data_8ZI6 # _model_server_result.job_id WwoA7luqcwmhzSQFUcGJpg _model_server_result.datetime_utc '2025-07-17 04:30:09' _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 8zi6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 8ZI6 # _exptl.entry_id 8ZI6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 2 _entity.src_method nat _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 8ZI6 _cell.length_a 111.78 _cell.length_b 111.78 _cell.length_c 91.77 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ZI6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # 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 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,H 1 1 B,F 2 1 C,G 3 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 D N N ? 2 F 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 373 n n N1 C6 UPG sing 374 n n N1 C1C UPG sing 375 n n C2 N3 UPG sing 376 n n C2 O2 UPG doub 377 n n N3 C4 UPG sing 378 n n N3 HN3 UPG sing 379 n n C4 C5 UPG sing 380 n n C4 O4 UPG doub 381 n n C5 C6 UPG doub 382 n n C5 H5 UPG sing 383 n n C6 H6 UPG sing 384 n n C1C C2C UPG sing 385 n n C1C O4C UPG sing 386 n n C1C H1C UPG sing 387 n n C2C O2C UPG sing 388 n n C2C C3C UPG sing 389 n n C2C H2C UPG sing 390 n n O2C HO2C UPG sing 391 n n C3C C4C UPG sing 392 n n C3C O3C UPG sing 393 n n C3C H3C UPG sing 394 n n C4C O4C UPG sing 395 n n C4C C5C UPG sing 396 n n C4C H4C UPG sing 397 n n O3C HO3C UPG sing 398 n n C5C O5C UPG sing 399 n n C5C H5C1 UPG sing 400 n n C5C H5C2 UPG sing 401 n n O5C PA UPG sing 402 n n PA O1A UPG doub 403 n n PA O2A UPG sing 404 n n PA O3A UPG sing 405 n n O2A HOA2 UPG sing 406 n n O3A PB UPG sing 407 n n PB O1B UPG doub 408 n n PB O2B UPG sing 409 n n PB O3B UPG sing 410 n n O2B HOB2 UPG sing 411 n n O3B C1' UPG sing 412 n n C1' C2' UPG sing 413 n n C1' O5' UPG sing 414 n n C1' H1' UPG sing 415 n n C2' C3' UPG sing 416 n n C2' O2' UPG sing 417 n n C2' H2' UPG sing 418 n n C3' C4' UPG sing 419 n n C3' O3' UPG sing 420 n n C3' H3' UPG sing 421 n n C4' C5' UPG sing 422 n n C4' O4' UPG sing 423 n n C4' H4' UPG sing 424 n n C5' C6' UPG sing 425 n n C5' O5' UPG sing 426 n n C5' H5' UPG sing 427 n n C6' O6' UPG sing 428 n n C6' "H6'1" UPG sing 429 n n C6' "H6'2" UPG sing 430 n n O2' HO2' UPG sing 431 n n O3' HO3' UPG sing 432 n n O4' HO4' UPG sing 433 n n O6' HO6' UPG sing 434 n n # _atom_sites.entry_id 8ZI6 _atom_sites.fract_transf_matrix[1][1] 0.008946 _atom_sites.fract_transf_matrix[1][2] 0.005165 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01033 _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] 0.010897 _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 D 2 UPG A 1 501 2 UPG UPG . E 3 IPA A 1 502 3 IPA IPA . F 2 UPG B 1 501 4 UPG UPG . G 4 PO4 C 1 501 1 PO4 PO4 . H 5 HOH A 1 601 1 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 -19.738 4.803 -11.797 1 41.9 ? N1 UPG 501 A 1 HETATM 2 C C2 UPG . . . D 2 -19.401 5.322 -13.045 1 46.36 ? C2 UPG 501 A 1 HETATM 3 N N3 UPG . . . D 2 -20.451 5.81 -13.783 1 49.53 ? N3 UPG 501 A 1 HETATM 4 C C4 UPG . . . D 2 -21.78 5.838 -13.411 1 48.36 ? C4 UPG 501 A 1 HETATM 5 C C5 UPG . . . D 2 -22.052 5.287 -12.111 1 43.85 ? C5 UPG 501 A 1 HETATM 6 C C6 UPG . . . D 2 -21.046 4.797 -11.367 1 40.22 ? C6 UPG 501 A 1 HETATM 7 O O2 UPG . . . D 2 -18.259 5.349 -13.477 1 43.85 ? O2 UPG 501 A 1 HETATM 8 O O4 UPG . . . D 2 -22.608 6.308 -14.191 1 46.98 ? O4 UPG 501 A 1 HETATM 9 C C1C UPG . . . D 2 -18.639 4.274 -10.951 1 36.68 ? C1C UPG 501 A 1 HETATM 10 C C2C UPG . . . D 2 -18.224 5.216 -9.821 1 34.92 ? C2C UPG 501 A 1 HETATM 11 O O2C UPG . . . D 2 -17.297 6.194 -10.241 1 31.62 ? O2C UPG 501 A 1 HETATM 12 C C3C UPG . . . D 2 -17.585 4.238 -8.824 1 35.39 ? C3C UPG 501 A 1 HETATM 13 C C4C UPG . . . D 2 -18.424 2.966 -9.02 1 36.83 ? C4C UPG 501 A 1 HETATM 14 O O4C UPG . . . D 2 -19.086 3.104 -10.31 1 36.61 ? O4C UPG 501 A 1 HETATM 15 O O3C UPG . . . D 2 -16.199 4.018 -9.06 1 34.56 ? O3C UPG 501 A 1 HETATM 16 C C5C UPG . . . D 2 -19.47 2.726 -7.965 1 38.01 ? C5C UPG 501 A 1 HETATM 17 O O5C UPG . . . D 2 -18.83 2.309 -6.73 1 40.61 ? O5C UPG 501 A 1 HETATM 18 P PA UPG . . . D 2 -19.633 2.647 -5.381 1 36.45 ? PA UPG 501 A 1 HETATM 19 O O1A UPG . . . D 2 -19.695 4.134 -5.272 1 33.01 ? O1A UPG 501 A 1 HETATM 20 O O2A UPG . . . D 2 -19.013 1.915 -4.249 1 35.02 ? O2A UPG 501 A 1 HETATM 21 O O3A UPG . . . D 2 -21.084 2.018 -5.713 1 37.7 ? O3A UPG 501 A 1 HETATM 22 P PB UPG . . . D 2 -21.671 0.623 -6.29 1 44.24 ? PB UPG 501 A 1 HETATM 23 O O1B UPG . . . D 2 -20.872 0.043 -7.408 1 52.73 ? O1B UPG 501 A 1 HETATM 24 O O2B UPG . . . D 2 -23.126 0.75 -6.592 1 39.8 ? O2B UPG 501 A 1 HETATM 25 O O3B UPG . . . D 2 -21.423 -0.37 -5.059 1 53.14 ? O3B UPG 501 A 1 # _model_server_stats.io_time_ms 91 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #