data_5KM5 # _model_server_result.job_id FPpIzi7TAQOI4FDXwOizPA _model_server_result.datetime_utc '2024-11-23 18:47:09' _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 5km5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 5KM5 # _exptl.entry_id 5KM5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 400.284 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-methyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-1,5-dihydro-1,4,5,6,8-pentaazaacenaphthylen-3-amine _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 90 _cell.angle_gamma 90 _cell.entry_id 5KM5 _cell.length_a 38.129 _cell.length_b 76.045 _cell.length_c 77.821 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KM5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C13 H17 N6 O7 P' _chem_comp.formula_weight 400.284 _chem_comp.id TR5 _chem_comp.mon_nstd_flag . _chem_comp.name 5-methyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-1,5-dihydro-1,4,5,6,8-pentaazaacenaphthylen-3-amine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Triciribine phosphate' # 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 O2' C2' TR5 sing 336 n n C2 N3 TR5 doub 337 n y C2 N1 TR5 sing 338 n y O3' C3' TR5 sing 339 n n N3 C4 TR5 sing 340 n y N1 C6 TR5 doub 341 n y C2' C3' TR5 sing 342 n n C2' C1' TR5 sing 343 n n C3' C4' TR5 sing 344 n n C4 C5 TR5 doub 345 n y C4 N9 TR5 sing 346 n y C6 C5 TR5 sing 347 n y C6 N61 TR5 sing 348 n n C62 N61 TR5 sing 349 n n C1' N9 TR5 sing 350 n n C1' O4' TR5 sing 351 n n C5 C7 TR5 sing 352 n y N9 C8 TR5 sing 353 n y N61 N71 TR5 sing 354 n n C4' C5' TR5 sing 355 n n C4' O4' TR5 sing 356 n n C5' O5' TR5 sing 357 n n C7 C8 TR5 doub 358 n y C7 C72 TR5 sing 359 n n N71 C72 TR5 doub 360 n n C72 N73 TR5 sing 361 n n O5' PB TR5 sing 362 n n O2 PB TR5 doub 363 n n O1 PB TR5 sing 364 n n PB O3 TR5 sing 365 n n O3 H1 TR5 sing 366 n n O1 H2 TR5 sing 367 n n C5' H3 TR5 sing 368 n n C5' H4 TR5 sing 369 n n C4' H5 TR5 sing 370 n n C3' H6 TR5 sing 371 n n O3' H7 TR5 sing 372 n n C2' H8 TR5 sing 373 n n O2' H9 TR5 sing 374 n n C1' H10 TR5 sing 375 n n C8 H11 TR5 sing 376 n n C2 H12 TR5 sing 377 n n C62 H13 TR5 sing 378 n n C62 H14 TR5 sing 379 n n C62 H15 TR5 sing 380 n n N73 H16 TR5 sing 381 n n N73 H17 TR5 sing 382 n n # _atom_sites.entry_id 5KM5 _atom_sites.fract_transf_matrix[1][1] 0.026227 _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] 0.01315 _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] 0.01285 _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 C 2 CL A 1 201 1 CL CL . D 3 PG4 A 1 202 1 PG4 PG4 . E 4 TR5 B 1 201 1 TR5 TCN . F 5 HOH A 1 301 3 HOH HOH . F 5 HOH A 2 302 6 HOH HOH . F 5 HOH A 3 303 4 HOH HOH . F 5 HOH A 4 304 54 HOH HOH . F 5 HOH A 5 305 12 HOH HOH . F 5 HOH A 6 306 47 HOH HOH . F 5 HOH A 7 307 19 HOH HOH . F 5 HOH A 8 308 38 HOH HOH . F 5 HOH A 9 309 35 HOH HOH . F 5 HOH A 10 310 22 HOH HOH . F 5 HOH A 11 311 27 HOH HOH . F 5 HOH A 12 312 1 HOH HOH . F 5 HOH A 13 313 34 HOH HOH . F 5 HOH A 14 314 49 HOH HOH . F 5 HOH A 15 315 40 HOH HOH . F 5 HOH A 16 316 21 HOH HOH . F 5 HOH A 17 317 2 HOH HOH . F 5 HOH A 18 318 14 HOH HOH . F 5 HOH A 19 319 25 HOH HOH . F 5 HOH A 20 320 37 HOH HOH . F 5 HOH A 21 321 18 HOH HOH . F 5 HOH A 22 322 33 HOH HOH . F 5 HOH A 23 323 3 HOH HOH . F 5 HOH A 24 324 59 HOH HOH . F 5 HOH A 25 325 52 HOH HOH . F 5 HOH A 26 326 31 HOH HOH . F 5 HOH A 27 327 28 HOH HOH . G 5 HOH B 1 301 6 HOH HOH . G 5 HOH B 2 302 5 HOH HOH . G 5 HOH B 3 303 1 HOH HOH . G 5 HOH B 4 304 30 HOH HOH . G 5 HOH B 5 305 13 HOH HOH . G 5 HOH B 6 306 8 HOH HOH . G 5 HOH B 7 307 7 HOH HOH . G 5 HOH B 8 308 26 HOH HOH . G 5 HOH B 9 309 3 HOH HOH . G 5 HOH B 10 310 20 HOH HOH . G 5 HOH B 11 311 10 HOH HOH . G 5 HOH B 12 312 11 HOH HOH . G 5 HOH B 13 313 5 HOH HOH . G 5 HOH B 14 314 24 HOH HOH . G 5 HOH B 15 315 2 HOH HOH . G 5 HOH B 16 316 23 HOH HOH . G 5 HOH B 17 317 51 HOH HOH . G 5 HOH B 18 318 42 HOH HOH . G 5 HOH B 19 319 17 HOH HOH . G 5 HOH B 20 320 2 HOH HOH . G 5 HOH B 21 321 7 HOH HOH . G 5 HOH B 22 322 4 HOH HOH . G 5 HOH B 23 323 9 HOH HOH . G 5 HOH B 24 324 50 HOH HOH . G 5 HOH B 25 325 58 HOH HOH . G 5 HOH B 26 326 4 HOH HOH . G 5 HOH B 27 327 16 HOH HOH . G 5 HOH B 28 328 55 HOH HOH . G 5 HOH B 29 329 32 HOH HOH . G 5 HOH B 30 330 15 HOH HOH . G 5 HOH B 31 331 1 HOH HOH . G 5 HOH B 32 332 57 HOH HOH . G 5 HOH B 33 333 36 HOH HOH . G 5 HOH B 34 334 45 HOH HOH . G 5 HOH B 35 335 43 HOH HOH . G 5 HOH B 36 336 44 HOH HOH . G 5 HOH B 37 337 39 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 O O2 TR5 . . . E 4 -12.263 0.822 -1.255 1 26.83 ? O2 TR5 201 B 1 HETATM 2 P PB TR5 . . . E 4 -12.021 0.602 0.221 1 28.49 ? PB TR5 201 B 1 HETATM 3 O O3 TR5 . . . E 4 -13.236 0.472 1.1 1 29.84 ? O3 TR5 201 B 1 HETATM 4 O O1 TR5 . . . E 4 -10.895 1.406 0.819 1 27.03 ? O1 TR5 201 B 1 HETATM 5 O O5' TR5 . . . E 4 -11.446 -0.874 0.25 1 26.9 ? O5' TR5 201 B 1 HETATM 6 C C5' TR5 . . . E 4 -10.815 -1.395 1.414 1 24.35 ? C5' TR5 201 B 1 HETATM 7 C C4' TR5 . . . E 4 -10.861 -2.896 1.381 1 25.56 ? C4' TR5 201 B 1 HETATM 8 O O4' TR5 . . . E 4 -9.893 -3.461 2.298 1 24.1 ? O4' TR5 201 B 1 HETATM 9 C C3' TR5 . . . E 4 -12.225 -3.499 1.762 1 25.7 ? C3' TR5 201 B 1 HETATM 10 O O3' TR5 . . . E 4 -12.687 -4.345 0.7 1 23.5 ? O3' TR5 201 B 1 HETATM 11 C C2' TR5 . . . E 4 -11.914 -4.332 3.015 1 25.1 ? C2' TR5 201 B 1 HETATM 12 O O2' TR5 . . . E 4 -12.686 -5.504 3.138 1 25.05 ? O2' TR5 201 B 1 HETATM 13 C C1' TR5 . . . E 4 -10.436 -4.645 2.813 1 24.82 ? C1' TR5 201 B 1 HETATM 14 N N9 TR5 . . . E 4 -9.706 -5.042 4.022 1 24.81 ? N9 TR5 201 B 1 HETATM 15 C C8 TR5 . . . E 4 -9.857 -4.522 5.287 1 26.93 ? C8 TR5 201 B 1 HETATM 16 C C7 TR5 . . . E 4 -8.931 -5.249 6.128 1 28.91 ? C7 TR5 201 B 1 HETATM 17 C C5 TR5 . . . E 4 -8.309 -6.13 5.318 1 25.76 ? C5 TR5 201 B 1 HETATM 18 C C4 TR5 . . . E 4 -8.773 -6.022 4.058 1 24.43 ? C4 TR5 201 B 1 HETATM 19 N N3 TR5 . . . E 4 -8.218 -6.876 3.163 1 24.81 ? N3 TR5 201 B 1 HETATM 20 C C2 TR5 . . . E 4 -7.265 -7.768 3.519 1 22.88 ? C2 TR5 201 B 1 HETATM 21 N N1 TR5 . . . E 4 -6.791 -7.895 4.772 1 25.82 ? N1 TR5 201 B 1 HETATM 22 C C6 TR5 . . . E 4 -7.296 -7.088 5.732 1 25.24 ? C6 TR5 201 B 1 HETATM 23 N N61 TR5 . . . E 4 -6.941 -7.07 7.087 1 27.44 ? N61 TR5 201 B 1 HETATM 24 C C62 TR5 . . . E 4 -5.924 -7.988 7.61 1 27.72 ? C62 TR5 201 B 1 HETATM 25 N N71 TR5 . . . E 4 -7.574 -6.158 7.956 1 27.92 ? N71 TR5 201 B 1 HETATM 26 C C72 TR5 . . . E 4 -8.514 -5.272 7.559 1 30.26 ? C72 TR5 201 B 1 HETATM 27 N N73 TR5 . . . E 4 -9.122 -4.353 8.554 1 26.61 ? N73 TR5 201 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #