data_2GN9 # _model_server_result.job_id 733X-l51DePaDVULtQVQnA _model_server_result.datetime_utc '2024-12-21 14:09:48' _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 2gn9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":334}' # _entry.id 2GN9 # _exptl.entry_id 2GN9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 743.405 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _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 2GN9 _cell.length_a 112.376 _cell.length_b 112.376 _cell.length_c 107.349 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GN9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS hexameric 6 author_and_software_defined_assembly 1 PISA dimeric 2 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,B,C,D,E,F,G,H,I 1 1,2,3 B,E,F,G,I 2 1 A,C,D,H 2 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_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 56.188 97.320471 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -56.188 97.320471 0 # 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 E N N # _chem_comp.formula 'C21 H28 N7 O17 P3' _chem_comp.formula_weight 743.405 _chem_comp.id NAP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE" # 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 PA O1A NAP doub 262 n n PA O2A NAP sing 263 n n PA O5B NAP sing 264 n n PA O3 NAP sing 265 n n O2A HOA2 NAP sing 266 n n O5B C5B NAP sing 267 n n C5B C4B NAP sing 268 n n C5B H51A NAP sing 269 n n C5B H52A NAP sing 270 n n C4B O4B NAP sing 271 n n C4B C3B NAP sing 272 n n C4B H4B NAP sing 273 n n O4B C1B NAP sing 274 n n C3B O3B NAP sing 275 n n C3B C2B NAP sing 276 n n C3B H3B NAP sing 277 n n O3B HO3A NAP sing 278 n n C2B O2B NAP sing 279 n n C2B C1B NAP sing 280 n n C2B H2B NAP sing 281 n n O2B P2B NAP sing 282 n n C1B N9A NAP sing 283 n n C1B H1B NAP sing 284 n n N9A C8A NAP sing 285 n y N9A C4A NAP sing 286 n y C8A N7A NAP doub 287 n y C8A H8A NAP sing 288 n n N7A C5A NAP sing 289 n y C5A C6A NAP sing 290 n y C5A C4A NAP doub 291 n y C6A N6A NAP sing 292 n n C6A N1A NAP doub 293 n y N6A H61A NAP sing 294 n n N6A H62A NAP sing 295 n n N1A C2A NAP sing 296 n y C2A N3A NAP doub 297 n y C2A H2A NAP sing 298 n n N3A C4A NAP sing 299 n y O3 PN NAP sing 300 n n PN O1N NAP doub 301 n n PN O2N NAP sing 302 n n PN O5D NAP sing 303 n n O5D C5D NAP sing 304 n n C5D C4D NAP sing 305 n n C5D H51N NAP sing 306 n n C5D H52N NAP sing 307 n n C4D O4D NAP sing 308 n n C4D C3D NAP sing 309 n n C4D H4D NAP sing 310 n n O4D C1D NAP sing 311 n n C3D O3D NAP sing 312 n n C3D C2D NAP sing 313 n n C3D H3D NAP sing 314 n n O3D HO3N NAP sing 315 n n C2D O2D NAP sing 316 n n C2D C1D NAP sing 317 n n C2D H2D NAP sing 318 n n O2D HO2N NAP sing 319 n n C1D N1N NAP sing 320 n n C1D H1D NAP sing 321 n n N1N C2N NAP sing 322 n y N1N C6N NAP doub 323 n y C2N C3N NAP doub 324 n y C2N H2N NAP sing 325 n n C3N C7N NAP sing 326 n n C3N C4N NAP sing 327 n y C7N O7N NAP doub 328 n n C7N N7N NAP sing 329 n n N7N H71N NAP sing 330 n n N7N H72N NAP sing 331 n n C4N C5N NAP doub 332 n y C4N H4N NAP sing 333 n n C5N C6N NAP sing 334 n y C5N H5N NAP sing 335 n n C6N H6N NAP sing 336 n n P2B O1X NAP doub 337 n n P2B O2X NAP sing 338 n n P2B O3X NAP sing 339 n n O2X HOP2 NAP sing 340 n n O3X HOP3 NAP sing 341 n n # _atom_sites.entry_id 2GN9 _atom_sites.fract_transf_matrix[1][1] 0.008899 _atom_sites.fract_transf_matrix[1][2] 0.005138 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010275 _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] 0.009315 _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 NAP A 1 334 334 NAP NAP . D 3 UPG A 1 335 335 UPG UPG . E 2 NAP B 1 334 334 NAP NAP . F 3 UPG B 1 335 335 UPG UPG . G 4 MES B 1 336 336 MES MES . H 5 HOH A 1 336 1 HOH HOH . H 5 HOH A 2 337 2 HOH HOH . H 5 HOH A 3 338 8 HOH HOH . H 5 HOH A 4 339 16 HOH HOH . H 5 HOH A 5 340 17 HOH HOH . H 5 HOH A 6 341 18 HOH HOH . H 5 HOH A 7 342 20 HOH HOH . H 5 HOH A 8 343 22 HOH HOH . H 5 HOH A 9 344 23 HOH HOH . H 5 HOH A 10 345 24 HOH HOH . H 5 HOH A 11 346 25 HOH HOH . H 5 HOH A 12 347 26 HOH HOH . H 5 HOH A 13 348 27 HOH HOH . H 5 HOH A 14 349 31 HOH HOH . H 5 HOH A 15 350 32 HOH HOH . H 5 HOH A 16 351 35 HOH HOH . H 5 HOH A 17 352 36 HOH HOH . H 5 HOH A 18 353 39 HOH HOH . H 5 HOH A 19 354 41 HOH HOH . H 5 HOH A 20 355 44 HOH HOH . H 5 HOH A 21 356 45 HOH HOH . H 5 HOH A 22 357 46 HOH HOH . H 5 HOH A 23 358 48 HOH HOH . H 5 HOH A 24 359 49 HOH HOH . H 5 HOH A 25 360 53 HOH HOH . H 5 HOH A 26 361 56 HOH HOH . H 5 HOH A 27 362 57 HOH HOH . H 5 HOH A 28 363 58 HOH HOH . H 5 HOH A 29 364 59 HOH HOH . H 5 HOH A 30 365 60 HOH HOH . H 5 HOH A 31 366 64 HOH HOH . H 5 HOH A 32 367 66 HOH HOH . H 5 HOH A 33 368 70 HOH HOH . H 5 HOH A 34 369 74 HOH HOH . I 5 HOH B 1 337 3 HOH HOH . I 5 HOH B 2 338 4 HOH HOH . I 5 HOH B 3 339 5 HOH HOH . I 5 HOH B 4 340 6 HOH HOH . I 5 HOH B 5 341 7 HOH HOH . I 5 HOH B 6 342 9 HOH HOH . I 5 HOH B 7 343 10 HOH HOH . I 5 HOH B 8 344 11 HOH HOH . I 5 HOH B 9 345 12 HOH HOH . I 5 HOH B 10 346 13 HOH HOH . I 5 HOH B 11 347 14 HOH HOH . I 5 HOH B 12 348 15 HOH HOH . I 5 HOH B 13 349 19 HOH HOH . I 5 HOH B 14 350 21 HOH HOH . I 5 HOH B 15 351 28 HOH HOH . I 5 HOH B 16 352 29 HOH HOH . I 5 HOH B 17 353 30 HOH HOH . I 5 HOH B 18 354 33 HOH HOH . I 5 HOH B 19 355 34 HOH HOH . I 5 HOH B 20 356 37 HOH HOH . I 5 HOH B 21 357 38 HOH HOH . I 5 HOH B 22 358 40 HOH HOH . I 5 HOH B 23 359 42 HOH HOH . I 5 HOH B 24 360 43 HOH HOH . I 5 HOH B 25 361 47 HOH HOH . I 5 HOH B 26 362 50 HOH HOH . I 5 HOH B 27 363 51 HOH HOH . I 5 HOH B 28 364 52 HOH HOH . I 5 HOH B 29 365 54 HOH HOH . I 5 HOH B 30 366 55 HOH HOH . I 5 HOH B 31 367 61 HOH HOH . I 5 HOH B 32 368 62 HOH HOH . I 5 HOH B 33 369 63 HOH HOH . I 5 HOH B 34 370 65 HOH HOH . I 5 HOH B 35 371 67 HOH HOH . I 5 HOH B 36 372 68 HOH HOH . I 5 HOH B 37 373 69 HOH HOH . I 5 HOH B 38 374 71 HOH HOH . I 5 HOH B 39 375 72 HOH HOH . I 5 HOH B 40 376 73 HOH HOH . I 5 HOH B 41 377 75 HOH HOH . I 5 HOH B 42 378 76 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 PA NAP . . . E 2 25.942 52.875 6.63 1 43.09 ? PA NAP 334 B 1 HETATM 2 O O1A NAP . . . E 2 26.685 51.465 6.875 1 28.55 ? O1A NAP 334 B 1 HETATM 3 O O2A NAP . . . E 2 25.503 53.134 5.098 1 32.74 ? O2A NAP 334 B 1 HETATM 4 O O5B NAP . . . E 2 24.606 53.088 7.535 1 39.73 ? O5B NAP 334 B 1 HETATM 5 C C5B NAP . . . E 2 23.566 53.871 7.01 1 45.91 ? C5B NAP 334 B 1 HETATM 6 C C4B NAP . . . E 2 22.276 53.257 7.484 1 44.36 ? C4B NAP 334 B 1 HETATM 7 O O4B NAP . . . E 2 21.236 54.207 7.313 1 45.69 ? O4B NAP 334 B 1 HETATM 8 C C3B NAP . . . E 2 21.938 52.083 6.626 1 44.5 ? C3B NAP 334 B 1 HETATM 9 O O3B NAP . . . E 2 22.165 50.919 7.405 1 49.09 ? O3B NAP 334 B 1 HETATM 10 C C2B NAP . . . E 2 20.478 52.215 6.327 1 44.13 ? C2B NAP 334 B 1 HETATM 11 O O2B NAP . . . E 2 19.759 51.132 6.925 1 45.42 ? O2B NAP 334 B 1 HETATM 12 C C1B NAP . . . E 2 20.051 53.498 6.997 1 41 ? C1B NAP 334 B 1 HETATM 13 N N9A NAP . . . E 2 19.129 54.296 6.137 1 37.67 ? N9A NAP 334 B 1 HETATM 14 C C8A NAP . . . E 2 19.411 54.655 4.867 1 37.48 ? C8A NAP 334 B 1 HETATM 15 N N7A NAP . . . E 2 18.38 55.35 4.377 1 33.02 ? N7A NAP 334 B 1 HETATM 16 C C5A NAP . . . E 2 17.46 55.381 5.45 1 34.57 ? C5A NAP 334 B 1 HETATM 17 C C6A NAP . . . E 2 16.165 55.999 5.481 1 27.86 ? C6A NAP 334 B 1 HETATM 18 N N6A NAP . . . E 2 15.727 56.639 4.362 1 22.18 ? N6A NAP 334 B 1 HETATM 19 N N1A NAP . . . E 2 15.444 55.903 6.643 1 33.26 ? N1A NAP 334 B 1 HETATM 20 C C2A NAP . . . E 2 16.024 55.208 7.709 1 38.07 ? C2A NAP 334 B 1 HETATM 21 N N3A NAP . . . E 2 17.235 54.607 7.728 1 37.88 ? N3A NAP 334 B 1 HETATM 22 C C4A NAP . . . E 2 17.946 54.719 6.545 1 32.01 ? C4A NAP 334 B 1 HETATM 23 O O3 NAP . . . E 2 26.822 54.147 7 1 22.28 ? O3 NAP 334 B 1 HETATM 24 P PN NAP . . . E 2 27.354 54.593 8.429 1 35.93 ? PN NAP 334 B 1 HETATM 25 O O1N NAP . . . E 2 26.771 53.729 9.667 1 33.29 ? O1N NAP 334 B 1 HETATM 26 O O2N NAP . . . E 2 28.957 54.547 8.27 1 48.04 ? O2N NAP 334 B 1 HETATM 27 O O5D NAP . . . E 2 27.028 56.161 8.482 1 42.17 ? O5D NAP 334 B 1 HETATM 28 C C5D NAP . . . E 2 25.972 56.534 9.325 1 53.99 ? C5D NAP 334 B 1 HETATM 29 C C4D NAP . . . E 2 26.056 58.016 9.571 1 51.96 ? C4D NAP 334 B 1 HETATM 30 O O4D NAP . . . E 2 27.355 58.303 10.086 1 54.61 ? O4D NAP 334 B 1 HETATM 31 C C3D NAP . . . E 2 25.879 58.769 8.288 1 55 ? C3D NAP 334 B 1 HETATM 32 O O3D NAP . . . E 2 24.704 59.562 8.396 1 54.25 ? O3D NAP 334 B 1 HETATM 33 C C2D NAP . . . E 2 27.084 59.612 8.152 1 58.25 ? C2D NAP 334 B 1 HETATM 34 O O2D NAP . . . E 2 26.707 60.964 7.96 1 58.98 ? O2D NAP 334 B 1 HETATM 35 C C1D NAP . . . E 2 27.854 59.459 9.432 1 61.51 ? C1D NAP 334 B 1 HETATM 36 N N1N NAP . . . E 2 29.325 59.342 9.19 1 69.24 ? N1N NAP 334 B 1 HETATM 37 C C2N NAP . . . E 2 29.755 58.457 8.204 1 77.19 ? C2N NAP 334 B 1 HETATM 38 C C3N NAP . . . E 2 31.151 58.388 8.008 1 80 ? C3N NAP 334 B 1 HETATM 39 C C7N NAP . . . E 2 31.737 57.472 6.972 1 79.65 ? C7N NAP 334 B 1 HETATM 40 O O7N NAP . . . E 2 32.558 57.831 6.143 1 76.83 ? O7N NAP 334 B 1 HETATM 41 N N7N NAP . . . E 2 31.273 56.181 7.041 1 76.84 ? N7N NAP 334 B 1 HETATM 42 C C4N NAP . . . E 2 32.02 59.202 8.804 1 77.8 ? C4N NAP 334 B 1 HETATM 43 C C5N NAP . . . E 2 31.488 60.082 9.795 1 70.96 ? C5N NAP 334 B 1 HETATM 44 C C6N NAP . . . E 2 30.098 60.149 9.989 1 70.12 ? C6N NAP 334 B 1 HETATM 45 P P2B NAP . . . E 2 18.601 50.409 6.04 1 43.69 ? P2B NAP 334 B 1 HETATM 46 O O1X NAP . . . E 2 18.212 48.941 6.567 1 52.69 ? O1X NAP 334 B 1 HETATM 47 O O2X NAP . . . E 2 17.368 51.451 6.055 1 53.96 ? O2X NAP 334 B 1 HETATM 48 O O3X NAP . . . E 2 19.123 50.472 4.513 1 42.9 ? O3X NAP 334 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 48 #