data_3NJ4 # _model_server_result.job_id 1HSFVHMnFdFKbQt9lP6uvw _model_server_result.datetime_utc '2025-09-04 15:19:55' _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 3nj4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":604}' # _entry.id 3NJ4 # _exptl.entry_id 3NJ4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 279.227 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S,5S)-4-(6-amino-9H-purin-9-yl)-3-fluoro-5-hydroxy-2-(hydroxymethyl)cyclopent-2-en-1-one _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 107.01 _cell.angle_gamma 90 _cell.entry_id 3NJ4 _cell.length_a 91.201 _cell.length_b 81.939 _cell.length_c 129.599 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NJ4 _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,H,I,J,K,L,M,N,O,P _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 F N N ? 3 H N N ? 3 J N N ? 3 L N N # _chem_comp.formula 'C11 H10 F N5 O3' _chem_comp.formula_weight 279.227 _chem_comp.id AFX _chem_comp.mon_nstd_flag . _chem_comp.name (4S,5S)-4-(6-amino-9H-purin-9-yl)-3-fluoro-5-hydroxy-2-(hydroxymethyl)cyclopent-2-en-1-one _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 C1 O1 AFX sing 1 n n C1 C4' AFX sing 2 n n F1 C5' AFX sing 3 n n N1 C2 AFX doub 4 n y N1 C6 AFX sing 5 n y C2 N3 AFX sing 6 n y N3 C4 AFX doub 7 n y C4 C5 AFX sing 8 n y C4 N9 AFX sing 9 n y C5 C6 AFX doub 10 n y C5 N7 AFX sing 11 n y C6 N6 AFX sing 12 n n N7 C8 AFX doub 13 n y C8 N9 AFX sing 14 n y N9 C1' AFX sing 15 n n C1' C2' AFX sing 16 n n C1' C5' AFX sing 17 n n C2' O2' AFX sing 18 n n C2' C3' AFX sing 19 n n C3' O3' AFX doub 20 n n C3' C4' AFX sing 21 n n C4' C5' AFX doub 22 n n C1 H1 AFX sing 23 n n C1 H1A AFX sing 24 n n O1 HO1 AFX sing 25 n n C2 H2 AFX sing 26 n n N6 HN6 AFX sing 27 n n N6 HN6A AFX sing 28 n n C8 H8 AFX sing 29 n n C1' H1' AFX sing 30 n n C2' H2' AFX sing 31 n n O2' HO2' AFX sing 32 n n # _atom_sites.entry_id 3NJ4 _atom_sites.fract_transf_matrix[1][1] 0.010965 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003354 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012204 _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] 0.008069 _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 2 NAD A 1 501 501 NAD NAH . F 3 AFX A 1 601 601 AFX ADC . G 2 NAD B 1 502 502 NAD NAH . H 3 AFX B 1 602 602 AFX ADC . I 2 NAD C 1 503 503 NAD NAH . J 3 AFX C 1 603 603 AFX ADC . K 2 