data_4P5D # _model_server_result.job_id V3fZMeBq5FBpkbTWmWMSkQ _model_server_result.datetime_utc '2024-12-04 16:41:01' _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 4p5d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 4P5D # _exptl.entry_id 4P5D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 458.361 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-(naphthalen-2-yl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 4P5D _cell.length_a 178.2 _cell.length_b 178.2 _cell.length_c 56.922 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4P5D _symmetry.cell_setting . _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA Dimeric 2 author_and_software_defined_assembly 1 PISA Dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,F 1 1,3 B,D,E,G 2 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' 7_554 y,x,-z-2/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 -37.948 3 'crystal symmetry operation' 11_554 -x+y,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -28.461 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _chem_comp.formula 'C20 H19 N4 O7 P' _chem_comp.formula_weight 458.361 _chem_comp.id N6P _chem_comp.mon_nstd_flag . _chem_comp.name 6-(naphthalen-2-yl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "6-Naphthylpurine riboside 5'-monophosphate" # 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 O6 P1 N6P doub 237 n n P1 O7 N6P sing 238 n n P1 O5 N6P sing 239 n n P1 O4 N6P sing 240 n n O4 C20 N6P sing 241 n n O1 C19 N6P sing 242 n n O1 C16 N6P sing 243 n n C20 C19 N6P sing 244 n n C15 N3 N6P doub 245 n y C15 N4 N6P sing 246 n y N3 C14 N6P sing 247 n y C8 C9 N6P doub 248 n y C8 C7 N6P sing 249 n y C19 C18 N6P sing 250 n n C9 C10 N6P sing 251 n y N4 C16 N6P sing 252 n n N4 C13 N6P sing 253 n y C6 C7 N6P doub 254 n y C6 C5 N6P sing 255 n y C16 C17 N6P sing 256 n n C7 C2 N6P sing 257 n y C14 C13 N6P doub 258 n y C14 C11 N6P sing 259 n y C10 C11 N6P sing 260 n n C10 C1 N6P doub 261 n y C13 N2 N6P sing 262 n y C5 C4 N6P doub 263 n y C18 C17 N6P sing 264 n n C18 O3 N6P sing 265 n n C11 N1 N6P doub 266 n y C17 O2 N6P sing 267 n n C2 C1 N6P sing 268 n y C2 C3 N6P doub 269 n y N2 C12 N6P doub 270 n y C4 C3 N6P sing 271 n y N1 C12 N6P sing 272 n y C1 H1 N6P sing 273 n n C3 H2 N6P sing 274 n n C4 H3 N6P sing 275 n n C5 H4 N6P sing 276 n n C6 H5 N6P sing 277 n n C8 H6 N6P sing 278 n n C9 H7 N6P sing 279 n n C12 H8 N6P sing 280 n n C15 H9 N6P sing 281 n n C16 H10 N6P sing 282 n n C17 H11 N6P sing 283 n n O2 H12 N6P sing 284 n n C18 H13 N6P sing 285 n n O3 H14 N6P sing 286 n n C19 H15 N6P sing 287 n n C20 H16 N6P sing 288 n n C20 H17 N6P sing 289 n n O5 H18 N6P sing 290 n n O7 H19 N6P sing 291 n n # _atom_sites.entry_id 4P5D _atom_sites.fract_transf_matrix[1][1] 0.005612 _atom_sites.fract_transf_matrix[1][2] 0.00324 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00648 _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] 0.017568 _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 N6P C 1 201 201 N6P N6P . D 2 N6P A 1 201 201 N6P N6P . E 3 SO4 A 1 202 1 SO4 SO4 . F 4 HOH C 1 301 82 HOH HOH . F 4 HOH C 2 302 120 HOH HOH . F 4 HOH C 3 303 123 HOH HOH . F 4 HOH C 4 304 15 HOH HOH . F 4 HOH C 5 305 53 HOH HOH . F 4 HOH C 6 306 19 HOH HOH . F 4 HOH C 7 307 39 HOH HOH . F 4 HOH C 8 308 10 HOH HOH . F 4 HOH C 9 309 2 HOH HOH . F 4 HOH C 10 310 103 HOH HOH . F 4 HOH C 11 311 40 HOH HOH . F 4 HOH C 12 312 36 HOH HOH . F 4 HOH C 13 313 87 HOH HOH . F 4 HOH C 14 314 86 HOH HOH . F 4 HOH C 15 315 142 HOH HOH . F 4 HOH C 16 316 31 HOH HOH . F 4 HOH C 17 317 20 HOH HOH . F 4 HOH C 18 318 43 HOH HOH . F 4 HOH C 19 319 129 HOH HOH . F 4 HOH C 20 320 62 HOH HOH . F 4 HOH C 21 321 12 HOH HOH . F 4 HOH C 22 322 22 HOH HOH . F 4 HOH C 23 323 24 HOH HOH . F 4 HOH C 24 324 28 HOH HOH . F 4 HOH C 25 325 45 HOH HOH . F 4 HOH C 26 326 46 HOH HOH . F 4 HOH C 27 327 52 HOH HOH . F 4 HOH C 28 328 57 HOH HOH . F 4 HOH C 29 329 61 HOH HOH . F 4 HOH C 30 330 67 HOH HOH . F 4 HOH C 31 331 72 HOH HOH . F 4 HOH C 32 332 73 HOH HOH . F 4 HOH C 33 333 75 HOH HOH . F 4 HOH C 34 334 77 HOH HOH . F 4 HOH C 35 335 79 HOH HOH . F 4 HOH C 36 336 80 HOH HOH . F 4 HOH C 37 337 90 HOH HOH . F 4 HOH C 38 338 98 HOH HOH . F 4 HOH C 39 339 100 HOH HOH . F 4 HOH C 40 340 102 HOH HOH . F 4 HOH C 41 341 104 HOH HOH . F 4 HOH C 42 342 106 HOH HOH . F 4 HOH C 43 343 110 HOH HOH . F 4 HOH C 44 344 116 HOH HOH . F 4 HOH C 45 345 121 HOH HOH . F 4 HOH C 46 346 127 HOH HOH . F 4 HOH C 47 347 128 HOH HOH . F 4 HOH C 48 348 131 HOH HOH . F 4 HOH C 49 349 136 HOH HOH . F 4 HOH C 50 350 137 HOH HOH . F 4 HOH C 51 351 140 HOH HOH . F 4 HOH C 52 352 141 HOH HOH . F 4 HOH C 53 353 146 HOH HOH . G 4 HOH A 1 301 32 HOH HOH . G 4 HOH A 2 302 35 HOH HOH . G 4 HOH A 3 303 41 HOH HOH . G 4 HOH A 4 304 49 HOH HOH . G 4 HOH A 5 305 6 HOH HOH . G 4 HOH A 6 306 25 HOH HOH . G 4 HOH A 7 307 125 HOH HOH . G 4 HOH A 8 308 33 HOH HOH . G 4 HOH A 9 309 144 HOH HOH . G 4 HOH A 10 310 16 HOH HOH . G 4 HOH A 11 311 23 HOH HOH . G 4 HOH A 12 312 114 HOH HOH . G 4 HOH A 13 313 65 HOH HOH . G 4 HOH A 14 314 7 HOH HOH . G 4 HOH A 15 315 3 HOH HOH . G 4 HOH A 16 316 108 HOH HOH . G 4 HOH A 17 317 81 HOH HOH . G 4 HOH A 18 318 63 HOH HOH . G 4 HOH A 19 319 1 HOH HOH . G 4 HOH A 20 320 21 HOH HOH . G 4 HOH A 21 321 74 HOH HOH . G 4 HOH A 22 322 14 HOH HOH . G 4 HOH A 23 323 89 HOH HOH . G 4 HOH A 24 324 97 HOH HOH . G 4 HOH A 25 325 76 HOH HOH . G 4 HOH A 26 326 11 HOH HOH . G 4 HOH A 27 327 99 HOH HOH . G 4 HOH A 28 328 85 HOH HOH . G 4 HOH A 29 329 38 HOH HOH . G 4 HOH A 30 330 134 HOH HOH . G 4 HOH A 31 331 50 HOH HOH . G 4 HOH A 32 332 71 HOH HOH . G 4 HOH A 33 333 29 HOH HOH . G 4 HOH A 34 334 84 HOH HOH . G 4 HOH A 35 335 88 HOH HOH . G 4 HOH A 36 336 37 HOH HOH . G 4 HOH A 37 337 115 HOH HOH . G 4 HOH A 38 338 96 HOH HOH . G 4 HOH A 39 339 44 HOH HOH . G 4 HOH A 40 340 132 HOH HOH . G 4 HOH A 41 341 101 HOH HOH . G 4 HOH A 42 342 133 HOH HOH . G 4 HOH A 43 343 54 HOH HOH . G 4 HOH A 44 344 34 HOH HOH . G 4 HOH A 45 345 92 HOH HOH . G 4 HOH A 46 346 51 HOH HOH . G 4 HOH A 47 347 95 HOH HOH . G 4 HOH A 48 348 93 HOH HOH . G 4 HOH A 49 349 143 HOH HOH . G 4 HOH A 50 350 58 HOH HOH . G 4 HOH A 51 351 30 HOH HOH . G 4 HOH A 52 352 4 HOH HOH . G 4 HOH A 53 353 5 HOH HOH . G 4 HOH A 54 354 8 HOH HOH . G 4 HOH A 55 355 9 HOH HOH . G 4 HOH A 56 356 13 HOH HOH . G 4 HOH A 57 357 17 HOH HOH . G 4 HOH A 58 358 18 HOH HOH . G 4 HOH A 59 359 26 HOH HOH . G 4 HOH A 60 360 27 HOH HOH . G 4 HOH A 61 361 42 HOH HOH . G 4 HOH A 62 362 47 HOH HOH . G 4 HOH A 63 363 48 HOH HOH . G 4 HOH A 64 364 55 HOH HOH . G 4 HOH A 65 365 56 HOH HOH . G 4 HOH A 66 366 59 HOH HOH . G 4 HOH A 67 367 60 HOH HOH . G 4 HOH A 68 368 64 HOH HOH . G 4 HOH A 69 369 66 HOH HOH . G 4 HOH A 70 370 68 HOH HOH . G 4 HOH A 71 371 69 HOH HOH . G 4 HOH A 72 372 70 HOH HOH . G 4 HOH A 73 373 78 HOH HOH . G 4 HOH A 74 374 83 HOH HOH . G 4 HOH A 75 375 91 HOH HOH . G 4 HOH A 76 376 94 HOH HOH . G 4 HOH A 77 377 105 HOH HOH . G 4 HOH A 78 378 107 HOH HOH . G 4 HOH A 79 379 109 HOH HOH . G 4 HOH A 80 380 111 HOH HOH . G 4 HOH A 81 381 112 HOH HOH . G 4 HOH A 82 382 113 HOH HOH . G 4 HOH A 83 383 117 HOH HOH . G 4 HOH A 84 384 118 HOH HOH . G 4 HOH A 85 385 119 HOH HOH . G 4 HOH A 86 386 122 HOH HOH . G 4 HOH A 87 387 124 HOH HOH . G 4 HOH A 88 388 130 HOH HOH . G 4 HOH A 89 389 135 HOH HOH . G 4 HOH A 90 390 139 HOH HOH . G 4 HOH A 91 391 145 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 C1 N6P . . . C 2 13.303 77.012 -5.083 1 53.5 ? C1 N6P 201 C 1 HETATM 2 C C2 N6P . . . C 2 14.19 78.06 -5.335 1 56.12 ? C2 N6P 201 C 1 HETATM 3 C C3 N6P . . . C 2 15.287 78.273 -4.486 1 69.24 ? C3 N6P 201 C 1 HETATM 4 C C4 N6P . . . C 2 16.171 79.319 -4.73 1 69.88 ? C4 N6P 201 C 1 HETATM 5 C C5 N6P . . . C 2 15.957 80.159 -5.823 1 65.4 ? C5 N6P 201 C 1 HETATM 6 C C6 N6P . . . C 2 14.861 79.954 -6.664 1 53.52 ? C6 N6P 201 C 1 HETATM 7 C C7 N6P . . . C 2 13.982 78.904 -6.418 1 51.63 ? C7 N6P 201 C 1 HETATM 8 C C8 N6P . . . C 2 12.89 78.7 -7.263 1 53.73 ? C8 N6P 201 C 1 HETATM 9 C C9 N6P . . . C 2 12.014 77.655 -7.017 1 56.95 ? C9 N6P 201 C 1 HETATM 10 C C10 N6P . . . C 2 12.242 76.779 -5.943 1 50.25 ? C10 N6P 201 C 1 HETATM 11 C C11 N6P . . . C 2 11.264 75.668 -5.611 1 40.19 ? C11 N6P 201 C 1 HETATM 12 N N1 N6P . . . C 2 11.49 74.888 -4.527 1 40.89 ? N1 N6P 201 C 1 HETATM 13 C C12 N6P . . . C 2 10.638 73.944 -4.145 1 39.55 ? C12 N6P 201 C 1 HETATM 14 N N2 N6P . . . C 2 9.494 73.688 -4.814 1 38.76 ? N2 N6P 201 C 1 HETATM 15 C C13 N6P . . . C 2 9.17 74.434 -5.911 1 36.54 ? C13 N6P 201 C 1 HETATM 16 C C14 N6P . . . C 2 10.048 75.459 -6.344 1 37.91 ? C14 N6P 201 C 1 HETATM 17 N N3 N6P . . . C 2 9.482 76.024 -7.446 1 36.91 ? N3 N6P 201 C 1 HETATM 18 C C15 N6P . . . C 2 8.306 75.394 -7.688 1 36.23 ? C15 N6P 201 C 1 HETATM 19 N N4 N6P . . . C 2 8.106 74.439 -6.784 1 41.35 ? N4 N6P 201 C 1 HETATM 20 C C16 N6P . . . C 2 7.008 73.606 -6.674 1 40.25 ? C16 N6P 201 C 1 HETATM 21 O O1 N6P . . . C 2 5.982 74.075 -7.82 1 33.62 ? O1 N6P 201 C 1 HETATM 22 C C17 N6P . . . C 2 6.4 73.897 -5.503 1 37.89 ? C17 N6P 201 C 1 HETATM 23 O O2 N6P . . . C 2 6.039 72.702 -4.696 1 37.43 ? O2 N6P 201 C 1 HETATM 24 C C18 N6P . . . C 2 5.113 74.723 -5.779 1 36.3 ? C18 N6P 201 C 1 HETATM 25 O O3 N6P . . . C 2 3.988 74.13 -5.344 1 36.65 ? O3 N6P 201 C 1 HETATM 26 C C19 N6P . . . C 2 5.032 74.854 -7.325 1 39.49 ? C19 N6P 201 C 1 HETATM 27 C C20 N6P . . . C 2 5.213 76.302 -7.746 1 32.68 ? C20 N6P 201 C 1 HETATM 28 O O4 N6P . . . C 2 5.264 76.297 -9.189 1 36.93 ? O4 N6P 201 C 1 HETATM 29 P P1 N6P . . . C 2 5.69 77.618 -9.974 1 33.72 ? P1 N6P 201 C 1 HETATM 30 O O5 N6P . . . C 2 7.056 78.013 -9.571 1 34.87 ? O5 N6P 201 C 1 HETATM 31 O O6 N6P . . . C 2 5.62 77.29 -11.467 1 36.46 ? O6 N6P 201 C 1 HETATM 32 O O7 N6P . . . C 2 4.726 78.728 -9.648 1 34.7 ? O7 N6P 201 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #