data_1R4F # _model_server_result.job_id bqrWWFu9XPD23IsQOVmWZA _model_server_result.datetime_utc '2024-11-28 10:44:28' _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 1r4f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":330}' # _entry.id 1R4F # _exptl.entry_id 1R4F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 266.253 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-DEAZA-ADENOSINE _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 102.291 _cell.angle_gamma 90 _cell.entry_id 1R4F _cell.length_a 51.996 _cell.length_b 74.865 _cell.length_c 81.369 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1R4F _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _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 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 A OD2 ASP 22 A ASP 10 1_555 C CA CA . A CA 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc2 A OD1 ASP 27 A ASP 15 1_555 C CA CA . A CA 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? metalc ? metalc3 A OD2 ASP 27 A ASP 15 1_555 C CA CA . A CA 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? metalc ? metalc4 A O THR 149 A THR 137 1_555 C CA CA . A CA 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc5 A OD2 ASP 273 A ASP 261 1_555 C CA CA . A CA 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc6 C CA CA . A CA 328 1_555 F O HOH . A HOH 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc7 C CA CA . A CA 328 1_555 F O HOH . A HOH 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.108 ? metalc ? metalc8 C CA CA . A CA 328 1_555 F O HOH . A HOH 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? metalc ? metalc9 B OD2 ASP 22 B ASP 10 1_555 D CA CA . B CA 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc10 B OD1 ASP 27 B ASP 15 1_555 D CA CA . B CA 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? metalc ? metalc11 B OD2 ASP 27 B ASP 15 1_555 D CA CA . B CA 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc12 B O THR 149 B THR 137 1_555 D CA CA . B CA 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc13 B OD2 ASP 273 B ASP 261 1_555 D CA CA . B CA 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc14 D CA CA . B CA 329 1_555 E O3' AD3 . B AD3 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc15 D CA CA . B CA 329 1_555 E O2' AD3 . B AD3 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc16 D CA CA . B CA 329 1_555 G O HOH . B HOH 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? # _chem_comp.formula 'C11 H14 N4 O4' _chem_comp.formula_weight 266.253 _chem_comp.id AD3 _chem_comp.mon_nstd_flag . _chem_comp.name 3-DEAZA-ADENOSINE _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 O5' C5' AD3 sing 1 n n O5' HO5' AD3 sing 2 n n C5' C4' AD3 sing 3 n n C5' "H5'1" AD3 sing 4 n n C5' "H5'2" AD3 sing 5 n n C4' O4' AD3 sing 6 n n C4' C3' AD3 sing 7 n n C4' H4' AD3 sing 8 n n O4' C1' AD3 sing 9 n n C3' O3' AD3 sing 10 n n C3' C2' AD3 sing 11 n n C3' H3' AD3 sing 12 n n O3' HO3' AD3 sing 13 n n C2' O2' AD3 sing 14 n n C2' C1' AD3 sing 15 n n C2' H2' AD3 sing 16 n n O2' HO2' AD3 sing 17 n n C1' N9 AD3 sing 18 n n C1' H1' AD3 sing 19 n n N9 C8 AD3 sing 20 n y N9 C4 AD3 sing 21 n y C8 N7 AD3 doub 22 n y C8 H8 AD3 sing 23 n n N7 C5 AD3 sing 24 n y C5 C6 AD3 sing 25 n y C5 C4 AD3 doub 26 n y C6 N6 AD3 sing 27 n n C6 N1 AD3 doub 28 n y N6 HN61 AD3 sing 29 n n N6 HN62 AD3 sing 30 n n N1 C2 AD3 sing 31 n y C2 C3 AD3 doub 32 n y C2 H2 AD3 sing 33 n n C3 C4 AD3 sing 34 n y C3 H3 AD3 sing 35 n n # _atom_sites.entry_id 1R4F _atom_sites.fract_transf_matrix[1][1] 0.019232 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00419 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013357 _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] 0.012578 _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 CA A 1 328 328 CA CA . D 2 CA B 1 329 328 CA CA . E 3 AD3 B 1 330 200 AD3 AD3 . F 4 HOH A 1 329 2 HOH HOH . F 4 HOH A 2 330 3 HOH HOH . F 4 HOH A 3 331 4 HOH HOH . F 4 HOH A 4 332 5 HOH HOH . F 4 HOH A 5 333 6 HOH HOH . F 4 HOH A 6 334 7 HOH HOH . F 4 HOH A 7 335 8 HOH HOH . F 4 HOH A 8 336 9 HOH HOH . F 4 HOH A 9 337 10 HOH HOH . F 4 HOH A 10 338 11 HOH HOH . F 4 HOH A 11 339 12 HOH HOH . F 4 HOH A 12 340 13 HOH HOH . F 4 HOH A 13 341 14 HOH HOH . F 4 HOH A 14 342 15 HOH HOH . F 4 HOH A 15 343 16 HOH HOH . F 4 HOH A 16 344 17 HOH HOH . F 4 HOH A 17 345 18 HOH HOH . F 4 HOH A 18 346 19 HOH HOH . F 4 HOH A 19 347 20 HOH HOH . F 4 HOH A 20 348 21 HOH HOH . F 4 HOH A 21 349 22 HOH HOH . F 4 HOH A 22 350 23 HOH HOH . F 4 HOH A 23 351 24 HOH HOH . F 4 HOH A 24 352 25 HOH HOH . F 4 HOH A 25 353 26 HOH HOH . F 4 HOH A 26 354 27 HOH HOH . F 4 HOH A 27 355 28 HOH HOH . F 4 HOH A 28 356 29 HOH HOH . F 4 HOH A 29 357 30 HOH HOH . F 4 HOH A 30 358 31 HOH HOH . F 4 HOH A 31 359 32 HOH HOH . F 4 HOH A 32 360 35 HOH HOH . F 4 HOH A 33 361 36 HOH HOH . F 4 HOH A 34 362 37 HOH HOH . F 4 HOH A 35 363 38 HOH HOH . F 4 HOH A 36 364 39 HOH HOH . F 4 HOH A 37 365 40 HOH HOH . F 4 HOH A 38 366 41 HOH HOH . F 4 HOH A 39 367 42 HOH HOH . F 4 HOH A 40 368 43 HOH HOH . F 4 HOH A 41 369 44 HOH HOH . F 4 HOH A 42 370 45 HOH HOH . F 4 HOH A 43 371 46 HOH HOH . F 4 HOH A 44 372 47 HOH HOH . F 4 HOH A 45 373 48 HOH HOH . F 4 HOH A 46 374 49 HOH HOH . F 4 HOH A 47 375 50 HOH HOH . F 4 HOH A 48 376 51 HOH HOH . F 4 HOH A 49 377 52 HOH HOH . F 4 HOH A 50 378 53 HOH HOH . F 4 HOH A 51 379 54 HOH HOH . F 4 HOH A 52 380 55 HOH HOH . F 4 HOH A 53 381 56 HOH HOH . F 4 HOH A 54 382 57 HOH HOH . F 4 HOH A 55 383 58 HOH HOH . F 4 HOH A 56 384 59 HOH HOH . F 4 HOH A 57 385 60 HOH HOH . F 4 HOH A 58 386 61 HOH HOH . F 4 HOH A 59 387 62 HOH HOH . F 4 HOH A 60 388 63 HOH HOH . F 4 HOH A 61 389 64 HOH HOH . F 4 HOH A 62 390 65 HOH HOH . F 4 HOH A 63 391 66 HOH HOH . F 4 HOH A 64 392 67 HOH HOH . F 4 HOH A 65 393 68 HOH HOH . F 4 HOH A 66 394 69 HOH HOH . F 4 HOH A 67 395 70 HOH HOH . F 4 HOH A 68 396 71 HOH HOH . F 4 HOH A 69 397 72 HOH HOH . F 4 HOH A 70 398 73 HOH HOH . F 4 HOH A 71 399 74 HOH HOH . F 4 HOH A 72 400 75 HOH HOH . F 4 HOH A 73 401 76 HOH HOH . F 4 HOH A 74 402 77 HOH HOH . F 4 HOH A 75 403 78 HOH HOH . F 4 HOH A 76 404 79 HOH HOH . F 4 HOH A 77 405 80 HOH HOH . F 4 HOH A 78 406 81 HOH HOH . F 4 HOH A 79 407 82 HOH HOH . F 4 HOH A 80 408 83 HOH HOH . F 4 HOH A 81 409 84 HOH HOH . F 4 HOH A 82 410 85 HOH HOH . F 4 HOH A 83 411 86 HOH HOH . F 4 HOH A 84 412 87 HOH HOH . F 4 HOH A 85 413 88 HOH HOH . F 4 HOH A 86 414 89 HOH HOH . F 4 HOH A 87 415 150 HOH HOH . F 4 HOH A 88 416 153 HOH HOH . G 4 HOH B 1 331 1 HOH HOH . G 4 HOH B 2 332 33 HOH HOH . G 4 HOH B 3 333 34 HOH HOH . G 4 HOH B 4 334 90 HOH HOH . G 4 HOH B 5 335 91 HOH HOH . G 4 HOH B 6 336 92 HOH HOH . G 4 HOH B 7 337 93 HOH HOH . G 4 HOH B 8 338 94 HOH HOH . G 4 HOH B 9 339 95 HOH HOH . G 4 HOH B 10 340 96 HOH HOH . G 4 HOH B 11 341 97 HOH HOH . G 4 HOH B 12 342 98 HOH HOH . G 4 HOH B 13 343 99 HOH HOH . G 4 HOH B 14 344 100 HOH HOH . G 4 HOH B 15 345 101 HOH HOH . G 4 HOH B 16 346 102 HOH HOH . G 4 HOH B 17 347 103 HOH HOH . G 4 HOH B 18 348 104 HOH HOH . G 4 HOH B 19 349 105 HOH HOH . G 4 HOH B 20 350 106 HOH HOH . G 4 HOH B 21 351 107 HOH HOH . G 4 HOH B 22 352 108 HOH HOH . G 4 HOH B 23 353 109 HOH HOH . G 4 HOH B 24 354 110 HOH HOH . G 4 HOH B 25 355 111 HOH HOH . G 4 HOH B 26 356 112 HOH HOH . G 4 HOH B 27 357 113 HOH HOH . G 4 HOH B 28 358 114 HOH HOH . G 4 HOH B 29 359 115 HOH HOH . G 4 HOH B 30 360 116 HOH HOH . G 4 HOH B 31 361 117 HOH HOH . G 4 HOH B 32 362 118 HOH HOH . G 4 HOH B 33 363 119 HOH HOH . G 4 HOH B 34 364 120 HOH HOH . G 4 HOH B 35 365 121 HOH HOH . G 4 HOH B 36 366 122 HOH HOH . G 4 HOH B 37 367 123 HOH HOH . G 4 HOH B 38 368 124 HOH HOH . G 4 HOH B 39 369 125 HOH HOH . G 4 HOH B 40 370 126 HOH HOH . G 4 HOH B 41 371 