . C 2 57.379 38.297 23.981 1 35.84 ? C4 UPG 501 A 1 HETATM 5 C C5 UPG . . . C 2 57.745 39.607 24.46 1 35.79 ? C5 UPG 501 A 1 HETATM 6 C C6 UPG . . . C 2 59.015 39.89 24.719 1 35.39 ? C6 UPG 501 A 1 HETATM 7 O O2 UPG . . . C 2 60.723 36.869 23.948 1 33.24 ? O2 UPG 501 A 1 HETATM 8 O O4 UPG . . . C 2 56.264 37.876 23.701 1 37.31 ? O4 UPG 501 A 1 HETATM 9 C C1C UPG . . . C 2 61.49 39.319 24.871 1 36.87 ? C1C UPG 501 A 1 HETATM 10 C C2C UPG . . . C 2 62.105 40.313 23.904 1 39.31 ? C2C UPG 501 A 1 HETATM 11 O O2C UPG . . . C 2 62.528 39.723 22.656 1 42.57 ? O2C UPG 501 A 1 HETATM 12 C C3C UPG . . . C 2 63.241 40.938 24.734 1 38.4 ? C3C UPG 501 A 1 HETATM 13 C C4C UPG . . . C 2 62.562 41.017 26.119 1 38.48 ? C4C UPG 501 A 1 HETATM 14 O O4C UPG . . . C 2 61.594 39.915 26.14 1 36.29 ? O4C UPG 501 A 1 HETATM 15 O O3C UPG . . . C 2 64.539 40.302 24.598 1 41.88 ? O3C UPG 501 A 1 HETATM 16 C C5C UPG . . . C 2 61.711 42.253 26.427 1 40.3 ? C5C UPG 501 A 1 HETATM 17 O O5C UPG . . . C 2 61.828 43.289 25.428 1 50.3 ? O5C UPG 501 A 1 HETATM 18 P PA UPG . . . C 2 60.571 44.217 24.995 1 49.82 ? PA UPG 501 A 1 HETATM 19 O O1A UPG . . . C 2 59.413 43.454 24.41 1 55 ? O1A UPG 501 A 1 HETATM 20 O O2A UPG . . . C 2 60.898 45.228 23.93 1 53.58 ? O2A UPG 501 A 1 HETATM 21 O O3A UPG . . . C 2 60.193 44.973 26.403 1 51.68 ? O3A UPG 501 A 1 HETATM 22 P PB UPG . . . C 2 58.619 45.396 26.684 1 50 ? PB UPG 501 A 1 HETATM 23 O O1B UPG . . . C 2 58.312 46.728 25.886 1 52.67 ? O1B UPG 501 A 1 HETATM 24 O O2B UPG . . . C 2 57.763 44.274 26.395 1 47.54 ? O2B UPG 501 A 1 HETATM 25 O O3B UPG . . . C 2 58.579 45.635 28.294 1 45.95 ? O3B UPG 501 A 1 HETATM 26 C C1' UPG . . . C 2 58.718 44.639 29.279 1 44.15 ? C1' UPG 501 A 1 HETATM 27 C C2' UPG . . . C 2 57.821 44.926 30.512 1 43.29 ? C2' UPG 501 A 1 HETATM 28 C C3' UPG . . . C 2 58.285 46.272 31.209 1 40.69 ? C3' UPG 501 A 1 HETATM 29 C C4' UPG . . . C 2 59.702 46.139 31.638 1 41.19 ? C4' UPG 501 A 1 HETATM 30 C C5' UPG . . . C 2 60.643 45.811 30.423 1 43.3 ? C5' UPG 501 A 1 HETATM 31 C C6' UPG . . . C 2 62.08 45.676 30.88 1 44.12 ? C6' UPG 501 A 1 HETATM 32 O O2' UPG . . . C 2 56.435 45.098 30.179 1 44.79 ? O2' UPG 501 A 1 HETATM 33 O O3' UPG . . . C 2 57.497 46.58 32.357 1 39.02 ? O3' UPG 501 A 1 HETATM 34 O O4' UPG . . . C 2 60.06 47.361 32.24 1 42.01 ? O4' UPG 501 A 1 HETATM 35 O O5' UPG . . . C 2 60.186 44.577 29.749 1 41.23 ? O5' UPG 501 A 1 HETATM 36 O O6' UPG . . . C 2 62.94 45.663 29.762 1 50.8 ? O6' UPG 501 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 1028 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 36 #