data_6KVJ # _model_server_result.job_id rgVya7CIq8QF7rRzT0iQ3g _model_server_result.datetime_utc '2025-07-17 04:05:58' _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 6kvj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":801}' # _entry.id 6KVJ # _exptl.entry_id 6KVJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 536.276 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE" _entity.pdbx_number_of_molecules 1 _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 6KVJ _cell.length_a 98.244 _cell.length_b 98.244 _cell.length_c 90.367 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KVJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C14 H22 N2 O16 P2' _chem_comp.formula_weight 536.276 _chem_comp.id UDX _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms UDP-ALPHA-D-XYLOPYRANOSE # 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 C1' C2' UDX sing 358 n n C1' O5' UDX sing 359 n n C1' O3B UDX sing 360 n n C1' H1' UDX sing 361 n n C2' O2' UDX sing 362 n n C2' C3' UDX sing 363 n n C2' "H2'1" UDX sing 364 n n O2' "HO'2" UDX sing 365 n n C3' O3' UDX sing 366 n n C3' C4' UDX sing 367 n n C3' "H3'1" UDX sing 368 n n O3' "HO'3" UDX sing 369 n n C4' O4' UDX sing 370 n n C4' C5' UDX sing 371 n n C4' "H4'1" UDX sing 372 n n O4' "HO'4" UDX sing 373 n n C5' O5' UDX sing 374 n n C5' "H5'1" UDX sing 375 n n C5' "H5'2" UDX sing 376 n n PB O1B UDX doub 377 n n PB O2B UDX sing 378 n n PB O3B UDX sing 379 n n PB O3A UDX sing 380 n n O2B HOB2 UDX sing 381 n n O3A PA UDX sing 382 n n PA O1A UDX doub 383 n n PA O2A UDX sing 384 n n PA O5D UDX sing 385 n n O2A HOA2 UDX sing 386 n n O5D C5D UDX sing 387 n n C5D C4D UDX sing 388 n n C5D H5A1 UDX sing 389 n n C5D H5A2 UDX sing 390 n n C4D O4D UDX sing 391 n n C4D C3D UDX sing 392 n n C4D H4A1 UDX sing 393 n n O4D C1D UDX sing 394 n n C3D O3D UDX sing 395 n n C3D C2D UDX sing 396 n n C3D H3A1 UDX sing 397 n n O3D HOA3 UDX sing 398 n n C2D O2D UDX sing 399 n n C2D C1D UDX sing 400 n n C2D H2A1 UDX sing 401 n n O2D HOC2 UDX sing 402 n n C1D N1 UDX sing 403 n n C1D "H1'1" UDX sing 404 n n N1 C6 UDX sing 405 n n N1 C2 UDX sing 406 n n C6 C5 UDX doub 407 n n C6 H61 UDX sing 408 n n C2 O2 UDX doub 409 n n C2 N3 UDX sing 410 n n N3 C4 UDX sing 411 n n N3 HN3 UDX sing 412 n n C4 O4 UDX doub 413 n n C4 C5 UDX sing 414 n n C5 H51 UDX sing 415 n n # _atom_sites.entry_id 6KVJ _atom_sites.fract_transf_matrix[1][1] 0.010179 _atom_sites.fract_transf_matrix[1][2] 0.005877 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011753 _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] 0.011066 _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 B 2 UDX A 1 801 801 UDX UDX . C 3 HOH A 1 901 11 HOH HOH . C 3 HOH A 2 902 6 HOH HOH . C 3 HOH A 3 903 8 HOH HOH . C 3 HOH A 4 904 4 HOH HOH . C 3 HOH A 5 905 1 HOH HOH . C 3 HOH A 6 906 3 HOH HOH . C 3 HOH A 7 907 2 HOH HOH . C 3 HOH A 8 908 9 HOH HOH . C 3 HOH A 9 909 7 HOH HOH . C 3 HOH A 10 910 5 HOH HOH . C 3 HOH A 11 911 10 HOH HOH . C 3 HOH A 12 912 12 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 C C1' UDX . . . B 2 25.807 12.031 11.411 0.95 68.39 ? C1' UDX 801 A 1 HETATM 2 C C2' UDX . . . B 2 26.209 13.485 11.456 0.95 59.55 ? C2' UDX 801 A 1 HETATM 3 O O2' UDX . . . B 2 25.538 14.058 10.347 0.95 66.61 ? O2' UDX 801 A 1 HETATM 4 C C3' UDX . . . B 2 27.692 13.702 11.201 0.95 47.73 ? C3' UDX 801 A 1 HETATM 5 O O3' UDX . . . B 2 28.283 14.651 12.053 0.95 49.73 ? O3' UDX 801 A 1 HETATM 6 C C4' UDX . . . B 2 28.455 12.431 11.35 0.95 56.38 ? C4' UDX 801 A 1 HETATM 7 O O4' UDX . . . B 2 29.703 12.725 10.813 0.95 65.63 ? O4' UDX 801 A 1 HETATM 8 C C5' UDX . . . B 2 27.865 11.38 10.442 0.95 74.03 ? C5' UDX 801 A 1 HETATM 9 O O5' UDX . . . B 2 26.454 11.524 10.243 0.95 83.98 ? O5' UDX 801 A 1 HETATM 10 P PB UDX . . . B 2 23.826 10.396 11.425 0.95 38.02 ? PB UDX 801 A 1 HETATM 11 O O1B UDX . . . B 2 22.608 10.298 12.182 0.95 41.68 -1 O1B UDX 801 A 1 HETATM 12 O O2B UDX . . . B 2 23.74 9.948 10.079 0.95 48.33 ? O2B UDX 801 A 1 HETATM 13 O O3B UDX . . . B 2 24.398 11.831 11.362 0.95 55.45 ? O3B UDX 801 A 1 HETATM 14 O O3A UDX . . . B 2 24.986 9.495 11.986 0.95 42.26 ? O3A UDX 801 A 1 HETATM 15 P PA UDX . . . B 2 25.751 9.25 13.331 0.95 29.03 ? PA UDX 801 A 1 HETATM 16 O O1A UDX . . . B 2 25.797 7.838 13.506 0.95 42.21 -1 O1A UDX 801 A 1 HETATM 17 O O2A UDX . . . B 2 26.963 9.986 13.165 0.95 34.57 ? O2A UDX 801 A 1 HETATM 18 O O5D UDX . . . B 2 24.971 9.822 14.518 0.95 34.67 ? O5D UDX 801 A 1 HETATM 19 C C5D UDX . . . B 2 23.79 9.197 14.899 0.95 38.17 ? C5D UDX 801 A 1 HETATM 20 C C4D UDX . . . B 2 23.545 9.225 16.379 0.95 38.21 ? C4D UDX 801 A 1 HETATM 21 O O4D UDX . . . B 2 22.28 8.642 16.575 0.95 41.75 ? O4D UDX 801 A 1 HETATM 22 C C3D UDX . . . B 2 24.496 8.347 17.142 0.95 37.61 ? C3D UDX 801 A 1 HETATM 23 O O3D UDX . . . B 2 25.118 9.142 18.134 0.95 47.41 ? O3D UDX 801 A 1 HETATM 24 C C2D UDX . . . B 2 23.651 7.252 17.737 0.95 39.48 ? C2D UDX 801 A 1 HETATM 25 O O2D UDX . . . B 2 23.992 6.884 19.056 0.95 36.19 ? O2D UDX 801 A 1 HETATM 26 C C1D UDX . . . B 2 22.29 7.856 17.721 0.95 38.33 ? C1D UDX 801 A 1 HETATM 27 N N1 UDX . . . B 2 21.298 6.838 17.594 0.95 32.61 ? N1 UDX 801 A 1 HETATM 28 C C6 UDX . . . B 2 21.133 6.207 16.459 0.95 30.19 ? C6 UDX 801 A 1 HETATM 29 C C2 UDX . . . B 2 20.505 6.51 18.683 0.95 30.51 ? C2 UDX 801 A 1 HETATM 30 O O2 UDX . . . B 2 20.626 7.088 19.75 0.95 31 ? O2 UDX 801 A 1 HETATM 31 N N3 UDX . . . B 2 19.583 5.595 18.569 0.95 30.83 ? N3 UDX 801 A 1 HETATM 32 C C4 UDX . . . B 2 19.398 4.947 17.436 0.95 30.43 ? C4 UDX 801 A 1 HETATM 33 O O4 UDX . . . B 2 18.548 4.099 17.342 0.95 31.23 ? O4 UDX 801 A 1 HETATM 34 C C5 UDX . . . B 2 20.171 5.23 16.348 0.95 32.59 ? C5 UDX 801 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 34 #