data_3EJL # _model_server_result.job_id rCSva50rJ6dvO9ENxe2ODQ _model_server_result.datetime_utc '2024-11-23 02:27:23' _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 3ejl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":314}' # _entry.id 3EJL # _exptl.entry_id 3EJL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 326.172 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _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 122.35 _cell.angle_gamma 90 _cell.entry_id 3EJL _cell.length_a 157.435 _cell.length_b 94.642 _cell.length_c 131.988 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EJL _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 PISA dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,I,J 1 1 C,D,G,H,K,L 2 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 3 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id D _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 199 _struct_conn.ptnr1_auth_asym_id D _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 199 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id D _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 210 _struct_conn.ptnr2_auth_asym_id D _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 210 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 2.036 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C9 H12 F N2 O8 P' _chem_comp.formula_weight 326.172 _chem_comp.id UFP _chem_comp.mon_nstd_flag . _chem_comp.name "5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna linking' _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 N1 C2 UFP sing 362 n n N1 C6 UFP sing 363 n n N1 C1' UFP sing 364 n n C2 N3 UFP sing 365 n n C2 O2 UFP doub 366 n n N3 C4 UFP sing 367 n n N3 HN3 UFP sing 368 n n C4 C5 UFP sing 369 n n C4 O4 UFP doub 370 n n C5 C6 UFP doub 371 n n C5 F5 UFP sing 372 n n C6 H6 UFP sing 373 n n C1' C2' UFP sing 374 n n C1' O4' UFP sing 375 n n C1' H1' UFP sing 376 n n C2' C3' UFP sing 377 n n C2' "H2'1" UFP sing 378 n n C2' "H2'2" UFP sing 379 n n C3' C4' UFP sing 380 n n C3' O3' UFP sing 381 n n C3' H3' UFP sing 382 n n C4' O4' UFP sing 383 n n C4' C5' UFP sing 384 n n C4' H4' UFP sing 385 n n O3' HO3' UFP sing 386 n n C5' O5' UFP sing 387 n n C5' "H5'1" UFP sing 388 n n C5' "H5'2" UFP sing 389 n n O5' P UFP sing 390 n n P O1P UFP doub 391 n n P O2P UFP sing 392 n n P O3P UFP sing 393 n n O2P HOP2 UFP sing 394 n n O3P HOP3 UFP sing 395 n n # _atom_sites.entry_id 3EJL _atom_sites.fract_transf_matrix[1][1] 0.006352 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004023 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010566 _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] 0.008968 _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 E 2 PO4 B 1 616 616 PO4 PO4 . F 2 PO4 B 1 314 616 PO4 PO4 . G 2 PO4 D 1 616 616 PO4 PO4 . H 3 UFP D 1 314 165 UFP UFP . I 4 HOH A 1 314 8 HOH HOH . I 4 HOH A 2 315 23 HOH HOH . I 4 HOH A 3 316 34 HOH HOH . I 4 HOH A 4 317 36 HOH HOH . I 4 HOH A 5 318 42 HOH HOH . I 4 HOH A 6 319 43 HOH HOH . I 4 HOH A 7 320 46 HOH HOH . I 4 HOH A 8 321 47 HOH HOH . J 4 HOH B 1 315 1 HOH HOH . J 4 HOH B 2 316 2 HOH HOH . J 4 HOH B 3 317 3 HOH HOH . J 4 HOH B 4 318 4 HOH HOH . J 4 HOH B 5 319 6 HOH HOH . J 4 HOH B 6 320 21 HOH HOH . J 4 HOH B 7 321 30 HOH HOH . J 4 HOH B 8 322 31 HOH HOH . J 4 HOH B 9 323 37 HOH HOH . J 4 HOH B 10 324 39 HOH HOH . J 4 HOH B 11 325 41 HOH HOH . K 4 HOH C 1 314 7 HOH HOH . K 4 HOH C 2 315 11 HOH HOH . K 4 HOH C 3 316 13 HOH HOH . K 4 HOH C 4 317 28 HOH HOH . K 4 HOH C 5 318 29 HOH HOH . K 4 HOH C 6 319 32 HOH HOH . K 4 HOH C 7 320 35 HOH HOH . K 4 HOH C 8 321 40 HOH HOH . L 4 HOH D 1 315 5 HOH HOH . L 4 HOH D 2 316 10 HOH HOH . L 4 HOH D 3 317 14 HOH HOH . L 4 HOH D 4 318 33 HOH HOH . L 4 HOH D 5 319 38 HOH HOH . L 4 HOH D 6 320 44 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 N N1 UFP . . . H 3 -75.498 -12.913 41.564 1 91.88 ? N1 UFP 314 D 1 HETATM 2 C C2 UFP . . . H 3 -74.548 -12.76 42.579 1 92.05 ? C2 UFP 314 D 1 HETATM 3 N N3 UFP . . . H 3 -73.98 -11.524 42.812 1 93.25 ? N3 UFP 314 D 1 HETATM 4 C C4 UFP . . . H 3 -74.342 -10.42 42.063 1 95.22 ? C4 UFP 314 D 1 HETATM 5 C C5 UFP . . . H 3 -75.319 -10.561 41.015 1 95.08 ? C5 UFP 314 D 1 HETATM 6 C C6 UFP . . . H 3 -75.879 -11.799 40.789 1 93.75 ? C6 UFP 314 D 1 HETATM 7 O O2 UFP . . . H 3 -74.203 -13.717 43.279 1 91.07 ? O2 UFP 314 D 1 HETATM 8 O O4 UFP . . . H 3 -73.836 -9.332 42.288 1 96.08 ? O4 UFP 314 D 1 HETATM 9 F F5 UFP . . . H 3 -75.684 -9.488 40.272 1 97.03 ? F5 UFP 314 D 1 HETATM 10 C C1' UFP . . . H 3 -76.147 -14.245 41.355 1 89.18 ? C1' UFP 314 D 1 HETATM 11 C C2' UFP . . . H 3 -77.592 -13.88 41.654 1 87.78 ? C2' UFP 314 D 1 HETATM 12 C C3' UFP . . . H 3 -78.374 -14.948 40.953 1 85.57 ? C3' UFP 314 D 1 HETATM 13 C C4' UFP . . . H 3 -77.325 -15.881 40.432 1 83.08 ? C4' UFP 314 D 1 HETATM 14 O O3' UFP . . . H 3 -79.288 -15.669 41.807 1 85.31 ? O3' UFP 314 D 1 HETATM 15 O O4' UFP . . . H 3 -76.334 -14.867 39.986 1 86.33 ? O4' UFP 314 D 1 HETATM 16 C C5' UFP . . . H 3 -78.336 -16.636 39.597 1 77.62 ? C5' UFP 314 D 1 HETATM 17 O O5' UFP . . . H 3 -78.066 -17.772 38.843 1 68.91 ? O5' UFP 314 D 1 HETATM 18 P P UFP . . . H 3 -79.608 -18.082 38.396 1 63.5 ? P UFP 314 D 1 HETATM 19 O O1P UFP . . . H 3 -80.155 -16.825 37.551 1 66.89 ? O1P UFP 314 D 1 HETATM 20 O O2P UFP . . . H 3 -79.799 -19.37 37.488 1 63.02 ? O2P UFP 314 D 1 HETATM 21 O O3P UFP . . . H 3 -80.476 -18.298 39.754 1 67.29 ? O3P UFP 314 D 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #