data_8KBF # _model_server_result.job_id Z_fcz8PO4Z0aVaDc0Ng96g _model_server_result.datetime_utc '2024-11-28 11:14:32' _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 8kbf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":201}' # _entry.id 8KBF # _exptl.entry_id 8KBF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 541.3 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R,3R,3aS,5S,6R,7S,8R,11R,13S,15aR)-2-(6-amino-9H-purin-9-yl)-3,6,7,11,13-pentahydroxyoctahydro-2H,5H,11H,13H-5,8-epoxy-11lambda~5~,13lambda~5~-furo[2,3-g][1,3,5,9,2,4]tetraoxadiphosphacyclotetradecine-11,13-dione _entity.pdbx_number_of_molecules 2 _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 8KBF _cell.length_a 101.27 _cell.length_b 101.27 _cell.length_c 101.27 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8KBF _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 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 F N N # _chem_comp.formula 'C15 H21 N5 O13 P2' _chem_comp.formula_weight 541.3 _chem_comp.id OJC _chem_comp.mon_nstd_flag . _chem_comp.name (2R,3R,3aS,5S,6R,7S,8R,11R,13S,15aR)-2-(6-amino-9H-purin-9-yl)-3,6,7,11,13-pentahydroxyoctahydro-2H,5H,11H,13H-5,8-epoxy-11lambda~5~,13lambda~5~-furo[2,3-g][1,3,5,9,2,4]tetraoxadiphosphacyclotetradecine-11,13-dione _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 N4 C1 OJC sing 276 n n C1 N OJC doub 277 n y C1 C2 OJC sing 278 n y N C OJC sing 279 n y C2 N3 OJC sing 280 n y C2 C3 OJC doub 281 n y C N1 OJC doub 282 n y N3 C4 OJC doub 283 n y C3 N1 OJC sing 284 n y C3 N2 OJC sing 285 n y C4 N2 OJC sing 286 n y N2 C5 OJC sing 287 n n O12 C6 OJC sing 288 n n C5 C6 OJC sing 289 n n C5 O OJC sing 290 n n C6 C7 OJC sing 291 n n O C8 OJC sing 292 n n O6 P1 OJC sing 293 n n C7 O9 OJC sing 294 n n C7 C8 OJC sing 295 n n O9 C14 OJC sing 296 n n C8 C9 OJC sing 297 n n O4 P1 OJC sing 298 n n O4 P OJC sing 299 n n O1 C9 OJC sing 300 n n O1 P OJC sing 301 n n P1 O7 OJC sing 302 n n P1 O5 OJC doub 303 n n C10 O7 OJC sing 304 n n C10 C11 OJC sing 305 n n C12 C13 OJC sing 306 n n C12 O11 OJC sing 307 n n C12 C11 OJC sing 308 n n O3 P OJC sing 309 n n C13 C14 OJC sing 310 n n C13 O10 OJC sing 311 n n C14 O8 OJC sing 312 n n P O2 OJC doub 313 n n C11 O8 OJC sing 314 n n C H8 OJC sing 315 n n C10 H14 OJC sing 316 n n C10 H15 OJC sing 317 n n C11 H4 OJC sing 318 n n C12 H5 OJC sing 319 n n C13 H6 OJC sing 320 n n C14 H7 OJC sing 321 n n C4 H9 OJC sing 322 n n C5 H OJC sing 323 n n C6 H1 OJC sing 324 n n C7 H2 OJC sing 325 n n C8 H3 OJC sing 326 n n C9 H10 OJC sing 327 n n C9 H11 OJC sing 328 n n N4 H20 OJC sing 329 n n N4 H19 OJC sing 330 n n O10 H16 OJC sing 331 n n O11 H17 OJC sing 332 n n O12 H18 OJC sing 333 n n O3 H12 OJC sing 334 n n O6 H13 OJC sing 335 n n # _atom_sites.entry_id 8KBF _atom_sites.fract_transf_matrix[1][1] 0.009875 _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] 0.009875 _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] 0.009875 _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 3 OJC A 1 201 201 OJC 13C . F 3 OJC B 1 201 201 OJC 13C . G 4 HOH A 1 301 1 HOH HOH . G 4 HOH A 2 302 43 HOH HOH . G 4 HOH A 3 303 41 HOH HOH . G 4 HOH A 4 304 45 HOH HOH . G 4 HOH A 5 305 20 HOH HOH . G 4 HOH A 6 306 7 HOH HOH . G 4 HOH A 7 307 36 HOH HOH . G 4 HOH A 8 308 16 HOH HOH . G 4 HOH A 9 309 5 HOH HOH . G 4 HOH A 10 310 40 HOH HOH . G 4 HOH A 11 311 25 HOH HOH . G 4 HOH A 12 312 42 HOH HOH . G 4 HOH A 13 313 21 HOH HOH . G 4 HOH A 14 314 50 HOH HOH . G 4 HOH A 15 315 2 HOH HOH . G 4 HOH A 16 316 12 HOH HOH . G 4 HOH A 17 317 39 HOH HOH . G 4 HOH A 18 318 3 HOH HOH . G 4 HOH A 19 319 23 HOH HOH . G 4 HOH A 20 320 27 HOH HOH . G 4 HOH A 21 321 35 HOH HOH . G 4 HOH A 22 322 53 HOH HOH . H 4 HOH B 1 301 48 HOH HOH . H 4 HOH B 2 302 18 HOH HOH . H 4 HOH B 3 303 15 HOH HOH . H 4 HOH B 4 304 10 HOH HOH . H 4 HOH B 5 305 6 HOH HOH . H 4 HOH B 6 306 28 HOH HOH . H 4 HOH B 7 307 30 HOH HOH . H 4 HOH B 8 308 13 HOH HOH . H 4 HOH B 9 309 29 HOH HOH . H 4 HOH B 10 310 17 HOH HOH . H 4 HOH B 11 311 8 HOH HOH . H 4 HOH B 12 312 33 HOH HOH . H 4 HOH B 13 313 4 HOH HOH . H 4 HOH B 14 314 14 HOH HOH . H 4 HOH B 15 315 26 HOH HOH . H 4 HOH B 16 316 19 HOH HOH . H 4 HOH B 17 317 11 HOH HOH . H 4 HOH B 18 318 37 HOH HOH . H 4 HOH B 19 319 24 HOH HOH . H 4 HOH B 20 320 32 HOH HOH . H 4 HOH B 21 321 22 HOH HOH . H 4 HOH B 22 322 47 HOH HOH . H 4 HOH B 23 323 46 HOH HOH . H 4 HOH B 24 324 31 HOH HOH . H 4 HOH B 25 325 44 HOH HOH . H 4 HOH B 26 326 52 HOH HOH . H 4 HOH B 27 327 34 HOH HOH . H 4 HOH B 28 328 51 HOH HOH . H 4 HOH B 29 329 49 HOH HOH . I 4 HOH C 1 101 9 HOH HOH . J 4 HOH D 1 101 38 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 N OJC . . . F 3 27.446 -0.663 -22.825 0.96 52.76 ? N OJC 201 B 1 HETATM 2 C C OJC . . . F 3 27.472 -1.998 -22.802 0.96 52.69 ? C OJC 201 B 1 HETATM 3 O O OJC . . . F 3 31.459 -4.336 -21.265 0.96 53.55 ? O OJC 201 B 1 HETATM 4 C C1 OJC . . . F 3 28.337 0.014 -22.063 0.96 46.15 ? C1 OJC 201 B 1 HETATM 5 C C2 OJC . . . F 3 29.249 -0.739 -21.301 0.96 49.38 ? C2 OJC 201 B 1 HETATM 6 C C3 OJC . . . F 3 29.15 -2.117 -21.376 0.96 43.71 ? C3 OJC 201 B 1 HETATM 7 C C10 OJC . . . F 3 26.495 -5.399 -25.108 0.96 78.49 ? C10 OJC 201 B 1 HETATM 8 C C11 OJC . . . F 3 26.372 -6.306 -23.908 0.96 56.76 ? C11 OJC 201 B 1 HETATM 9 C C12 OJC . . . F 3 26.048 -5.611 -22.579 0.96 59.69 ? C12 OJC 201 B 1 HETATM 10 C C13 OJC . . . F 3 26.806 -6.447 -21.539 0.96 41.92 ? C13 OJC 201 B 1 HETATM 11 C C14 OJC . . . F 3 27.8 -7.266 -22.344 0.96 42.84 ? C14 OJC 201 B 1 HETATM 12 C C4 OJC . . . F 3 30.766 -1.507 -20.02 0.96 45.12 ? C4 OJC 201 B 1 HETATM 13 C C5 OJC . . . F 3 30.525 -3.978 -20.253 0.96 50.61 ? C5 OJC 201 B 1 HETATM 14 C C6 OJC . . . F 3 29.47 -5.091 -20.217 0.96 46.77 ? C6 OJC 201 B 1 HETATM 15 C C7 OJC . . . F 3 29.52 -5.581 -21.67 0.96 48.44 ? C7 OJC 201 B 1 HETATM 16 C C8 OJC . . . F 3 31.027 -5.543 -21.918 0.96 48.35 ? C8 OJC 201 B 1 HETATM 17 C C9 OJC . . . F 3 31.43 -5.505 -23.377 0.96 49.82 ? C9 OJC 201 B 1 HETATM 18 N N1 OJC . . . F 3 28.282 -2.809 -22.125 0.96 50.42 ? N1 OJC 201 B 1 HETATM 19 N N2 OJC . . . F 3 30.143 -2.602 -20.553 0.96 47.71 ? N2 OJC 201 B 1 HETATM 20 N N3 OJC . . . F 3 30.271 -0.367 -20.435 0.96 42.78 ? N3 OJC 201 B 1 HETATM 21 N N4 OJC . . . F 3 28.32 1.349 -22.085 0.96 35 ? N4 OJC 201 B 1 HETATM 22 O O1 OJC . . . F 3 30.563 -4.565 -24.056 0.96 51.03 ? O1 OJC 201 B 1 HETATM 23 O O10 OJC . . . F 3 26.076 -7.491 -20.926 0.96 50.9 ? O10 OJC 201 B 1 HETATM 24 O O11 OJC . . . F 3 24.697 -5.279 -22.255 0.96 61.29 ? O11 OJC 201 B 1 HETATM 25 O O12 OJC . . . F 3 29.881 -6.131 -19.356 0.96 64.39 ? O12 OJC 201 B 1 HETATM 26 O O2 OJC . . . F 3 30.589 -2.943 -25.96 0.96 49.14 ? O2 OJC 201 B 1 HETATM 27 O O3 OJC . . . F 3 31.828 -5.143 -26.211 0.96 64.91 ? O3 OJC 201 B 1 HETATM 28 O O4 OJC . . . F 3 29.245 -5.056 -25.949 0.96 57.19 ? O4 OJC 201 B 1 HETATM 29 O O5 OJC . . . F 3 28.704 -6.139 -28.141 0.96 91.64 ? O5 OJC 201 B 1 HETATM 30 O O6 OJC . . . F 3 27.561 -3.936 -27.54 0.96 53.69 ? O6 OJC 201 B 1 HETATM 31 O O7 OJC . . . F 3 27.109 -6.108 -26.222 0.96 62.74 ? O7 OJC 201 B 1 HETATM 32 O O8 OJC . . . F 3 27.675 -6.867 -23.688 0.96 65.8 ? O8 OJC 201 B 1 HETATM 33 O O9 OJC . . . F 3 29.063 -6.924 -21.835 0.96 56.44 ? O9 OJC 201 B 1 HETATM 34 P P OJC . . . F 3 30.686 -4.387 -25.643 0.96 50.85 ? P OJC 201 B 1 HETATM 35 P P1 OJC . . . F 3 28.132 -5.247 -27.103 0.96 73.88 ? P1 OJC 201 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 35 #