data_1XK5 # _model_server_result.job_id jINLJRaz2Lvqu539TM2PCA _model_server_result.datetime_utc '2025-03-09 04:42:02' _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 1xk5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":400}' # _entry.id 1XK5 # _exptl.entry_id 1XK5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 832.501 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2,2,7-TRIMETHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE" _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 1XK5 _cell.length_a 57.47 _cell.length_b 57.47 _cell.length_c 130.09 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XK5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C23 H35 N10 O18 P3' _chem_comp.formula_weight 832.501 _chem_comp.id TPG _chem_comp.mon_nstd_flag n _chem_comp.name "2,2,7-TRIMETHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE" _chem_comp.type 'rna 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 OBB CBF TPG doub 306 n n CBF NBE TPG sing 307 n n CBF CBG TPG sing 308 n n NBE CBM TPG sing 309 n n NBE HBE TPG sing 310 n n CBM NBV TPG sing 311 n n CBM NBN TPG doub 312 n n NBV CBZ TPG sing 313 n n NBV CBW TPG sing 314 n n CBZ HBZ1 TPG sing 315 n n CBZ HBZ2 TPG sing 316 n n CBZ HBZ3 TPG sing 317 n n CBW HBW1 TPG sing 318 n n CBW HBW2 TPG sing 319 n n CBW HBW3 TPG sing 320 n n NBN CBO TPG sing 321 n n CBO CBG TPG doub 322 n n CBO NBP TPG sing 323 n n CBG NBH TPG sing 324 n n NBH CBC TPG sing 325 n n NBH CBI TPG sing 326 n n CBC HBC1 TPG sing 327 n n CBC HBC2 TPG sing 328 n n CBC HBC3 TPG sing 329 n n CBI NBP TPG sing 330 n n CBI HBI1 TPG sing 331 n n CBI HBI2 TPG sing 332 n n NBP CBQ TPG sing 333 n n CBQ OBR TPG sing 334 n n CBQ CBX TPG sing 335 n n CBQ HBQ TPG sing 336 n n OBR CBS TPG sing 337 n n CBX OCA TPG sing 338 n n CBX CBY TPG sing 339 n n CBX HBX TPG sing 340 n n OCA HCA TPG sing 341 n n CBY OCB TPG sing 342 n n CBY CBS TPG sing 343 n n CBY HBY TPG sing 344 n n OCB HCB TPG sing 345 n n CBS CBT TPG sing 346 n n CBS HBS TPG sing 347 n n CBT OBU TPG sing 348 n n CBT HBT1 TPG sing 349 n n CBT HBT2 TPG sing 350 n n OBU PBK TPG sing 351 n n PBK OBL TPG doub 352 n n PBK OBJ TPG sing 353 n n PBK OBD TPG sing 354 n n OBJ HBJ TPG sing 355 n n OBD PAZ TPG sing 356 n n PAZ OBA TPG doub 357 n n PAZ OAY TPG sing 358 n n PAZ OAX TPG sing 359 n n OAY HAY TPG sing 360 n n OAX PAT TPG sing 361 n n PAT OAU TPG doub 362 n n PAT OAS TPG sing 363 n n PAT O5' TPG sing 364 n n OAS HAS TPG sing 365 n n O5' C5' TPG sing 366 n n C5' C4' TPG sing 367 n n C5' H5' TPG sing 368 n n C5' "H5''" TPG sing 369 n n C4' O4' TPG sing 370 n n C4' C3' TPG sing 371 n n C4' H4' TPG sing 372 n n O4' C1' TPG sing 373 n n C3' O3' TPG sing 374 n n C3' C2' TPG sing 375 n n C3' H3' TPG sing 376 n n O3' H2 TPG sing 377 n n C2' O2' TPG sing 378 n n C2' C1' TPG sing 379 n n C2' H1 TPG sing 380 n n O2' H2' TPG sing 381 n n C1' N9 TPG sing 382 n n C1' H1' TPG sing 383 n n N9 C8 TPG sing 384 n y N9 C4 TPG sing 385 n y C8 N7 TPG doub 386 n y C8 H8 TPG sing 387 n n N7 C5 TPG sing 388 n y C5 C4 TPG doub 389 n y C5 C6 TPG sing 390 n n C4 N3 TPG sing 391 n n N3 C2 TPG doub 392 n n C2 N2 TPG sing 393 n n C2 N1 TPG sing 394 n n N2 HN21 TPG sing 395 n n N2 HN22 TPG sing 396 n n N1 C6 TPG sing 397 n n N1 HN1 TPG sing 398 n n C6 O6 TPG doub 399 n n # _atom_sites.entry_id 1XK5 _atom_sites.fract_transf_matrix[1][1] 0.0174 _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] 0.0174 _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] 0.007687 _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 B 2 TPG A 1 400 400 TPG DRG . C 3 HOH A 1 1 1 HOH HOH . C 3 HOH A 2 2 2 HOH HOH . C 3 HOH A 3 3 3 HOH HOH . C 3 HOH A 4 4 4 HOH HOH . C 3 HOH A 5 5 5 HOH HOH . C 3 HOH A 6 6 6 HOH HOH . C 3 HOH A 7 7 7 HOH HOH . C 3 HOH A 8 8 8 HOH HOH . C 3 HOH A 9 9 9 HOH HOH . C 3 HOH A 10 10 10 HOH HOH . C 3 HOH A 11 11 11 HOH HOH . C 3 HOH A 12 12 12 HOH HOH . C 3 HOH A 13 13 13 HOH HOH . C 3 HOH A 14 14 14 HOH HOH . C 3 HOH A 15 15 15 HOH HOH . C 3 HOH A 16 16 16 HOH HOH . C 3 HOH A 17 17 17 HOH HOH . C 3 HOH A 18 18 18 HOH HOH . C 3 HOH A 19 19 19 HOH HOH . C 3 HOH A 20 20 20 HOH HOH . C 3 HOH A 21 21 21 HOH HOH . C 3 HOH A 22 22 22 HOH HOH . C 3 HOH A 23 23 23 HOH HOH . C 3 HOH A 24 24 24 HOH HOH . C 3 HOH A 25 25 25 HOH HOH . C 3 HOH A 26 26 26 HOH HOH . C 3 HOH A 27 27 27 HOH HOH . C 3 HOH A 28 28 28 HOH HOH . C 3 HOH A 29 29 29 HOH HOH . C 3 HOH A 30 30 30 HOH HOH . C 3 HOH A 31 31 31 HOH HOH . C 3 HOH A 32 32 32 HOH HOH . C 3 HOH A 33 33 33 HOH HOH . C 3 HOH A 34 34 34 HOH HOH . C 3 HOH A 35 35 35 HOH HOH . C 3 HOH A 36 36 36 HOH HOH . C 3 HOH A 37 37 37 HOH HOH . C 3 HOH A 38 38 38 HOH HOH . C 3 HOH A 39 39 39 HOH HOH . C 3 HOH A 40 40 40 HOH HOH . C 3 HOH A 41 41 41 HOH HOH . C 3 HOH A 42 42 42 HOH HOH . C 3 HOH A 43 43 43 HOH HOH . C 3 HOH A 44 44 44 HOH HOH . C 3 HOH A 45 45 45 HOH HOH . C 3 HOH A 46 46 46 HOH HOH . C 3 HOH A 47 47 47 HOH HOH . C 3 HOH A 48 48 48 HOH HOH . C 3 HOH A 49 49 49 HOH HOH . C 3 HOH A 50 50 50 HOH HOH . C 3 HOH A 51 51 51 HOH HOH . C 3 HOH A 52 52 52 HOH HOH . C 3 HOH A 53 53 53 HOH HOH . C 3 HOH A 54 54 54 HOH HOH . C 3 HOH A 55 55 55 HOH HOH . C 3 HOH A 56 56 56 HOH HOH . C 3 HOH A 57 57 57 HOH HOH . C 3 HOH A 58 58 58 HOH HOH . C 3 HOH A 59 59 59 HOH HOH . C 3 HOH A 60 60 60 HOH HOH . C 3 HOH A 61 61 61 HOH HOH . C 3 HOH A 62 62 62 HOH HOH . C 3 HOH A 63 63 63 HOH HOH . C 3 HOH A 64 64 64 HOH HOH . C 3 HOH A 65 65 65 HOH HOH . C 3 HOH A 66 66 66 HOH HOH . C 3 HOH A 67 67 67 HOH HOH . C 3 HOH A 68 68 68 HOH HOH . C 3 HOH A 69 69 69 HOH HOH . C 3 HOH A 70 70 70 HOH HOH . C 3 HOH A 71 71 71 HOH HOH . C 3 HOH A 72 72 72 HOH HOH . C 3 HOH A 73 73 73 HOH HOH . C 3 HOH A 74 74 74 HOH HOH . C 3 HOH A 75 75 75 HOH HOH . C 3 HOH A 76 76 76 HOH HOH . C 3 HOH A 77 77 77 HOH HOH . C 3 HOH A 78 78 78 HOH HOH . C 3 HOH A 79 79 79 HOH HOH . C 3 HOH A 80 80 80 HOH HOH . C 3 HOH A 81 81 81 HOH HOH . C 3 HOH A 82 82 82 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 OBB TPG . . . B 2 13.343 40.165 11.728 1 54.16 ? OBB TPG 400 A 1 HETATM 2 C CBF TPG . . . B 2 13.12 38.96 11.831 1 57.5 ? CBF TPG 400 A 1 HETATM 3 N NBE TPG . . . B 2 13.66 38.236 12.903 1 57.24 ? NBE TPG 400 A 1 HETATM 4 C CBM TPG . . . B 2 13.402 36.863 13.007 1 56.27 ? CBM TPG 400 A 1 HETATM 5 N NBV TPG . . . B 2 13.938 36.146 13.993 1 57.49 ? NBV TPG 400 A 1 HETATM 6 C CBZ TPG . . . B 2 13.67 34.704 14.094 1 56.8 ? CBZ TPG 400 A 1 HETATM 7 C CBW TPG . . . B 2 14.811 36.787 14.987 1 54.93 ? CBW TPG 400 A 1 HETATM 8 N NBN TPG . . . B 2 12.636 36.268 12.08 1 55.52 ? NBN TPG 400 A 1 HETATM 9 C CBO TPG . . . B 2 12.105 36.94 11.045 1 59.69 ? CBO TPG 400 A 1 HETATM 10 C CBG TPG . . . B 2 12.332 38.306 10.888 1 58.09 ? CBG TPG 400 A 1 HETATM 11 N NBH TPG . . . B 2 11.796 38.701 9.736 1 56.41 ? NBH TPG 400 A 1 HETATM 12 C CBC TPG . . . B 2 11.941 40.044 9.131 1 54.66 ? CBC TPG 400 A 1 HETATM 13 C CBI TPG . . . B 2 11.018 37.607 9.142 1 59.48 ? CBI TPG 400 A 1 HETATM 14 N NBP TPG . . . B 2 11.409 36.484 10.006 1 62.09 ? NBP TPG 400 A 1 HETATM 15 C CBQ TPG . . . B 2 11.064 35.068 9.738 1 67.39 ? CBQ TPG 400 A 1 HETATM 16 O OBR TPG . . . B 2 12.135 34.523 8.945 1 71.67 ? OBR TPG 400 A 1 HETATM 17 C CBX TPG . . . B 2 9.799 34.877 8.898 1 69.39 ? CBX TPG 400 A 1 HETATM 18 O OCA TPG . . . B 2 9.336 33.53 9.029 1 68.62 ? OCA TPG 400 A 1 HETATM 19 C CBY TPG . . . B 2 10.363 35.14 7.505 1 72.93 ? CBY TPG 400 A 1 HETATM 20 O OCB TPG . . . B 2 9.489 34.6 6.51 1 74.66 ? OCB TPG 400 A 1 HETATM 21 C CBS TPG . . . B 2 11.648 34.321 7.607 1 74.46 ? CBS TPG 400 A 1 HETATM 22 C CBT TPG . . . B 2 12.665 34.735 6.543 1 79.44 ? CBT TPG 400 A 1 HETATM 23 O OBU TPG . . . B 2 12.089 34.611 5.241 1 86.14 ? OBU TPG 400 A 1 HETATM 24 P PBK TPG . . . B 2 12.635 35.519 4.03 1 89.63 ? PBK TPG 400 A 1 HETATM 25 O OBL TPG . . . B 2 13.873 36.369 4.613 1 87.98 ? OBL TPG 400 A 1 HETATM 26 O OBJ TPG . . . B 2 11.577 36.403 3.492 1 90.47 ? OBJ TPG 400 A 1 HETATM 27 O OBD TPG . . . B 2 13.231 34.495 2.939 1 90.77 ? OBD TPG 400 A 1 HETATM 28 P PAZ TPG . . . B 2 14.794 34.107 2.933 1 91.52 ? PAZ TPG 400 A 1 HETATM 29 O OBA TPG . . . B 2 15.179 33.205 1.655 1 92.95 ? OBA TPG 400 A 1 HETATM 30 O OAY TPG . . . B 2 15.807 34.894 3.671 1 91.2 ? OAY TPG 400 A 1 HETATM 31 O OAX TPG . . . B 2 14.61 32.854 3.929 1 91.57 ? OAX TPG 400 A 1 HETATM 32 P PAT TPG . . . B 2 15.878 32.212 4.689 1 91.7 ? PAT TPG 400 A 1 HETATM 33 O OAU TPG . . . B 2 16.5 30.965 3.88 1 89.52 ? OAU TPG 400 A 1 HETATM 34 O OAS TPG . . . B 2 16.657 32.962 5.698 1 91.83 ? OAS TPG 400 A 1 HETATM 35 O O5' TPG . . . B 2 14.985 31.281 5.653 1 90.22 ? O5' TPG 400 A 1 HETATM 36 C C5' TPG . . . B 2 14.158 31.834 6.682 1 87.04 ? C5' TPG 400 A 1 HETATM 37 C C4' TPG . . . B 2 14.854 31.847 8.045 1 85.44 ? C4' TPG 400 A 1 HETATM 38 O O4' TPG . . . B 2 15.877 32.851 8.153 1 84.7 ? O4' TPG 400 A 1 HETATM 39 C C3' TPG . . . B 2 13.883 32.243 9.156 1 84.33 ? C3' TPG 400 A 1 HETATM 40 O O3' TPG . . . B 2 13.026 31.137 9.452 1 82.81 ? O3' TPG 400 A 1 HETATM 41 C C2' TPG . . . B 2 14.908 32.4 10.276 1 83.24 ? C2' TPG 400 A 1 HETATM 42 O O2' TPG . . . B 2 15.403 31.115 10.662 1 84.3 ? O2' TPG 400 A 1 HETATM 43 C C1' TPG . . . B 2 16.009 33.179 9.551 1 82.15 ? C1' TPG 400 A 1 HETATM 44 N N9 TPG . . . B 2 15.823 34.64 9.718 1 78.82 ? N9 TPG 400 A 1 HETATM 45 C C8 TPG . . . B 2 15.274 35.468 8.832 1 76.77 ? C8 TPG 400 A 1 HETATM 46 N N7 TPG . . . B 2 15.352 36.718 9.283 1 75.63 ? N7 TPG 400 A 1 HETATM 47 C C5 TPG . . . B 2 15.95 36.689 10.47 1 75.73 ? C5 TPG 400 A 1 HETATM 48 C C4 TPG . . . B 2 16.244 35.36 10.755 1 77.01 ? C4 TPG 400 A 1 HETATM 49 N N3 TPG . . . B 2 16.847 35.02 11.905 1 75.45 ? N3 TPG 400 A 1 HETATM 50 C C2 TPG . . . B 2 17.193 35.938 12.82 1 73.73 ? C2 TPG 400 A 1 HETATM 51 N N2 TPG . . . B 2 17.778 35.563 13.954 1 71.98 ? N2 TPG 400 A 1 HETATM 52 N N1 TPG . . . B 2 16.927 37.293 12.583 1 73.36 ? N1 TPG 400 A 1 HETATM 53 C C6 TPG . . . B 2 16.298 37.671 11.39 1 74.26 ? C6 TPG 400 A 1 HETATM 54 O O6 TPG . . . B 2 16.079 38.858 11.153 1 72.78 ? O6 TPG 400 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 54 #