data_6JEN # _model_server_result.job_id 6HJ_fCyEED8xHMj2c-og3Q _model_server_result.datetime_utc '2024-12-08 05:55:14' _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 6jen # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":502}' # _entry.id 6JEN # _exptl.entry_id 6JEN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 568.293 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE" _entity.pdbx_number_of_molecules 3 _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 6JEN _cell.length_a 56.718 _cell.length_b 136.883 _cell.length_c 205.136 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JEN _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 1 1 B,F,G 2 1 C,H,I 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 ? 3 E N N ? 3 G N N ? 3 I N N # _chem_comp.formula 'C15 H23 F N2 O16 P2' _chem_comp.formula_weight 568.293 _chem_comp.id U2F _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE" _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 C1 O1 U2F sing 392 n n C1 C2 U2F sing 393 n n C1 O5 U2F sing 394 n n C1 H1 U2F sing 395 n n O1 PB U2F sing 396 n n PB O1B U2F doub 397 n n PB O2B U2F sing 398 n n PB O3A U2F sing 399 n n O3A PA U2F sing 400 n n PA O1A U2F doub 401 n n PA O2A U2F sing 402 n n PA O5' U2F sing 403 n n O5' C5' U2F sing 404 n n C5' C4' U2F sing 405 n n C5' "H5'1" U2F sing 406 n n C5' "H5'2" U2F sing 407 n n C4' O4' U2F sing 408 n n C4' C3' U2F sing 409 n n C4' H4' U2F sing 410 n n O4' C1' U2F sing 411 n n C1' C2' U2F sing 412 n n C1' N1 U2F sing 413 n n C1' H1' U2F sing 414 n n C2' C3' U2F sing 415 n n C2' O2' U2F sing 416 n n C2' H2' U2F sing 417 n n C3' O3' U2F sing 418 n n C3' H3' U2F sing 419 n n O3' HB U2F sing 420 n n O2' HA U2F sing 421 n n N1 C6' U2F sing 422 n n N1 C9' U2F sing 423 n n C6' O6' U2F doub 424 n n C6' N3 U2F sing 425 n n N3 C7' U2F sing 426 n n N3 H3 U2F sing 427 n n C7' O7' U2F doub 428 n n C7' C8' U2F sing 429 n n C8' C9' U2F doub 430 n n C8' H8' U2F sing 431 n n C9' H9' U2F sing 432 n n C2 F1 U2F sing 433 n n C2 C3 U2F sing 434 n n C2 H2 U2F sing 435 n n C3 O3 U2F sing 436 n n C3 C4 U2F sing 437 n n C3 HC U2F sing 438 n n O3 HD U2F sing 439 n n C4 O4 U2F sing 440 n n C4 C5 U2F sing 441 n n C4 H4 U2F sing 442 n n O4 HE U2F sing 443 n n C5 C6 U2F sing 444 n n C5 O5 U2F sing 445 n n C5 H5 U2F sing 446 n n C6 O6 U2F sing 447 n n C6 H6C1 U2F sing 448 n n C6 H6C2 U2F sing 449 n n O6 H6 U2F sing 450 n n HO1 O2A U2F sing 451 n n HO2 O2B U2F sing 452 n n # _atom_sites.entry_id 6JEN _atom_sites.fract_transf_matrix[1][1] 0.017631 _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] 0.007306 _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] 0.004875 _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 3RL A 1 501 501 3RL 3RL . E 3 U2F A 1 502 1 U2F U2F . F 2 3RL B 1 501 501 3RL 3RL . G 3 U2F B 1 502 2 U2F U2F . H 2 3RL C 1 501 501 3RL 3RL . I 3 U2F C 1 502 3 U2F U2F . # 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 U2F . . . G 3 22.771 45.16 75.821 1 83.5 ? C1 U2F 502 B 1 HETATM 2 O O1 U2F . . . G 3 22.285 44.759 77.075 1 89.98 ? O1 U2F 502 B 1 HETATM 3 P PB U2F . . . G 3 21.801 43.258 77.367 1 81.2 ? PB U2F 502 B 1 HETATM 4 O O1B U2F . . . G 3 20.343 43.149 77.066 1 71.57 ? O1B U2F 502 B 1 HETATM 5 O O2B U2F . . . G 3 22.726 42.306 76.685 1 82.01 ? O2B U2F 502 B 1 HETATM 6 O O3A U2F . . . G 3 22.018 43.155 78.953 1 82.08 ? O3A U2F 502 B 1 HETATM 7 P PA U2F . . . G 3 21.269 43.836 80.198 1 78.33 ? PA U2F 502 B 1 HETATM 8 O O1A U2F . . . G 3 21.051 45.281 79.894 1 80.72 ? O1A U2F 502 B 1 HETATM 9 O O2A U2F . . . G 3 21.999 43.479 81.45 1 68.26 ? O2A U2F 502 B 1 HETATM 10 O O5' U2F . . . G 3 19.861 43.067 80.165 1 80.54 ? O5' U2F 502 B 1 HETATM 11 C C5' U2F . . . G 3 19.827 41.673 80.565 1 78.92 ? C5' U2F 502 B 1 HETATM 12 C C4' U2F . . . G 3 18.406 41.169 80.504 1 80.94 ? C4' U2F 502 B 1 HETATM 13 O O4' U2F . . . G 3 18.378 39.755 80.831 1 78.03 ? O4' U2F 502 B 1 HETATM 14 C C1' U2F . . . G 3 17.872 39.568 82.137 1 74.3 ? C1' U2F 502 B 1 HETATM 15 C C2' U2F . . . G 3 17.654 40.953 82.748 1 73.26 ? C2' U2F 502 B 1 HETATM 16 C C3' U2F . . . G 3 17.423 41.805 81.496 1 74.24 ? C3' U2F 502 B 1 HETATM 17 O O3' U2F . . . G 3 16.083 41.709 81.029 1 61.67 ? O3' U2F 502 B 1 HETATM 18 O O2' U2F . . . G 3 16.531 40.918 83.603 1 75.09 ? O2' U2F 502 B 1 HETATM 19 N N1 U2F . . . G 3 18.833 38.75 82.902 1 83.19 ? N1 U2F 502 B 1 HETATM 20 C C6' U2F . . . G 3 18.31 37.833 83.796 1 87.02 ? C6' U2F 502 B 1 HETATM 21 O O6' U2F . . . G 3 17.107 37.684 83.967 1 81.79 ? O6' U2F 502 B 1 HETATM 22 N N3 U2F . . . G 3 19.244 37.099 84.481 1 104.09 ? N3 U2F 502 B 1 HETATM 23 C C7' U2F . . . G 3 20.618 37.186 84.367 1 92.23 ? C7' U2F 502 B 1 HETATM 24 O O7' U2F . . . G 3 21.328 36.453 85.056 1 90.38 ? O7' U2F 502 B 1 HETATM 25 C C8' U2F . . . G 3 21.081 38.158 83.42 1 86.49 ? C8' U2F 502 B 1 HETATM 26 C C9' U2F . . . G 3 20.19 38.891 82.735 1 89.15 ? C9' U2F 502 B 1 HETATM 27 C C2 U2F . . . G 3 24.023 45.98 76.042 1 83.3 ? C2 U2F 502 B 1 HETATM 28 F F1 U2F . . . G 3 24.91 45.243 76.847 1 69.55 ? F1 U2F 502 B 1 HETATM 29 C C3 U2F . . . G 3 23.717 47.292 76.737 1 75 ? C3 U2F 502 B 1 HETATM 30 O O3 U2F . . . G 3 24.898 48.09 76.764 1 66.33 ? O3 U2F 502 B 1 HETATM 31 C C4 U2F . . . G 3 22.613 48.017 75.977 1 78.25 ? C4 U2F 502 B 1 HETATM 32 O O4 U2F . . . G 3 22.227 49.195 76.679 1 62.17 ? O4 U2F 502 B 1 HETATM 33 C C5 U2F . . . G 3 21.398 47.108 75.825 1 82.11 ? C5 U2F 502 B 1 HETATM 34 C C6 U2F . . . G 3 20.285 47.74 75.022 1 85.71 ? C6 U2F 502 B 1 HETATM 35 O O6 U2F . . . G 3 19.231 46.811 74.777 1 80 ? O6 U2F 502 B 1 HETATM 36 O O5 U2F . . . G 3 21.789 45.911 75.129 1 84.03 ? O5 U2F 502 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #