data_6WJ3 # _model_server_result.job_id xxj-o5qONIfrTENVrtKYoQ _model_server_result.datetime_utc '2025-08-31 06:28:30' _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 6wj3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":500}' # _entry.id 6WJ3 # _exptl.entry_id 6WJ3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 444.185 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'xanthosine diphosphate' _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 90 _cell.entry_id 6WJ3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6WJ3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 ? _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 10 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H14 N4 O12 P2' _chem_comp.formula_weight 444.185 _chem_comp.id U3J _chem_comp.mon_nstd_flag . _chem_comp.name 'xanthosine diphosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O2 C2 U3J doub 401 n n O2A PA U3J doub 402 n n O4' C4' U3J sing 403 n n O4' C1' U3J sing 404 n n O1B PB U3J doub 405 n n C3' C4' U3J sing 406 n n C3' C2' U3J sing 407 n n C3' O3' U3J sing 408 n n C4' C5' U3J sing 409 n n C1' C2' U3J sing 410 n n C1' N9 U3J sing 411 n n C2' O2' U3J sing 412 n n N3 C2 U3J sing 413 n n N3 C4 U3J sing 414 n n C2 N1 U3J sing 415 n n PA O5' U3J sing 416 n n PA O3A U3J sing 417 n n PA O1A U3J sing 418 n n N9 C4 U3J sing 419 n y N9 C8 U3J sing 420 n y C4 C5 U3J doub 421 n y O5' C5' U3J sing 422 n n PB O3A U3J sing 423 n n PB O2B U3J sing 424 n n PB O3B U3J sing 425 n n N1 C6 U3J sing 426 n n C8 N7 U3J doub 427 n y C5 C6 U3J sing 428 n n C5 N7 U3J sing 429 n y C6 O6 U3J doub 430 n n N1 H1 U3J sing 431 n n C8 H2 U3J sing 432 n n N3 H3 U3J sing 433 n n C1' H4 U3J sing 434 n n C2' H5 U3J sing 435 n n C3' H6 U3J sing 436 n n C4' H7 U3J sing 437 n n C5' H8 U3J sing 438 n n C5' H9 U3J sing 439 n n O1A H10 U3J sing 440 n n O2' H11 U3J sing 441 n n O2B H12 U3J sing 442 n n O3' H13 U3J sing 443 n n O3B H14 U3J sing 444 n n # _atom_sites.entry_id 6WJ3 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 I 9 GDP F 1 500 500 GDP GDP . J 10 U3J G 1 500 500 U3J XPP . # 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 U3J . . . J 10 165.977 181.588 131.942 1 113.93 ? N1 U3J 500 G 1 HETATM 2 C C8 U3J . . . J 10 162.22 183.879 132.642 1 113.93 ? C8 U3J 500 G 1 HETATM 3 N N3 U3J . . . J 10 164.271 182.069 130.471 1 113.93 ? N3 U3J 500 G 1 HETATM 4 C C6 U3J . . . J 10 165.372 182.231 132.937 1 113.93 ? C6 U3J 500 G 1 HETATM 5 O O2 U3J . . . J 10 166.132 180.81 129.721 1 113.93 ? O2 U3J 500 G 1 HETATM 6 N N7 U3J . . . J 10 163.248 183.551 133.423 1 113.93 ? N7 U3J 500 G 1 HETATM 7 C C2 U3J . . . J 10 165.439 181.511 130.744 1 113.93 ? C2 U3J 500 G 1 HETATM 8 C C4 U3J . . . J 10 163.604 182.732 131.421 1 113.93 ? C4 U3J 500 G 1 HETATM 9 C C5 U3J . . . J 10 164.141 182.834 132.697 1 113.93 ? C5 U3J 500 G 1 HETATM 10 N N9 U3J . . . J 10 162.416 183.379 131.413 1 113.93 ? N9 U3J 500 G 1 HETATM 11 O O6 U3J . . . J 10 165.964 182.296 134.194 1 113.93 ? O6 U3J 500 G 1 HETATM 12 C C1' U3J . . . J 10 161.543 183.509 130.254 1 113.93 ? C1' U3J 500 G 1 HETATM 13 C C2' U3J . . . J 10 160.129 182.789 130.444 1 113.93 ? C2' U3J 500 G 1 HETATM 14 C C3' U3J . . . J 10 159.078 183.853 130.065 1 113.93 ? C3' U3J 500 G 1 HETATM 15 C C4' U3J . . . J 10 159.686 185.032 130.221 1 113.93 ? C4' U3J 500 G 1 HETATM 16 C C5' U3J . . . J 10 159.44 185.583 131.565 1 113.93 ? C5' U3J 500 G 1 HETATM 17 O O1A U3J . . . J 10 156.613 186.244 132.286 1 113.93 ? O1A U3J 500 G 1 HETATM 18 O O1B U3J . . . J 10 155.088 189.731 130.028 1 113.93 ? O1B U3J 500 G 1 HETATM 19 O O2' U3J . . . J 10 159.941 182.382 131.697 1 113.93 ? O2' U3J 500 G 1 HETATM 20 O O2A U3J . . . J 10 156.884 186.748 129.89 1 113.93 ? O2A U3J 500 G 1 HETATM 21 O O2B U3J . . . J 10 154.414 188.3 131.897 1 113.93 ? O2B U3J 500 G 1 HETATM 22 O O3' U3J . . . J 10 157.875 183.744 130.965 1 113.93 ? O3' U3J 500 G 1 HETATM 23 O O3A U3J . . . J 10 156.943 188.741 131.572 1 113.93 ? O3A U3J 500 G 1 HETATM 24 O O3B U3J . . . J 10 155.237 190.578 132.349 1 113.93 ? O3B U3J 500 G 1 HETATM 25 O O4' U3J . . . J 10 161.303 184.768 130.013 1 113.93 ? O4' U3J 500 G 1 HETATM 26 O O5' U3J . . . J 10 158.95 186.915 131.423 1 113.93 ? O5' U3J 500 G 1 HETATM 27 P PA U3J . . . J 10 157.327 187.128 131.277 1 113.93 ? PA U3J 500 G 1 HETATM 28 P PB U3J . . . J 10 155.376 189.349 131.459 1 113.93 ? PB U3J 500 G 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #