data_6JEM # _model_server_result.job_id I0Ej_hRbEaQwnR6NKNNbnQ _model_server_result.datetime_utc '2025-01-10 11:51:32' _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 6jem # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 6JEM # _exptl.entry_id 6JEM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 568.293 _entity.id 2 _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 6JEM _cell.length_a 57.374 _cell.length_b 137.616 _cell.length_c 208.956 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JEM _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 ? 2 D N N ? 2 F N N ? 2 H 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 386 n n C1 C2 U2F sing 387 n n C1 O5 U2F sing 388 n n C1 H1 U2F sing 389 n n O1 PB U2F sing 390 n n PB O1B U2F doub 391 n n PB O2B U2F sing 392 n n PB O3A U2F sing 393 n n O3A PA U2F sing 394 n n PA O1A U2F doub 395 n n PA O2A U2F sing 396 n n PA O5' U2F sing 397 n n O5' C5' U2F sing 398 n n C5' C4' U2F sing 399 n n C5' "H5'1" U2F sing 400 n n C5' "H5'2" U2F sing 401 n n C4' O4' U2F sing 402 n n C4' C3' U2F sing 403 n n C4' H4' U2F sing 404 n n O4' C1' U2F sing 405 n n C1' C2' U2F sing 406 n n C1' N1 U2F sing 407 n n C1' H1' U2F sing 408 n n C2' C3' U2F sing 409 n n C2' O2' U2F sing 410 n n C2' H2' U2F sing 411 n n C3' O3' U2F sing 412 n n C3' H3' U2F sing 413 n n O3' HB U2F sing 414 n n O2' HA U2F sing 415 n n N1 C6' U2F sing 416 n n N1 C9' U2F sing 417 n n C6' O6' U2F doub 418 n n C6' N3 U2F sing 419 n n N3 C7' U2F sing 420 n n N3 H3 U2F sing 421 n n C7' O7' U2F doub 422 n n C7' C8' U2F sing 423 n n C8' C9' U2F doub 424 n n C8' H8' U2F sing 425 n n C9' H9' U2F sing 426 n n C2 F1 U2F sing 427 n n C2 C3 U2F sing 428 n n C2 H2 U2F sing 429 n n C3 O3 U2F sing 430 n n C3 C4 U2F sing 431 n n C3 HC U2F sing 432 n n O3 HD U2F sing 433 n n C4 O4 U2F sing 434 n n C4 C5 U2F sing 435 n n C4 H4 U2F sing 436 n n O4 HE U2F sing 437 n n C5 C6 U2F sing 438 n n C5 O5 U2F sing 439 n n C5 H5 U2F sing 440 n n C6 O6 U2F sing 441 n n C6 H6C1 U2F sing 442 n n C6 H6C2 U2F sing 443 n n O6 H6 U2F sing 444 n n HO1 O2A U2F sing 445 n n HO2 O2B U2F sing 446 n n # _atom_sites.entry_id 6JEM _atom_sites.fract_transf_matrix[1][1] 0.017429 _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] 0.007267 _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] 0.004786 _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 U2F A 1 501 1 U2F U2F . E 3 STL A 1 502 1 STL STL . F 2 U2F B 1 501 2 U2F U2F . G 3 STL B 1 502 2 STL STL . H 2 U2F C 1 501 3 U2F U2F . I 3 STL C 1 502 3 STL STL . # 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 . . . D 2 9.796 25.889 25.95 1 111.9 ? C1 U2F 501 A 1 HETATM 2 O O1 U2F . . . D 2 8.74 26.435 25.203 1 104.05 ? O1 U2F 501 A 1 HETATM 3 P PB U2F . . . D 2 8.835 27.883 24.521 1 90.47 ? PB U2F 501 A 1 HETATM 4 O O1B U2F . . . D 2 10.268 28.201 24.249 1 115.52 ? O1B U2F 501 A 1 HETATM 5 O O2B U2F . . . D 2 8.047 28.858 25.333 1 96.05 ? O2B U2F 501 A 1 HETATM 6 O O3A U2F . . . D 2 8.081 27.632 23.127 1 85.26 ? O3A U2F 501 A 1 HETATM 7 P PA U2F . . . D 2 6.686 26.933 22.757 1 79.63 ? PA U2F 501 A 1 HETATM 8 O O1A U2F . . . D 2 6.547 25.685 23.565 1 68.09 ? O1A U2F 501 A 1 HETATM 9 O O2A U2F . . . D 2 6.582 26.83 21.271 1 89.11 ? O2A U2F 501 A 1 HETATM 10 O O5' U2F . . . D 2 5.642 28.03 23.288 1 79.08 ? O5' U2F 501 A 1 HETATM 11 C C5' U2F . . . D 2 5.327 29.161 22.437 1 92.53 ? C5' U2F 501 A 1 HETATM 12 C C4' U2F . . . D 2 4.208 29.958 23.061 1 94.99 ? C4' U2F 501 A 1 HETATM 13 O O4' U2F . . . D 2 4.238 31.32 22.557 1 111.43 ? O4' U2F 501 A 1 HETATM 14 C C1' U2F . . . D 2 3.098 31.57 21.761 1 91.94 ? C1' U2F 501 A 1 HETATM 15 C C2' U2F . . . D 2 2.442 30.217 21.484 1 96.56 ? C2' U2F 501 A 1 HETATM 16 C C3' U2F . . . D 2 2.784 29.461 22.772 1 87.68 ? C3' U2F 501 A 1 HETATM 17 O O3' U2F . . . D 2 1.897 29.792 23.833 1 86.07 ? O3' U2F 501 A 1 HETATM 18 O O2' U2F . . . D 2 1.052 30.396 21.305 1 87.61 ? O2' U2F 501 A 1 HETATM 19 N N1 U2F . . . D 2 3.524 32.262 20.529 1 79.61 ? N1 U2F 501 A 1 HETATM 20 C C6' U2F . . . D 2 2.671 33.224 20.019 1 68.41 ? C6' U2F 501 A 1 HETATM 21 O O6' U2F . . . D 2 1.603 33.51 20.544 1 72.63 ? O6' U2F 501 A 1 HETATM 22 N N3 U2F . . . D 2 3.113 33.837 18.874 1 67.19 ? N3 U2F 501 A 1 HETATM 23 C C7' U2F . . . D 2 4.295 33.592 18.202 1 73.06 ? C7' U2F 501 A 1 HETATM 24 O O7' U2F . . . D 2 4.552 34.229 17.18 1 70.1 ? O7' U2F 501 A 1 HETATM 25 C C8' U2F . . . D 2 5.123 32.582 18.793 1 72.39 ? C8' U2F 501 A 1 HETATM 26 C C9' U2F . . . D 2 4.717 31.965 19.914 1 72.69 ? C9' U2F 501 A 1 HETATM 27 C C2 U2F . . . D 2 10.738 25.19 24.994 1 93.64 ? C2 U2F 501 A 1 HETATM 28 F F1 U2F . . . D 2 11.091 26.088 23.97 1 98.14 ? F1 U2F 501 A 1 HETATM 29 C C3 U2F . . . D 2 10.095 23.97 24.366 1 85.86 ? C3 U2F 501 A 1 HETATM 30 O O3 U2F . . . D 2 11.077 23.263 23.613 1 66.59 ? O3 U2F 501 A 1 HETATM 31 C C4 U2F . . . D 2 9.536 23.076 25.466 1 85.04 ? C4 U2F 501 A 1 HETATM 32 O O4 U2F . . . D 2 8.827 21.98 24.894 1 64 ? O4 U2F 501 A 1 HETATM 33 C C5 U2F . . . D 2 8.588 23.873 26.355 1 93.39 ? C5 U2F 501 A 1 HETATM 34 C C6 U2F . . . D 2 8.043 23.066 27.51 1 93.1 ? C6 U2F 501 A 1 HETATM 35 O O6 U2F . . . D 2 7.438 23.906 28.49 1 88.04 ? O6 U2F 501 A 1 HETATM 36 O O5 U2F . . . D 2 9.3 24.987 26.924 1 118.45 ? O5 U2F 501 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 36 #