127 HOH HOH . G 4 HOH B 42 372 128 HOH HOH . G 4 HOH B 43 373 129 HOH HOH . G 4 HOH B 44 374 130 HOH HOH . G 4 HOH B 45 375 131 HOH HOH . G 4 HOH B 46 376 132 HOH HOH . G 4 HOH B 47 377 133 HOH HOH . G 4 HOH B 48 378 134 HOH HOH . G 4 HOH B 49 379 135 HOH HOH . G 4 HOH B 50 380 136 HOH HOH . G 4 HOH B 51 381 137 HOH HOH . G 4 HOH B 52 382 138 HOH HOH . G 4 HOH B 53 383 139 HOH HOH . G 4 HOH B 54 384 140 HOH HOH . G 4 HOH B 55 385 141 HOH HOH . G 4 HOH B 56 386 142 HOH HOH . G 4 HOH B 57 387 143 HOH HOH . G 4 HOH B 58 388 144 HOH HOH . G 4 HOH B 59 389 145 HOH HOH . G 4 HOH B 60 390 146 HOH HOH . G 4 HOH B 61 391 147 HOH HOH . G 4 HOH B 62 392 148 HOH HOH . G 4 HOH B 63 393 149 HOH HOH . G 4 HOH B 64 394 151 HOH HOH . G 4 HOH B 65 395 152 HOH HOH . G 4 HOH B 66 396 154 HOH HOH . G 4 HOH B 67 397 155 HOH HOH . G 4 HOH B 68 398 156 HOH HOH . G 4 HOH B 69 399 157 HOH HOH . G 4 HOH B 70 400 158 HOH HOH . G 4 HOH B 71 401 159 HOH HOH . G 4 HOH B 72 402 160 HOH HOH . G 4 HOH B 73 403 161 HOH HOH . G 4 HOH B 74 404 162 HOH HOH . G 4 HOH B 75 405 163 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 O5' AD3 . . . E 3 23.548 27.529 42.75 1 43.29 ? O5' AD3 330 B 1 HETATM 2 C C5' AD3 . . . E 3 24.369 28.622 42.309 1 46.72 ? C5' AD3 330 B 1 HETATM 3 C C4' AD3 . . . E 3 25.566 27.939 41.638 1 48.19 ? C4' AD3 330 B 1 HETATM 4 O O4' AD3 . . . E 3 25.157 27 40.572 1 49.55 ? O4' AD3 330 B 1 HETATM 5 C C3' AD3 . . . E 3 26.511 28.947 40.985 1 47.92 ? C3' AD3 330 B 1 HETATM 6 O O3' AD3 . . . E 3 27.848 28.627 41.427 1 43.67 ? O3' AD3 330 B 1 HETATM 7 C C2' AD3 . . . E 3 26.358 28.812 39.466 1 49.74 ? C2' AD3 330 B 1 HETATM 8 O O2' AD3 . . . E 3 27.595 28.862 38.74 1 45.36 ? O2' AD3 330 B 1 HETATM 9 C C1' AD3 . . . E 3 25.538 27.507 39.279 1 53.06 ? C1' AD3 330 B 1 HETATM 10 N N9 AD3 . . . E 3 24.386 27.689 38.304 1 58.89 ? N9 AD3 330 B 1 HETATM 11 C C8 AD3 . . . E 3 24.515 28.029 36.935 1 60.49 ? C8 AD3 330 B 1 HETATM 12 N N7 AD3 . . . E 3 23.389 28.106 36.264 1 62.83 ? N7 AD3 330 B 1 HETATM 13 C C5 AD3 . . . E 3 22.406 27.803 37.22 1 64.6 ? C5 AD3 330 B 1 HETATM 14 C C6 AD3 . . . E 3 20.936 27.705 37.16 1 66.49 ? C6 AD3 330 B 1 HETATM 15 N N6 AD3 . . . E 3 20.228 27.917 36.045 1 68.66 ? N6 AD3 330 B 1 HETATM 16 N N1 AD3 . . . E 3 20.264 27.373 38.327 1 66.42 ? N1 AD3 330 B 1 HETATM 17 C C2 AD3 . . . E 3 20.949 27.15 39.482 1 65.82 ? C2 AD3 330 B 1 HETATM 18 C C3 AD3 . . . E 3 22.3 27.205 39.683 1 64.04 ? C3 AD3 330 B 1 HETATM 19 C C4 AD3 . . . E 3 22.993 27.544 38.488 1 62.68 ? C4 AD3 330 B 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 19 #