data_9J9C # _model_server_result.job_id jdzXf5UgCVhnWLJoiffyOw _model_server_result.datetime_utc '2024-11-27 00:56:06' _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 9j9c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 9J9C # _exptl.entry_id 9J9C _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 7 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93.39 _cell.angle_gamma 90 _cell.entry_id 9J9C _cell.length_a 87.13 _cell.length_b 170.39 _cell.length_c 152.13 _cell.Z_PDB 14 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9J9C _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 ? monomeric 1 author_defined_assembly 5 ? monomeric 1 author_defined_assembly 6 ? monomeric 1 author_defined_assembly 7 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,H,I 1 1 B,J,K 2 1 C,L,M 3 1 D,N,O 4 1 E,P 5 1 F,Q,R 6 1 G,S 7 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 H N N ? 2 J N N ? 2 L N N ? 2 N N N ? 2 P N N ? 2 Q N N ? 2 S 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 379 n n C1 C2 U2F sing 380 n n C1 O5 U2F sing 381 n n C1 H1 U2F sing 382 n n O1 PB U2F sing 383 n n PB O1B U2F doub 384 n n PB O2B U2F sing 385 n n PB O3A U2F sing 386 n n O3A PA U2F sing 387 n n PA O1A U2F doub 388 n n PA O2A U2F sing 389 n n PA O5' U2F sing 390 n n O5' C5' U2F sing 391 n n C5' C4' U2F sing 392 n n C5' "H5'1" U2F sing 393 n n C5' "H5'2" U2F sing 394 n n C4' O4' U2F sing 395 n n C4' C3' U2F sing 396 n n C4' H4' U2F sing 397 n n O4' C1' U2F sing 398 n n C1' C2' U2F sing 399 n n C1' N1 U2F sing 400 n n C1' H1' U2F sing 401 n n C2' C3' U2F sing 402 n n C2' O2' U2F sing 403 n n C2' H2' U2F sing 404 n n C3' O3' U2F sing 405 n n C3' H3' U2F sing 406 n n O3' HB U2F sing 407 n n O2' HA U2F sing 408 n n N1 C6' U2F sing 409 n n N1 C9' U2F sing 410 n n C6' O6' U2F doub 411 n n C6' N3 U2F sing 412 n n N3 C7' U2F sing 413 n n N3 H3 U2F sing 414 n n C7' O7' U2F doub 415 n n C7' C8' U2F sing 416 n n C8' C9' U2F doub 417 n n C8' H8' U2F sing 418 n n C9' H9' U2F sing 419 n n C2 F1 U2F sing 420 n n C2 C3 U2F sing 421 n n C2 H2 U2F sing 422 n n C3 O3 U2F sing 423 n n C3 C4 U2F sing 424 n n C3 HC U2F sing 425 n n O3 HD U2F sing 426 n n C4 O4 U2F sing 427 n n C4 C5 U2F sing 428 n n C4 H4 U2F sing 429 n n O4 HE U2F sing 430 n n C5 C6 U2F sing 431 n n C5 O5 U2F sing 432 n n C5 H5 U2F sing 433 n n C6 O6 U2F sing 434 n n C6 H6C1 U2F sing 435 n n C6 H6C2 U2F sing 436 n n O6 H6 U2F sing 437 n n HO1 O2A U2F sing 438 n n HO2 O2B U2F sing 439 n n # _atom_sites.entry_id 9J9C _atom_sites.fract_transf_matrix[1][1] 0.011477 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00068 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005869 _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] 0.006585 _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 H 2 U2F A 1 501 501 U2F U2F . I 3 T83 A 1 502 502 T83 UNL . J 2 U2F B 1 501 501 U2F U2F . K 3 T83 B 1 502 502 T83 UNL . L 2 U2F C 1 501 501 U2F U2F . M 3 T83 C 1 502 502 T83 UNL . N 2 U2F D 1 501 501 U2F U2F . O 3 T83 D 1 502 502 T83 UNL . P 2 U2F E 1 501 501 U2F U2F . Q 2 U2F F 1 501 501 U2F U2F . R 3 T83 F 1 502 502 T83 UNL . S 2 U2F G 1 501 501 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 . . . J 2 42.88 41.547 69.841 1 84.15 ? C1 U2F 501 B 1 HETATM 2 O O1 U2F . . . J 2 41.548 41.775 70.244 1 75.61 ? O1 U2F 501 B 1 HETATM 3 P PB U2F . . . J 2 40.996 41.332 71.692 1 77.11 ? PB U2F 501 B 1 HETATM 4 O O1B U2F . . . J 2 39.716 42.069 71.959 1 60.43 ? O1B U2F 501 B 1 HETATM 5 O O2B U2F . . . J 2 41.05 39.838 71.814 1 93.35 ? O2B U2F 501 B 1 HETATM 6 O O3A U2F . . . J 2 42.089 41.993 72.661 1 59.55 ? O3A U2F 501 B 1 HETATM 7 P PA U2F . . . J 2 42.414 43.55 72.506 1 52.83 ? PA U2F 501 B 1 HETATM 8 O O1A U2F . . . J 2 41.549 44.164 71.446 1 41.06 ? O1A U2F 501 B 1 HETATM 9 O O2A U2F . . . J 2 43.896 43.629 72.354 1 49 ? O2A U2F 501 B 1 HETATM 10 O O5' U2F . . . J 2 41.948 44.134 73.921 1 50.45 ? O5' U2F 501 B 1 HETATM 11 C C5' U2F . . . J 2 40.511 44.17 74.2 1 45.91 ? C5' U2F 501 B 1 HETATM 12 C C4' U2F . . . J 2 39.916 45.481 73.75 1 43.82 ? C4' U2F 501 B 1 HETATM 13 O O4' U2F . . . J 2 38.573 45.611 74.281 1 47.94 ? O4' U2F 501 B 1 HETATM 14 C C1' U2F . . . J 2 38.539 46.496 75.384 1 52.65 ? C1' U2F 501 B 1 HETATM 15 C C2' U2F . . . J 2 39.98 46.932 75.638 1 49.71 ? C2' U2F 501 B 1 HETATM 16 C C3' U2F . . . J 2 40.614 46.745 74.254 1 48.35 ? C3' U2F 501 B 1 HETATM 17 O O3' U2F . . . J 2 40.301 47.83 73.394 1 54.24 ? O3' U2F 501 B 1 HETATM 18 O O2' U2F . . . J 2 39.974 48.291 76.01 1 54.84 ? O2' U2F 501 B 1 HETATM 19 N N1 U2F . . . J 2 37.882 45.803 76.527 1 61.31 ? N1 U2F 501 B 1 HETATM 20 C C6' U2F . . . J 2 37.128 46.551 77.433 1 59.42 ? C6' U2F 501 B 1 HETATM 21 O O6' U2F . . . J 2 37.013 47.768 77.379 1 62.28 ? O6' U2F 501 B 1 HETATM 22 N N3 U2F . . . J 2 36.523 45.829 78.434 1 56.95 ? N3 U2F 501 B 1 HETATM 23 C C7' U2F . . . J 2 36.579 44.457 78.622 1 73.34 ? C7' U2F 501 B 1 HETATM 24 O O7' U2F . . . J 2 35.999 43.936 79.581 1 58.5 ? O7' U2F 501 B 1 HETATM 25 C C8' U2F . . . J 2 37.356 43.752 77.636 1 84.66 ? C8' U2F 501 B 1 HETATM 26 C C9' U2F . . . J 2 37.963 44.435 76.648 1 70.88 ? C9' U2F 501 B 1 HETATM 27 C C2 U2F . . . J 2 43.551 42.817 69.328 1 84.38 ? C2 U2F 501 B 1 HETATM 28 F F1 U2F . . . J 2 42.636 43.59 68.581 1 88.46 ? F1 U2F 501 B 1 HETATM 29 C C3 U2F . . . J 2 44.749 42.423 68.473 1 75.1 ? C3 U2F 501 B 1 HETATM 30 O O3 U2F . . . J 2 45.733 43.454 68.422 1 64.62 ? O3 U2F 501 B 1 HETATM 31 C C4 U2F . . . J 2 45.353 41.158 69.077 1 71.55 ? C4 U2F 501 B 1 HETATM 32 O O4 U2F . . . J 2 46.593 40.914 68.441 1 77.95 ? O4 U2F 501 B 1 HETATM 33 C C5 U2F . . . J 2 44.377 39.978 68.868 1 71.26 ? C5 U2F 501 B 1 HETATM 34 C C6 U2F . . . J 2 44.444 38.919 69.937 1 68.61 ? C6 U2F 501 B 1 HETATM 35 O O6 U2F . . . J 2 43.161 38.286 70.027 1 85.13 ? O6 U2F 501 B 1 HETATM 36 O O5 U2F . . . J 2 43.02 40.483 68.905 1 75.04 ? O5 U2F 501 B 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 420 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 36 #