NAD D 1 504 504 NAD NAH . L 3 AFX D 1 604 604 AFX ADC . M 4 HOH A 1 433 2 HOH TIP . M 4 HOH A 2 434 4 HOH TIP . M 4 HOH A 3 435 8 HOH TIP . M 4 HOH A 4 436 10 HOH TIP . M 4 HOH A 5 437 15 HOH TIP . M 4 HOH A 6 438 16 HOH TIP . M 4 HOH A 7 439 26 HOH TIP . M 4 HOH A 8 440 28 HOH TIP . M 4 HOH A 9 441 37 HOH TIP . M 4 HOH A 10 442 40 HOH TIP . M 4 HOH A 11 443 41 HOH TIP . M 4 HOH A 12 444 42 HOH TIP . M 4 HOH A 13 445 45 HOH TIP . M 4 HOH A 14 446 46 HOH TIP . M 4 HOH A 15 447 47 HOH TIP . M 4 HOH A 16 448 51 HOH TIP . M 4 HOH A 17 449 54 HOH TIP . M 4 HOH A 18 450 60 HOH TIP . M 4 HOH A 19 451 61 HOH TIP . M 4 HOH A 20 452 63 HOH TIP . M 4 HOH A 21 453 65 HOH TIP . M 4 HOH A 22 454 66 HOH TIP . M 4 HOH A 23 455 74 HOH TIP . M 4 HOH A 24 456 85 HOH TIP . M 4 HOH A 25 457 91 HOH TIP . M 4 HOH A 26 458 93 HOH TIP . M 4 HOH A 27 459 96 HOH TIP . M 4 HOH A 28 460 104 HOH TIP . M 4 HOH A 29 461 105 HOH TIP . M 4 HOH A 30 462 107 HOH TIP . M 4 HOH A 31 463 113 HOH TIP . M 4 HOH A 32 464 114 HOH TIP . M 4 HOH A 33 465 115 HOH TIP . M 4 HOH A 34 466 123 HOH TIP . M 4 HOH A 35 467 125 HOH TIP . M 4 HOH A 36 468 126 HOH TIP . M 4 HOH A 37 469 132 HOH TIP . M 4 HOH A 38 470 147 HOH TIP . M 4 HOH A 39 471 156 HOH TIP . M 4 HOH A 40 472 157 HOH TIP . M 4 HOH A 41 473 160 HOH TIP . M 4 HOH A 42 474 170 HOH TIP . M 4 HOH A 43 475 171 HOH TIP . M 4 HOH A 44 476 174 HOH TIP . M 4 HOH A 45 477 175 HOH TIP . M 4 HOH A 46 478 176 HOH TIP . M 4 HOH A 47 479 184 HOH TIP . M 4 HOH A 48 480 188 HOH TIP . M 4 HOH A 49 481 190 HOH TIP . M 4 HOH A 50 482 192 HOH TIP . M 4 HOH A 51 483 195 HOH TIP . M 4 HOH A 52 484 196 HOH TIP . M 4 HOH A 53 485 203 HOH TIP . M 4 HOH A 54 486 210 HOH TIP . M 4 HOH A 55 487 214 HOH TIP . M 4 HOH A 56 488 216 HOH TIP . M 4 HOH A 57 489 220 HOH TIP . M 4 HOH A 58 490 223 HOH TIP . M 4 HOH A 59 491 227 HOH TIP . M 4 HOH A 60 492 231 HOH TIP . M 4 HOH A 61 493 243 HOH TIP . M 4 HOH A 62 494 244 HOH TIP . M 4 HOH A 63 495 247 HOH TIP . M 4 HOH A 64 496 249 HOH TIP . M 4 HOH A 65 497 250 HOH TIP . M 4 HOH A 66 498 255 HOH TIP . M 4 HOH A 67 499 257 HOH TIP . N 4 HOH B 1 433 3 HOH TIP . N 4 HOH B 2 434 5 HOH TIP . N 4 HOH B 3 435 6 HOH TIP . N 4 HOH B 4 436 9 HOH TIP . N 4 HOH B 5 437 12 HOH TIP . N 4 HOH B 6 438 20 HOH TIP . N 4 HOH B 7 439 21 HOH TIP . N 4 HOH B 8 440 23 HOH TIP . N 4 HOH B 9 441 27 HOH TIP . N 4 HOH B 10 442 29 HOH TIP . N 4 HOH B 11 443 30 HOH TIP . N 4 HOH B 12 444 31 HOH TIP . N 4 HOH B 13 445 33 HOH TIP . N 4 HOH B 14 446 35 HOH TIP . N 4 HOH B 15 447 43 HOH TIP . N 4 HOH B 16 448 48 HOH TIP . N 4 HOH B 17 449 49 HOH TIP . N 4 HOH B 18 450 56 HOH TIP . N 4 HOH B 19 451 58 HOH TIP . N 4 HOH B 20 452 67 HOH TIP . N 4 HOH B 21 453 68 HOH TIP . N 4 HOH B 22 454 72 HOH TIP . N 4 HOH B 23 455 73 HOH TIP . N 4 HOH B 24 456 75 HOH TIP . N 4 HOH B 25 457 76 HOH TIP . N 4 HOH B 26 458 78 HOH TIP . N 4 HOH B 27 459 79 HOH TIP . N 4 HOH B 28 460 81 HOH TIP . N 4 HOH B 29 461 84 HOH TIP . N 4 HOH B 30 462 86 HOH TIP . N 4 HOH B 31 463 90 HOH TIP . N 4 HOH B 32 464 92 HOH TIP . N 4 HOH B 33 465 94 HOH TIP . N 4 HOH B 34 466 98 HOH TIP . N 4 HOH B 35 467 99 HOH TIP . N 4 HOH B 36 468 101 HOH TIP . N 4 HOH B 37 469 108 HOH TIP . N 4 HOH B 38 470 109 HOH TIP . N 4 HOH B 39 471 110 HOH TIP . N 4 HOH B 40 472 116 HOH TIP . N 4 HOH B 41 473 117 HOH TIP . N 4 HOH B 42 474 118 HOH TIP . N 4 HOH B 43 475 119 HOH TIP . N 4 HOH B 44 476 121 HOH TIP . N 4 HOH B 45 477 124 HOH TIP . N 4 HOH B 46 478 127 HOH TIP . N 4 HOH B 47 479 131 HOH TIP . N 4 HOH B 48 480 134 HOH TIP . N 4 HOH B 49 481 135 HOH TIP . N 4 HOH B 50 482 136 HOH TIP . N 4 HOH B 51 483 139 HOH TIP . N 4 HOH B 52 484 140 HOH TIP . N 4 HOH B 53 485 145 HOH TIP . N 4 HOH B 54 486 149 HOH TIP . N 4 HOH B 55 487 150 HOH TIP . N 4 HOH B 56 488 152 HOH TIP . N 4 HOH B 57 489 153 HOH TIP . N 4 HOH B 58 490 155 HOH TIP . N 4 HOH B 59 491 162 HOH TIP . N 4 HOH B 60 492 168 HOH TIP . N 4 HOH B 61 493 172 HOH TIP . N 4 HOH B 62 494 173 HOH TIP . N 4 HOH B 63 495 177 HOH TIP . N 4 HOH B 64 496 178 HOH TIP . N 4 HOH B 65 497 180 HOH TIP . N 4 HOH B 66 498 181 HOH TIP . N 4 HOH B 67 499 182 HOH TIP . N 4 HOH B 68 500 186 HOH TIP . N 4 HOH B 69 501 187 HOH TIP . N 4 HOH B 70 503 189 HOH TIP . N 4 HOH B 71 504 197 HOH TIP . N 4 HOH B 72 505 209 HOH TIP . N 4 HOH B 73 506 212 HOH TIP . N 4 HOH B 74 507 213 HOH TIP . N 4 HOH B 75 508 218 HOH TIP . N 4 HOH B 76 509 224 HOH TIP . N 4 HOH B 77 510 225 HOH TIP . N 4 HOH B 78 511 226 HOH TIP . N 4 HOH B 79 512 230 HOH TIP . N 4 HOH B 80 513 233 HOH TIP . N 4 HOH B 81 514 234 HOH TIP . N 4 HOH B 82 515 235 HOH TIP . N 4 HOH B 83 516 237 HOH TIP . N 4 HOH B 84 517 240 HOH TIP . N 4 HOH B 85 518 242 HOH TIP . N 4 HOH B 86 519 246 HOH TIP . N 4 HOH B 87 520 248 HOH TIP . N 4 HOH B 88 521 252 HOH TIP . N 4 HOH B 89 522 253 HOH TIP . N 4 HOH B 90 523 254 HOH TIP . N 4 HOH B 91 524 256 HOH TIP . N 4 HOH B 92 525 258 HOH TIP . O 4 HOH C 1 433 11 HOH TIP . O 4 HOH C 2 434 13 HOH TIP . O 4 HOH C 3 435 14 HOH TIP . O 4 HOH C 4 436 18 HOH TIP . O 4 HOH C 5 437 32 HOH TIP . O 4 HOH C 6 438 39 HOH TIP . O 4 HOH C 7 439 50 HOH TIP . O 4 HOH C 8 440 70 HOH TIP . O 4 HOH C 9 441 71 HOH TIP . O 4 HOH C 10 442 77 HOH TIP . O 4 HOH C 11 443 82 HOH TIP . O 4 HOH C 12 444 87 HOH TIP . O 4 HOH C 13 445 89 HOH TIP . O 4 HOH C 14 446 100 HOH TIP . O 4 HOH C 15 447 102 HOH TIP . O 4 HOH C 16 448 103 HOH TIP . O 4 HOH C 17 449 106 HOH TIP . O 4 HOH C 18 450 111 HOH TIP . O 4 HOH C 19 451 120 HOH TIP . O 4 HOH C 20 452 129 HOH TIP . O 4 HOH C 21 453 137 HOH TIP . O 4 HOH C 22 454 142 HOH TIP . O 4 HOH C 23 455 143 HOH TIP . O 4 HOH C 24 456 144 HOH TIP . O 4 HOH C 25 457 146 HOH TIP . O 4 HOH C 26 458 148 HOH TIP . O 4 HOH C 27 459 154 HOH TIP . O 4 HOH C 28 460 158 HOH TIP . O 4 HOH C 29 461 159 HOH TIP . O 4 HOH C 30 462 169 HOH TIP . O 4 HOH C 31 463 191 HOH TIP . O 4 HOH C 32 464 201 HOH TIP . O 4 HOH C 33 465 202 HOH TIP . O 4 HOH C 34 466 204 HOH TIP . O 4 HOH C 35 467 207 HOH TIP . O 4 HOH C 36 468 211 HOH TIP . O 4 HOH C 37 469 217 HOH TIP . O 4 HOH C 38 470 219 HOH TIP . O 4 HOH C 39 471 228 HOH TIP . O 4 HOH C 40 472 238 HOH TIP . O 4 HOH C 41 473 241 HOH TIP . P 4 HOH D 1 433 1 HOH TIP . P 4 HOH D 2 434 7 HOH TIP . P 4 HOH D 3 435 17 HOH TIP . P 4 HOH D 4 436 19 HOH TIP . P 4 HOH D 5 437 22 HOH TIP . P 4 HOH D 6 438 24 HOH TIP . P 4 HOH D 7 439 25 HOH TIP . P 4 HOH D 8 440 34 HOH TIP . P 4 HOH D 9 441 36 HOH TIP . P 4 HOH D 10 442 38 HOH TIP . P 4 HOH D 11 443 44 HOH TIP . P 4 HOH D 12 444 52 HOH TIP . P 4 HOH D 13 445 53 HOH TIP . P 4 HOH D 14 446 55 HOH TIP . P 4 HOH D 15 447 57 HOH TIP . P 4 HOH D 16 448 59 HOH TIP . P 4 HOH D 17 449 62 HOH TIP . P 4 HOH D 18 450 64 HOH TIP . P 4 HOH D 19 451 69 HOH TIP . P 4 HOH D 20 452 80 HOH TIP . P 4 HOH D 21 453 83 HOH TIP . P 4 HOH D 22 454 88 HOH TIP . P 4 HOH D 23 455 95 HOH TIP . P 4 HOH D 24 456 97 HOH TIP . P 4 HOH D 25 457 112 HOH TIP . P 4 HOH D 26 458 122 HOH TIP . P 4 HOH D 27 459 128 HOH TIP . P 4 HOH D 28 460 130 HOH TIP . P 4 HOH D 29 461 133 HOH TIP . P 4 HOH D 30 462 138 HOH TIP . P 4 HOH D 31 463 141 HOH TIP . P 4 HOH D 32 464 151 HOH TIP . P 4 HOH D 33 465 161 HOH TIP . P 4 HOH D 34 466 163 HOH TIP . P 4 HOH D 35 467 164 HOH TIP . P 4 HOH D 36 468 165 HOH TIP . P 4 HOH D 37 469 166 HOH TIP . P 4 HOH D 38 470 167 HOH TIP . P 4 HOH D 39 471 179 HOH TIP . P 4 HOH D 40 472 183 HOH TIP . P 4 HOH D 41 473 185 HOH TIP . P 4 HOH D 42 474 193 HOH TIP . P 4 HOH D 43 475 194 HOH TIP . P 4 HOH D 44 476 198 HOH TIP . P 4 HOH D 45 477 199 HOH TIP . P 4 HOH D 46 478 200 HOH TIP . P 4 HOH D 47 479 205 HOH TIP . P 4 HOH D 48 480 206 HOH TIP . P 4 HOH D 49 481 208 HOH TIP . P 4 HOH D 50 482 215 HOH TIP . P 4 HOH D 51 483 221 HOH TIP . P 4 HOH D 52 484 222 HOH TIP . P 4 HOH D 53 485 229 HOH TIP . P 4 HOH D 54 486 232 HOH TIP . P 4 HOH D 55 487 236 HOH TIP . P 4 HOH D 56 488 239 HOH TIP . P 4 HOH D 57 489 245 HOH TIP . P 4 HOH D 58 490 251 HOH TIP . # 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 C1 AFX . . . L 3 -0.58 -4.389 73.777 1 30.44 ? C1 AFX 604 D 1 HETATM 2 F F1 AFX . . . L 3 0.961 -6.892 74.052 1 32.69 ? F1 AFX 604 D 1 HETATM 3 N N1 AFX . . . L 3 2.265 -11.647 77.845 1 30.89 ? N1 AFX 604 D 1 HETATM 4 O O1 AFX . . . L 3 -0.958 -5.17 72.649 1 31.75 ? O1 AFX 604 D 1 HETATM 5 C C2 AFX . . . L 3 1.066 -11.432 77.285 1 28.54 ? C2 AFX 604 D 1 HETATM 6 N N3 AFX . . . L 3 0.526 -10.255 76.916 1 29.18 ? N3 AFX 604 D 1 HETATM 7 C C4 AFX . . . L 3 1.367 -9.011 77.175 1 30.22 ? C4 AFX 604 D 1 HETATM 8 C C5 AFX . . . L 3 2.685 -9.192 77.776 1 30.74 ? C5 AFX 604 D 1 HETATM 9 C C6 AFX . . . L 3 3.083 -10.6 78.113 1 31.96 ? C6 AFX 604 D 1 HETATM 10 N N6 AFX . . . L 3 4.25 -10.873 78.662 1 33.26 ? N6 AFX 604 D 1 HETATM 11 N N7 AFX . . . L 3 3.363 -8.002 77.963 1 31.96 ? N7 AFX 604 D 1 HETATM 12 C C8 AFX . . . L 3 2.407 -7.165 77.445 1 30.49 ? C8 AFX 604 D 1 HETATM 13 N N9 AFX . . . L 3 1.201 -7.633 76.952 1 29.43 ? N9 AFX 604 D 1 HETATM 14 C C1' AFX . . . L 3 -0.035 -7.193 76.348 1 30.35 ? C1' AFX 604 D 1 HETATM 15 C C2' AFX . . . L 3 -0.981 -6.278 77.17 1 28.44 ? C2' AFX 604 D 1 HETATM 16 O O2' AFX . . . L 3 -2.054 -6.981 77.768 1 33.09 ? O2' AFX 604 D 1 HETATM 17 C C3' AFX . . . L 3 -1.299 -5.112 76.237 1 29.66 ? C3' AFX 604 D 1 HETATM 18 O O3' AFX . . . L 3 -2.048 -4.173 76.513 1 32.59 ? O3' AFX 604 D 1 HETATM 19 C C4' AFX . . . L 3 -0.548 -5.299 74.946 1 29.36 ? C4' AFX 604 D 1 HETATM 20 C C5' AFX . . . L 3 0.135 -6.425 75.063 1 29.9 ? C5' AFX 604 D 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #