data_2PNZ # _model_server_result.job_id jwprYdfHCGhkxBW6TzgdLQ _model_server_result.datetime_utc '2025-07-20 05:36:20' _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 2pnz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":279}' # _entry.id 2PNZ # _exptl.entry_id 2PNZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.221 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-MONOPHOSPHATE" _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 120 _cell.entry_id 2PNZ _cell.length_a 93.81 _cell.length_b 93.81 _cell.length_c 126.26 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PNZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -46.905 81.241843 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -93.81 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H14 N5 O8 P' _chem_comp.formula_weight 363.221 _chem_comp.id 5GP _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5'-MONOPHOSPHATE" _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 P O1P 5GP doub 1 n n P O2P 5GP sing 2 n n P O3P 5GP sing 3 n n P O5' 5GP sing 4 n n O2P HOP2 5GP sing 5 n n O3P HOP3 5GP sing 6 n n O5' C5' 5GP sing 7 n n C5' C4' 5GP sing 8 n n C5' "H5'1" 5GP sing 9 n n C5' "H5'2" 5GP sing 10 n n C4' O4' 5GP sing 11 n n C4' C3' 5GP sing 12 n n C4' H4' 5GP sing 13 n n O4' C1' 5GP sing 14 n n C3' O3' 5GP sing 15 n n C3' C2' 5GP sing 16 n n C3' H3' 5GP sing 17 n n O3' HO3' 5GP sing 18 n n C2' O2' 5GP sing 19 n n C2' C1' 5GP sing 20 n n C2' H2' 5GP sing 21 n n O2' HO2' 5GP sing 22 n n C1' N9 5GP sing 23 n n C1' H1' 5GP sing 24 n n N9 C8 5GP sing 25 n y N9 C4 5GP sing 26 n y C8 N7 5GP doub 27 n y C8 H8 5GP sing 28 n n N7 C5 5GP sing 29 n y C5 C6 5GP sing 30 n n C5 C4 5GP doub 31 n y C6 O6 5GP doub 32 n n C6 N1 5GP sing 33 n n N1 C2 5GP sing 34 n n N1 HN1 5GP sing 35 n n C2 N2 5GP sing 36 n n C2 N3 5GP doub 37 n n N2 HN21 5GP sing 38 n n N2 HN22 5GP sing 39 n n N3 C4 5GP sing 40 n n # _atom_sites.entry_id 2PNZ _atom_sites.fract_transf_matrix[1][1] 0.01066 _atom_sites.fract_transf_matrix[1][2] 0.006154 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012309 _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] 0.00792 _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 3 UDP A 1 250 250 UDP UDP . D 4 5GP A 1 279 279 5GP 5GP . E 5 MPD A 1 251 251 MPD MPD . F 5 MPD A 1 252 252 MPD MPD . G 5 MPD A 1 282 282 MPD MPD . H 5 MPD B 1 280 280 MPD MPD . I 5 MPD B 1 281 281 MPD MPD . J 6 HOH A 1 283 5 HOH HOH . J 6 HOH A 2 284 8 HOH HOH . J 6 HOH A 3 285 12 HOH HOH . J 6 HOH A 4 286 16 HOH HOH . J 6 HOH A 5 287 18 HOH HOH . J 6 HOH A 6 288 19 HOH HOH . J 6 HOH A 7 289 20 HOH HOH . J 6 HOH A 8 290 23 HOH HOH . J 6 HOH A 9 291 25 HOH HOH . J 6 HOH A 10 292 32 HOH HOH . J 6 HOH A 11 293 37 HOH HOH . J 6 HOH A 12 294 44 HOH HOH . J 6 HOH A 13 295 45 HOH HOH . J 6 HOH A 14 296 49 HOH HOH . J 6 HOH A 15 297 53 HOH HOH . J 6 HOH A 16 298 54 HOH HOH . J 6 HOH A 17 299 55 HOH HOH . J 6 HOH A 18 300 57 HOH HOH . J 6 HOH A 19 301 63 HOH HOH . J 6 HOH A 20 302 65 HOH HOH . J 6 HOH A 21 303 67 HOH HOH . J 6 HOH A 22 304 69 HOH HOH . J 6 HOH A 23 305 70 HOH HOH . J 6 HOH A 24 306 73 HOH HOH . J 6 HOH A 25 307 76 HOH HOH . J 6 HOH A 26 308 77 HOH HOH . J 6 HOH A 27 309 79 HOH HOH . J 6 HOH A 28 310 81 HOH HOH . J 6 HOH A 29 311 83 HOH HOH . J 6 HOH A 30 312 84 HOH HOH . J 6 HOH A 31 313 85 HOH HOH . J 6 HOH A 32 314 86 HOH HOH . J 6 HOH A 33 315 87 HOH HOH . J 6 HOH A 34 316 91 HOH HOH . J 6 HOH A 35 317 93 HOH HOH . J 6 HOH A 36 318 95 HOH HOH . J 6 HOH A 37 319 96 HOH HOH . J 6 HOH A 38 320 99 HOH HOH . J 6 HOH A 39 321 101 HOH HOH . J 6 HOH A 40 322 102 HOH HOH . J 6 HOH A 41 323 104 HOH HOH . J 6 HOH A 42 324 106 HOH HOH . J 6 HOH A 43 325 110 HOH HOH . J 6 HOH A 44 326 112 HOH HOH . J 6 HOH A 45 327 115 HOH HOH . J 6 HOH A 46 328 117 HOH HOH . J 6 HOH A 47 329 123 HOH HOH . J 6 HOH A 48 330 125 HOH HOH . J 6 HOH A 49 331 126 HOH HOH . J 6 HOH A 50 332 127 HOH HOH . J 6 HOH A 51 333 128 HOH HOH . J 6 HOH A 52 334 129 HOH HOH . J 6 HOH A 53 335 130 HOH HOH . J 6 HOH A 54 336 134 HOH HOH . J 6 HOH A 55 337 135 HOH HOH . J 6 HOH A 56 338 138 HOH HOH . J 6 HOH A 57 339 148 HOH HOH . J 6 HOH A 58 340 150 HOH HOH . J 6 HOH A 59 341 152 HOH HOH . J 6 HOH A 60 342 154 HOH HOH . J 6 HOH A 61 343 155 HOH HOH . J 6 HOH A 62 344 157 HOH HOH . J 6 HOH A 63 345 159 HOH HOH . J 6 HOH A 64 346 164 HOH HOH . J 6 HOH A 65 347 170 HOH HOH . J 6 HOH A 66 348 171 HOH HOH . J 6 HOH A 67 349 175 HOH HOH . J 6 HOH A 68 350 178 HOH HOH . J 6 HOH A 69 351 181 HOH HOH . J 6 HOH A 70 352 182 HOH HOH . J 6 HOH A 71 353 183 HOH HOH . J 6 HOH A 72 354 185 HOH HOH . J 6 HOH A 73 355 189 HOH HOH . J 6 HOH A 74 356 194 HOH HOH . J 6 HOH A 75 357 195 HOH HOH . J 6 HOH A 76 358 196 HOH HOH . J 6 HOH A 77 359 198 HOH HOH . J 6 HOH A 78 360 199 HOH HOH . J 6 HOH A 79 361 200 HOH HOH . J 6 HOH A 80 362 201 HOH HOH . J 6 HOH A 81 363 202 HOH HOH . J 6 HOH A 82 364 203 HOH HOH . J 6 HOH A 83 365 204 HOH HOH . J 6 HOH A 84 366 205 HOH HOH . J 6 HOH A 85 367 206 HOH HOH . J 6 HOH A 86 368 216 HOH HOH . J 6 HOH A 87 369 219 HOH HOH . J 6 HOH A 88 370 220 HOH HOH . J 6 HOH A 89 371 222 HOH HOH . J 6 HOH A 90 372 223 HOH HOH . J 6 HOH A 91 373 224 HOH HOH . J 6 HOH A 92 374 225 HOH HOH . J 6 HOH A 93 375 226 HOH HOH . J 6 HOH A 94 376 228 HOH HOH . J 6 HOH A 95 377 233 HOH HOH . J 6 HOH A 96 378 234 HOH HOH . J 6 HOH A 97 379 235 HOH HOH . J 6 HOH A 98 380 236 HOH HOH . J 6 HOH A 99 381 237 HOH HOH . J 6 HOH A 100 382 238 HOH HOH . K 6 HOH B 1 282 1 HOH HOH . K 6 HOH B 2 283 2 HOH HOH . K 6 HOH B 3 284 3 HOH HOH . K 6 HOH B 4 285 4 HOH HOH . K 6 HOH B 5 286 6 HOH HOH . K 6 HOH B 6 287 7 HOH HOH . K 6 HOH B 7 288 9 HOH HOH . K 6 HOH B 8 289 10 HOH HOH . K 6 HOH B 9 290 11 HOH HOH . K 6 HOH B 10 291 13 HOH HOH . K 6 HOH B 11 292 14 HOH HOH . K 6 HOH B 12 293 15 HOH HOH . K 6 HOH B 13 294 17 HOH HOH . K 6 HOH B 14 295 21 HOH HOH . K 6 HOH B 15 296 22 HOH HOH . K 6 HOH B 16 297 24 HOH HOH . K 6 HOH B 17 298 26 HOH HOH . K 6 HOH B 18 299 27 HOH HOH . K 6 HOH B 19 300 28 HOH HOH . K 6 HOH B 20 301 29 HOH HOH . K 6 HOH B 21 302 30 HOH HOH . K 6 HOH B 22 303 31 HOH HOH . K 6 HOH B 23 304 33 HOH HOH . K 6 HOH B 24 305 34 HOH HOH . K 6 HOH B 25 306 35 HOH HOH . K 6 HOH B 26 307 36 HOH HOH . K 6 HOH B 27 308 38 HOH HOH . K 6 HOH B 28 309 39 HOH HOH . K 6 HOH B 29 310 40 HOH HOH . K 6 HOH B 30 311 41 HOH HOH . K 6 HOH B 31 312 42 HOH HOH . K 6 HOH B 32 313 43 HOH HOH . K 6 HOH B 33 314 46 HOH HOH . K 6 HOH B 34 315 47 HOH HOH . K 6 HOH B 35 316 48 HOH HOH . K 6 HOH B 36 317 50 HOH HOH . K 6 HOH B 37 318 51 HOH HOH . K 6 HOH B 38 319 52 HOH HOH . K 6 HOH B 39 320 56 HOH HOH . K 6 HOH B 40 321 58 HOH HOH . K 6 HOH B 41 322 59 HOH HOH . K 6 HOH B 42 323 60 HOH HOH . K 6 HOH B 43 324 61 HOH HOH . K 6 HOH B 44 325 62 HOH HOH . K 6 HOH B 45 326 64 HOH HOH . K 6 HOH B 46 327 66 HOH HOH . K 6 HOH B 47 328 68 HOH HOH . K 6 HOH B 48 329 71 HOH HOH . K 6 HOH B 49 330 72 HOH HOH . K 6 HOH B 50 331 74 HOH HOH . K 6 HOH B 51 332 75 HOH HOH . K 6 HOH B 52 333 78 HOH HOH . K 6 HOH B 53 334 80 HOH HOH . K 6 HOH B 54 335 88 HOH HOH . K 6 HOH B 55 336 89 HOH HOH . K 6 HOH B 56 337 90 HOH HOH . K 6 HOH B 57 338 92 HOH HOH . K 6 HOH B 58 339 94 HOH HOH . K 6 HOH B 59 340 97 HOH HOH . K 6 HOH B 60 341 98 HOH HOH . K 6 HOH B 61 342 100 HOH HOH . K 6 HOH B 62 343 103 HOH HOH . K 6 HOH B 63 344 105 HOH HOH . K 6 HOH B 64 345 107 HOH HOH . K 6 HOH B 65 346 108 HOH HOH . K 6 HOH B 66 347 109 HOH HOH . K 6 HOH B 67 348 111 HOH HOH . K 6 HOH B 68 349 113 HOH HOH . K 6 HOH B 69 350 114 HOH HOH . K 6 HOH B 70 351 116 HOH HOH . K 6 HOH B 71 352 118 HOH HOH . K 6 HOH B 72 353 119 HOH HOH . K 6 HOH B 73 354 120 HOH HOH . K 6 HOH B 74 355 121 HOH HOH . K 6 HOH B 75 356 122 HOH HOH . K 6 HOH B 76 357 124 HOH HOH . K 6 HOH B 77 358 132 HOH HOH . K 6 HOH B 78 359 133 HOH HOH . K 6 HOH B 79 360 136 HOH HOH . K 6 HOH B 80 361 137 HOH HOH . K 6 HOH B 81 362 139 HOH HOH . K 6 HOH B 82 363 140 HOH HOH . K 6 HOH B 83 364 141 HOH HOH . K 6 HOH B 84 365 142 HOH HOH . K 6 HOH B 85 366 143 HOH HOH . K 6 HOH B 86 367 144 HOH HOH . K 6 HOH B 87 368 145 HOH HOH . K 6 HOH B 88 369 146 HOH HOH . K 6 HOH B 89 370 147 HOH HOH . K 6 HOH B 90 371 149 HOH HOH . K 6 HOH B 91 372 151 HOH HOH . K 6 HOH B 92 373 153 HOH HOH . K 6 HOH B 93 374 156 HOH HOH . K 6 HOH B 94 375 158 HOH HOH . K 6 HOH B 95 376 160 HOH HOH . K 6 HOH B 96 377 161 HOH HOH . K 6 HOH B 97 378 162 HOH HOH . K 6 HOH B 98 379 163 HOH HOH . K 6 HOH B 99 380 165 HOH HOH . K 6 HOH B 100 381 166 HOH HOH . K 6 HOH B 101 382 167 HOH HOH . K 6 HOH B 102 383 168 HOH HOH . K 6 HOH B 103 384 169 HOH HOH . K 6 HOH B 104 385 172 HOH HOH . K 6 HOH B 105 386 173 HOH HOH . K 6 HOH B 106 387 174 HOH HOH . K 6 HOH B 107 388 176 HOH HOH . K 6 HOH B 108 389 177 HOH HOH . K 6 HOH B 109 390 179 HOH HOH . K 6 HOH B 110 391 180 HOH HOH . K 6 HOH B 111 392 184 HOH HOH . K 6 HOH B 112 393 186 HOH HOH . K 6 HOH B 113 394 187 HOH HOH . K 6 HOH B 114 395 188 HOH HOH . K 6 HOH B 115 396 190 HOH HOH . K 6 HOH B 116 397 191 HOH HOH . K 6 HOH B 117 398 192 HOH HOH . K 6 HOH B 118 399 193 HOH HOH . K 6 HOH B 119 400 197 HOH HOH . K 6 HOH B 120 401 207 HOH HOH . K 6 HOH B 121 402 208 HOH HOH . K 6 HOH B 122 403 209 HOH HOH . K 6 HOH B 123 404 210 HOH HOH . K 6 HOH B 124 405 211 HOH HOH . K 6 HOH B 125 406 212 HOH HOH . K 6 HOH B 126 407 213 HOH HOH . K 6 HOH B 127 408 214 HOH HOH . K 6 HOH B 128 409 215 HOH HOH . K 6 HOH B 129 410 217 HOH HOH . K 6 HOH B 130 411 218 HOH HOH . K 6 HOH B 131 412 221 HOH HOH . K 6 HOH B 132 413 227 HOH HOH . K 6 HOH B 133 414 229 HOH HOH . K 6 HOH B 134 415 230 HOH HOH . K 6 HOH B 135 416 231 HOH HOH . K 6 HOH B 136 417 232 HOH HOH . K 6 HOH B 137 418 239 HOH HOH . K 6 HOH B 138 419 240 HOH HOH . K 6 HOH B 139 420 241 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 P P 5GP . . . D 4 -49.852 16.763 -24.036 0.8 66.98 ? P 5GP 279 A 1 HETATM 2 O O1P 5GP . . . D 4 -49.89 15.452 -24.817 0.8 64.84 ? O1P 5GP 279 A 1 HETATM 3 O O2P 5GP . . . D 4 -49.25 17.905 -24.841 0.8 65.96 ? O2P 5GP 279 A 1 HETATM 4 O O3P 5GP . . . D 4 -49.38 16.669 -22.577 0.8 64.52 ? O3P 5GP 279 A 1 HETATM 5 O O5' 5GP . . . D 4 -51.433 17.142 -23.933 0.8 64.96 ? O5' 5GP 279 A 1 HETATM 6 C C5' 5GP . . . D 4 -52.387 16.216 -23.413 0.8 64.16 ? C5' 5GP 279 A 1 HETATM 7 C C4' 5GP . . . D 4 -53.652 16.93 -22.935 0.8 63.77 ? C4' 5GP 279 A 1 HETATM 8 O O4' 5GP . . . D 4 -53.983 16.465 -21.617 0.8 65.39 ? O4' 5GP 279 A 1 HETATM 9 C C3' 5GP . . . D 4 -53.479 18.438 -22.883 0.8 63.84 ? C3' 5GP 279 A 1 HETATM 10 O O3' 5GP . . . D 4 -54.397 19.083 -23.784 0.8 57.82 ? O3' 5GP 279 A 1 HETATM 11 C C2' 5GP . . . D 4 -53.658 18.807 -21.41 0.8 66.52 ? C2' 5GP 279 A 1 HETATM 12 O O2' 5GP . . . D 4 -54.764 19.691 -21.225 0.8 69.13 ? O2' 5GP 279 A 1 HETATM 13 C C1' 5GP . . . D 4 -53.951 17.515 -20.655 0.8 67.25 ? C1' 5GP 279 A 1 HETATM 14 N N9 5GP . . . D 4 -52.899 17.221 -19.646 0.8 68.6 ? N9 5GP 279 A 1 HETATM 15 C C8 5GP . . . D 4 -51.674 16.74 -19.902 0.8 68.98 ? C8 5GP 279 A 1 HETATM 16 N N7 5GP . . . D 4 -50.983 16.606 -18.741 0.8 70.43 ? N7 5GP 279 A 1 HETATM 17 C C5 5GP . . . D 4 -51.799 17.005 -17.734 0.8 71.37 ? C5 5GP 279 A 1 HETATM 18 C C6 5GP . . . D 4 -51.658 17.085 -16.336 0.8 72.88 ? C6 5GP 279 A 1 HETATM 19 O O6 5GP . . . D 4 -50.578 16.741 -15.78 0.8 73.53 ? O6 5GP 279 A 1 HETATM 20 N N1 5GP . . . D 4 -52.687 17.54 -15.592 0.8 72.67 ? N1 5GP 279 A 1 HETATM 21 C C2 5GP . . . D 4 -53.841 17.913 -16.166 0.8 71.75 ? C2 5GP 279 A 1 HETATM 22 N N2 5GP . . . D 4 -54.861 18.376 -15.413 0.8 72.92 ? N2 5GP 279 A 1 HETATM 23 N N3 5GP . . . D 4 -54 17.844 -17.505 0.8 71.21 ? N3 5GP 279 A 1 HETATM 24 C C4 5GP . . . D 4 -53.002 17.393 -18.315 0.8 70.43 ? C4 5GP 279 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #