data_3RKW # _model_server_result.job_id uogREhg0MBnEmkK6B1Okzw _model_server_result.datetime_utc '2025-01-11 18:57:19' _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 3rkw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 3RKW # _exptl.entry_id 3RKW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 573.517 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description BIOTINYL-5-AMP _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 3RKW _cell.length_a 94.598 _cell.length_b 94.598 _cell.length_c 130.626 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RKW _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 94.598 0 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 'C20 H28 N7 O9 P S' _chem_comp.formula_weight 573.517 _chem_comp.id BT5 _chem_comp.mon_nstd_flag . _chem_comp.name BIOTINYL-5-AMP _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 CBB OBB BT5 sing 70 n n CBB OCB BT5 doub 71 n n CBB CAB BT5 sing 72 n n OBB P BT5 sing 73 n n CAB C9B BT5 sing 74 n n CAB H101 BT5 sing 75 n n CAB H102 BT5 sing 76 n n C9B C8B BT5 sing 77 n n C9B H9B1 BT5 sing 78 n n C9B H9B2 BT5 sing 79 n n C8B C7B BT5 sing 80 n n C8B H8B1 BT5 sing 81 n n C8B H8B2 BT5 sing 82 n n C7B C2B BT5 sing 83 n n C7B H7B1 BT5 sing 84 n n C7B H7B2 BT5 sing 85 n n C2B S1B BT5 sing 86 n n C2B C4B BT5 sing 87 n n C2B H2B BT5 sing 88 n n S1B C6B BT5 sing 89 n n C6B C5B BT5 sing 90 n n C6B H6B1 BT5 sing 91 n n C6B H6B2 BT5 sing 92 n n C5B N1B BT5 sing 93 n n C5B C4B BT5 sing 94 n n C5B H5B BT5 sing 95 n n N1B C3B BT5 sing 96 n n N1B H1B BT5 sing 97 n n C3B O3B BT5 doub 98 n n C3B N2B BT5 sing 99 n n N2B C4B BT5 sing 100 n n N2B H4 BT5 sing 101 n n C4B H4B BT5 sing 102 n n P OP1 BT5 doub 103 n n P OP2 BT5 sing 104 n n P O5' BT5 sing 105 n n OP2 H2P BT5 sing 106 n n O5' C5' BT5 sing 107 n n C5' C4' BT5 sing 108 n n C5' H5' BT5 sing 109 n n C5' "H5''" BT5 sing 110 n n C4' O4' BT5 sing 111 n n C4' C3' BT5 sing 112 n n C4' H4' BT5 sing 113 n n O4' C1' BT5 sing 114 n n C3' O3' BT5 sing 115 n n C3' C2' BT5 sing 116 n n C3' H3' BT5 sing 117 n n O3' H2 BT5 sing 118 n n C2' O2' BT5 sing 119 n n C2' C1' BT5 sing 120 n n C2' H1 BT5 sing 121 n n O2' H2' BT5 sing 122 n n C1' N9 BT5 sing 123 n n C1' H1' BT5 sing 124 n n N9 C8 BT5 sing 125 n y N9 C4 BT5 sing 126 n y C8 N7 BT5 doub 127 n y C8 H8 BT5 sing 128 n n N7 C5 BT5 sing 129 n y C5 C6 BT5 doub 130 n y C5 C4 BT5 sing 131 n y C6 N6 BT5 sing 132 n n C6 N1 BT5 sing 133 n y N6 HN61 BT5 sing 134 n n N6 HN62 BT5 sing 135 n n N1 C2 BT5 doub 136 n y C2 N3 BT5 sing 137 n y C2 H3 BT5 sing 138 n n N3 C4 BT5 doub 139 n y # _atom_sites.entry_id 3RKW _atom_sites.fract_transf_matrix[1][1] 0.010571 _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] 0.010571 _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] 0.007655 _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 BT5 A 1 500 500 BT5 BT5 . C 3 HOH A 1 324 1 HOH HOH . C 3 HOH A 2 325 2 HOH HOH . C 3 HOH A 3 326 3 HOH HOH . C 3 HOH A 4 327 4 HOH HOH . C 3 HOH A 5 328 5 HOH HOH . C 3 HOH A 6 329 6 HOH HOH . C 3 HOH A 7 330 7 HOH HOH . C 3 HOH A 8 331 8 HOH HOH . C 3 HOH A 9 332 9 HOH HOH . C 3 HOH A 10 333 10 HOH HOH . C 3 HOH A 11 334 11 HOH HOH . C 3 HOH A 12 335 12 HOH HOH . C 3 HOH A 13 336 13 HOH HOH . C 3 HOH A 14 337 14 HOH HOH . C 3 HOH A 15 338 15 HOH HOH . C 3 HOH A 16 339 16 HOH HOH . C 3 HOH A 17 340 17 HOH HOH . C 3 HOH A 18 341 18 HOH HOH . C 3 HOH A 19 342 19 HOH HOH . C 3 HOH A 20 343 20 HOH HOH . C 3 HOH A 21 344 21 HOH HOH . C 3 HOH A 22 345 22 HOH HOH . C 3 HOH A 23 346 23 HOH HOH . C 3 HOH A 24 347 24 HOH HOH . C 3 HOH A 25 348 25 HOH HOH . C 3 HOH A 26 349 26 HOH HOH . C 3 HOH A 27 350 27 HOH HOH . C 3 HOH A 28 351 28 HOH HOH . C 3 HOH A 29 352 29 HOH HOH . C 3 HOH A 30 353 30 HOH HOH . C 3 HOH A 31 354 31 HOH HOH . C 3 HOH A 32 355 32 HOH HOH . C 3 HOH A 33 356 33 HOH HOH . C 3 HOH A 34 357 34 HOH HOH . C 3 HOH A 35 358 35 HOH HOH . C 3 HOH A 36 359 36 HOH HOH . C 3 HOH A 37 360 37 HOH HOH . C 3 HOH A 38 361 38 HOH HOH . C 3 HOH A 39 362 39 HOH HOH . C 3 HOH A 40 363 40 HOH HOH . C 3 HOH A 41 364 41 HOH HOH . C 3 HOH A 42 365 42 HOH HOH . C 3 HOH A 43 366 43 HOH HOH . C 3 HOH A 44 367 44 HOH HOH . C 3 HOH A 45 368 45 HOH HOH . C 3 HOH A 46 369 46 HOH HOH . C 3 HOH A 47 370 47 HOH HOH . C 3 HOH A 48 371 48 HOH HOH . C 3 HOH A 49 372 49 HOH HOH . C 3 HOH A 50 373 50 HOH HOH . C 3 HOH A 51 374 51 HOH HOH . C 3 HOH A 52 375 52 HOH HOH . C 3 HOH A 53 376 53 HOH HOH . C 3 HOH A 54 377 54 HOH HOH . C 3 HOH A 55 378 55 HOH HOH . C 3 HOH A 56 379 56 HOH HOH . C 3 HOH A 57 380 57 HOH HOH . C 3 HOH A 58 381 58 HOH HOH . C 3 HOH A 59 382 59 HOH HOH . C 3 HOH A 60 383 60 HOH HOH . C 3 HOH A 61 384 61 HOH HOH . C 3 HOH A 62 385 62 HOH HOH . C 3 HOH A 63 386 63 HOH HOH . C 3 HOH A 64 387 64 HOH HOH . C 3 HOH A 65 388 65 HOH HOH . C 3 HOH A 66 389 66 HOH HOH . C 3 HOH A 67 390 67 HOH HOH . C 3 HOH A 68 391 68 HOH HOH . C 3 HOH A 69 392 69 HOH HOH . C 3 HOH A 70 393 70 HOH HOH . C 3 HOH A 71 394 71 HOH HOH . C 3 HOH A 72 395 72 HOH HOH . C 3 HOH A 73 396 73 HOH HOH . C 3 HOH A 74 397 74 HOH HOH . C 3 HOH A 75 398 75 HOH HOH . C 3 HOH A 76 399 76 HOH HOH . C 3 HOH A 77 400 77 HOH HOH . C 3 HOH A 78 401 78 HOH HOH . C 3 HOH A 79 402 79 HOH HOH . C 3 HOH A 80 403 80 HOH HOH . C 3 HOH A 81 404 81 HOH HOH . C 3 HOH A 82 405 82 HOH HOH . C 3 HOH A 83 406 83 HOH HOH . C 3 HOH A 84 407 84 HOH HOH . C 3 HOH A 85 408 85 HOH HOH . C 3 HOH A 86 409 86 HOH HOH . C 3 HOH A 87 410 87 HOH HOH . C 3 HOH A 88 411 88 HOH HOH . C 3 HOH A 89 412 89 HOH HOH . C 3 HOH A 90 413 90 HOH HOH . C 3 HOH A 91 414 91 HOH HOH . C 3 HOH A 92 415 92 HOH HOH . C 3 HOH A 93 416 93 HOH HOH . C 3 HOH A 94 417 94 HOH HOH . C 3 HOH A 95 418 95 HOH HOH . C 3 HOH A 96 419 96 HOH HOH . C 3 HOH A 97 420 97 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 C CBB BT5 . . . B 2 50.849 17.18 18.111 1 27.96 ? CBB BT5 500 A 1 HETATM 2 O OBB BT5 . . . B 2 51.986 17.91 18.476 1 37.9 ? OBB BT5 500 A 1 HETATM 3 C CAB BT5 . . . B 2 49.669 17.3 18.877 1 29.63 ? CAB BT5 500 A 1 HETATM 4 C C9B BT5 . . . B 2 49.797 16.974 20.244 1 45.83 ? C9B BT5 500 A 1 HETATM 5 C C8B BT5 . . . B 2 48.676 16.54 21.123 1 29.52 ? C8B BT5 500 A 1 HETATM 6 C C7B BT5 . . . B 2 48.597 17.155 22.565 1 39.18 ? C7B BT5 500 A 1 HETATM 7 C C2B BT5 . . . B 2 47.461 16.717 23.356 1 46.35 ? C2B BT5 500 A 1 HETATM 8 S S1B BT5 . . . B 2 47.305 17.291 24.904 1 31.4 ? S1B BT5 500 A 1 HETATM 9 C C6B BT5 . . . B 2 46.203 16.105 25.331 1 13.92 ? C6B BT5 500 A 1 HETATM 10 C C5B BT5 . . . B 2 46.864 14.757 24.862 1 21.21 ? C5B BT5 500 A 1 HETATM 11 N N1B BT5 . . . B 2 47.754 14.157 25.754 1 5.1 ? N1B BT5 500 A 1 HETATM 12 C C3B BT5 . . . B 2 49.088 14.661 25.388 1 17.33 ? C3B BT5 500 A 1 HETATM 13 O O3B BT5 . . . B 2 50.067 14.017 25.915 1 18.06 ? O3B BT5 500 A 1 HETATM 14 N N2B BT5 . . . B 2 49.054 14.689 23.879 1 13.47 ? N2B BT5 500 A 1 HETATM 15 C C4B BT5 . . . B 2 47.754 15.146 23.591 1 15.14 ? C4B BT5 500 A 1 HETATM 16 P P BT5 . . . B 2 53.275 18.095 17.676 1 28.99 ? P BT5 500 A 1 HETATM 17 O OP1 BT5 . . . B 2 52.919 18.796 16.46 1 34.32 ? OP1 BT5 500 A 1 HETATM 18 O OP2 BT5 . . . B 2 53.984 16.843 17.571 1 36.36 ? OP2 BT5 500 A 1 HETATM 19 O O5' BT5 . . . B 2 54.129 19.02 18.615 1 40.78 ? O5' BT5 500 A 1 HETATM 20 C C5' BT5 . . . B 2 53.684 20.241 19.03 1 33.79 ? C5' BT5 500 A 1 HETATM 21 C C4' BT5 . . . B 2 54.749 21.28 18.909 1 27.35 ? C4' BT5 500 A 1 HETATM 22 O O4' BT5 . . . B 2 54.179 22.61 18.869 1 48.36 ? O4' BT5 500 A 1 HETATM 23 C C3' BT5 . . . B 2 55.941 21.34 19.869 1 35.86 ? C3' BT5 500 A 1 HETATM 24 O O3' BT5 . . . B 2 57.061 20.612 19.418 1 27.16 ? O3' BT5 500 A 1 HETATM 25 C C2' BT5 . . . B 2 56.225 22.839 19.926 1 47.06 ? C2' BT5 500 A 1 HETATM 26 O O2' BT5 . . . B 2 56.939 23.235 18.758 1 39.7 ? O2' BT5 500 A 1 HETATM 27 C C1' BT5 . . . B 2 54.828 23.406 19.799 1 46.98 ? C1' BT5 500 A 1 HETATM 28 N N9 BT5 . . . B 2 54.071 23.355 21.048 1 42.67 ? N9 BT5 500 A 1 HETATM 29 C C8 BT5 . . . B 2 54.224 22.663 22.179 1 30.93 ? C8 BT5 500 A 1 HETATM 30 N N7 BT5 . . . B 2 53.188 22.975 22.992 1 21.92 ? N7 BT5 500 A 1 HETATM 31 C C5 BT5 . . . B 2 52.359 23.824 22.365 1 28.32 ? C5 BT5 500 A 1 HETATM 32 C C6 BT5 . . . B 2 51.177 24.507 22.627 1 24.13 ? C6 BT5 500 A 1 HETATM 33 N N6 BT5 . . . B 2 50.467 24.455 23.865 1 18.64 ? N6 BT5 500 A 1 HETATM 34 N N1 BT5 . . . B 2 50.717 25.345 21.696 1 26.61 ? N1 BT5 500 A 1 HETATM 35 C C2 BT5 . . . B 2 51.335 25.507 20.542 1 33.74 ? C2 BT5 500 A 1 HETATM 36 N N3 BT5 . . . B 2 52.449 24.892 20.264 1 32.11 ? N3 BT5 500 A 1 HETATM 37 C C4 BT5 . . . B 2 52.956 24.054 21.133 1 36.89 ? C4 BT5 500 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 37 #