data_1PD8 # _model_server_result.job_id gPt9wf4JEzBW-zklPzfrZQ _model_server_result.datetime_utc '2024-10-18 16:25:16' _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 1pd8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 1PD8 # _exptl.entry_id 1PD8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 745.421 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _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 1PD8 _cell.length_a 85.873 _cell.length_b 85.873 _cell.length_c 77.637 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PD8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C21 H30 N7 O17 P3' _chem_comp.formula_weight 745.421 _chem_comp.id NDP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _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 PA O1A NDP doub 291 n n PA O2A NDP sing 292 n n PA O5B NDP sing 293 n n PA O3 NDP sing 294 n n O2A HOA2 NDP sing 295 n n O5B C5B NDP sing 296 n n C5B C4B NDP sing 297 n n C5B H51A NDP sing 298 n n C5B H52A NDP sing 299 n n C4B O4B NDP sing 300 n n C4B C3B NDP sing 301 n n C4B H4B NDP sing 302 n n O4B C1B NDP sing 303 n n C3B O3B NDP sing 304 n n C3B C2B NDP sing 305 n n C3B H3B NDP sing 306 n n O3B HO3A NDP sing 307 n n C2B O2B NDP sing 308 n n C2B C1B NDP sing 309 n n C2B H2B NDP sing 310 n n O2B P2B NDP sing 311 n n C1B N9A NDP sing 312 n n C1B H1B NDP sing 313 n n N9A C8A NDP sing 314 n y N9A C4A NDP sing 315 n y C8A N7A NDP doub 316 n y C8A H8A NDP sing 317 n n N7A C5A NDP sing 318 n y C5A C6A NDP sing 319 n y C5A C4A NDP doub 320 n y C6A N6A NDP sing 321 n n C6A N1A NDP doub 322 n y N6A H61A NDP sing 323 n n N6A H62A NDP sing 324 n n N1A C2A NDP sing 325 n y C2A N3A NDP doub 326 n y C2A H2A NDP sing 327 n n N3A C4A NDP sing 328 n y O3 PN NDP sing 329 n n PN O1N NDP doub 330 n n PN O2N NDP sing 331 n n PN O5D NDP sing 332 n n O2N H21N NDP sing 333 n n O5D C5D NDP sing 334 n n C5D C4D NDP sing 335 n n C5D H51N NDP sing 336 n n C5D H52N NDP sing 337 n n C4D O4D NDP sing 338 n n C4D C3D NDP sing 339 n n C4D H4D NDP sing 340 n n O4D C1D NDP sing 341 n n C3D O3D NDP sing 342 n n C3D C2D NDP sing 343 n n C3D H3D NDP sing 344 n n O3D HO3N NDP sing 345 n n C2D O2D NDP sing 346 n n C2D C1D NDP sing 347 n n C2D H2D NDP sing 348 n n O2D HO2N NDP sing 349 n n C1D N1N NDP sing 350 n n C1D H1D NDP sing 351 n n N1N C2N NDP sing 352 n n N1N C6N NDP sing 353 n n C2N C3N NDP doub 354 n n C2N H2N NDP sing 355 n n C3N C7N NDP sing 356 n n C3N C4N NDP sing 357 n n C7N O7N NDP doub 358 n n C7N N7N NDP sing 359 n n N7N H71N NDP sing 360 n n N7N H72N NDP sing 361 n n C4N C5N NDP sing 362 n n C4N H41N NDP sing 363 n n C4N H42N NDP sing 364 n n C5N C6N NDP doub 365 n n C5N H5N NDP sing 366 n n C6N H6N NDP sing 367 n n P2B O1X NDP doub 368 n n P2B O2X NDP sing 369 n n P2B O3X NDP sing 370 n n O2X HOP2 NDP sing 371 n n O3X HOP3 NDP sing 372 n n # _atom_sites.entry_id 1PD8 _atom_sites.fract_transf_matrix[1][1] 0.011645 _atom_sites.fract_transf_matrix[1][2] 0.006723 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013447 _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] 0.01288 _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 B 2 NDP A 1 300 187 NDP COE . C 3 CO4 A 1 301 187 CO4 COE . D 4 HOH A 1 188 188 HOH WAT . D 4 HOH A 2 189 189 HOH WAT . D 4 HOH A 3 190 190 HOH WAT . D 4 HOH A 4 191 191 HOH WAT . D 4 HOH A 5 192 192 HOH WAT . D 4 HOH A 6 193 193 HOH WAT . D 4 HOH A 7 194 194 HOH WAT . D 4 HOH A 8 195 195 HOH WAT . D 4 HOH A 9 196 196 HOH WAT . D 4 HOH A 10 197 197 HOH WAT . D 4 HOH A 11 198 198 HOH WAT . D 4 HOH A 12 199 199 HOH WAT . D 4 HOH A 13 200 200 HOH WAT . D 4 HOH A 14 201 201 HOH WAT . D 4 HOH A 15 202 202 HOH WAT . D 4 HOH A 16 203 203 HOH WAT . D 4 HOH A 17 204 204 HOH WAT . D 4 HOH A 18 205 205 HOH WAT . D 4 HOH A 19 206 206 HOH WAT . D 4 HOH A 20 207 207 HOH WAT . D 4 HOH A 21 208 208 HOH WAT . D 4 HOH A 22 209 209 HOH WAT . D 4 HOH A 23 210 210 HOH WAT . D 4 HOH A 24 211 211 HOH WAT . D 4 HOH A 25 212 212 HOH WAT . D 4 HOH A 26 213 213 HOH WAT . D 4 HOH A 27 214 214 HOH WAT . D 4 HOH A 28 215 215 HOH WAT . D 4 HOH A 29 216 216 HOH WAT . D 4 HOH A 30 217 217 HOH WAT . D 4 HOH A 31 218 218 HOH WAT . D 4 HOH A 32 219 219 HOH WAT . D 4 HOH A 33 220 220 HOH WAT . D 4 HOH A 34 221 221 HOH WAT . D 4 HOH A 35 222 222 HOH WAT . D 4 HOH A 36 223 223 HOH WAT . D 4 HOH A 37 224 224 HOH WAT . D 4 HOH A 38 225 225 HOH WAT . D 4 HOH A 39 226 226 HOH WAT . D 4 HOH A 40 227 227 HOH WAT . D 4 HOH A 41 228 228 HOH WAT . D 4 HOH A 42 229 229 HOH WAT . D 4 HOH A 43 230 230 HOH WAT . D 4 HOH A 44 231 231 HOH WAT . D 4 HOH A 45 232 232 HOH WAT . D 4 HOH A 46 233 233 HOH WAT . D 4 HOH A 47 234 234 HOH WAT . D 4 HOH A 48 235 235 HOH WAT . D 4 HOH A 49 236 236 HOH WAT . D 4 HOH A 50 237 237 HOH WAT . D 4 HOH A 51 238 238 HOH WAT . D 4 HOH A 52 239 239 HOH WAT . D 4 HOH A 53 240 240 HOH WAT . D 4 HOH A 54 241 241 HOH WAT . D 4 HOH A 55 242 242 HOH WAT . D 4 HOH A 56 243 243 HOH WAT . D 4 HOH A 57 244 244 HOH WAT . D 4 HOH A 58 245 245 HOH WAT . D 4 HOH A 59 246 246 HOH WAT . D 4 HOH A 60 247 247 HOH WAT . D 4 HOH A 61 248 248 HOH WAT . D 4 HOH A 62 249 249 HOH WAT . D 4 HOH A 63 250 250 HOH WAT . D 4 HOH A 64 251 251 HOH WAT . D 4 HOH A 65 252 252 HOH WAT . D 4 HOH A 66 253 253 HOH WAT . D 4 HOH A 67 254 254 HOH WAT . # 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 NDP . . . B 2 26.334 8.526 8.984 1 30.17 ? PA NDP 300 A 1 HETATM 2 O O1A NDP . . . B 2 26.866 9.552 8.185 1 28.75 ? O1A NDP 300 A 1 HETATM 3 O O2A NDP . . . B 2 25.03 8.26 8.243 1 30.34 ? O2A NDP 300 A 1 HETATM 4 O O5B NDP . . . B 2 26.498 8.671 10.405 1 32.56 ? O5B NDP 300 A 1 HETATM 5 C C5B NDP . . . B 2 26.147 7.703 11.512 1 34.65 ? C5B NDP 300 A 1 HETATM 6 C C4B NDP . . . B 2 25.486 8.372 12.746 1 35.96 ? C4B NDP 300 A 1 HETATM 7 O O4B NDP . . . B 2 24.643 9.307 12.323 1 35.57 ? O4B NDP 300 A 1 HETATM 8 C C3B NDP . . . B 2 24.603 7.394 13.574 1 36.54 ? C3B NDP 300 A 1 HETATM 9 O O3B NDP . . . B 2 25.743 6.706 14.336 1 37.71 ? O3B NDP 300 A 1 HETATM 10 C C2B NDP . . . B 2 23.946 8.491 14.454 1 36.41 ? C2B NDP 300 A 1 HETATM 11 O O2B NDP . . . B 2 24.624 9.18 15.365 1 35.73 ? O2B NDP 300 A 1 HETATM 12 C C1B NDP . . . B 2 23.451 9.405 13.221 1 36.88 ? C1B NDP 300 A 1 HETATM 13 N N9A NDP . . . B 2 22.417 8.848 12.479 1 38.65 ? N9A NDP 300 A 1 HETATM 14 C C8A NDP . . . B 2 22.657 8.164 11.312 1 39.04 ? C8A NDP 300 A 1 HETATM 15 N N7A NDP . . . B 2 21.463 7.724 10.813 1 39.7 ? N7A NDP 300 A 1 HETATM 16 C C5A NDP . . . B 2 20.522 8.238 11.746 1 40.12 ? C5A NDP 300 A 1 HETATM 17 C C6A NDP . . . B 2 18.995 8.19 11.87 1 41.21 ? C6A NDP 300 A 1 HETATM 18 N N6A NDP . . . B 2 18.364 7.516 10.819 1 42.31 ? N6A NDP 300 A 1 HETATM 19 N N1A NDP . . . B 2 18.415 8.774 12.944 1 41.02 ? N1A NDP 300 A 1 HETATM 20 C C2A NDP . . . B 2 19.23 9.372 13.815 1 40.52 ? C2A NDP 300 A 1 HETATM 21 N N3A NDP . . . B 2 20.546 9.494 13.836 1 39.96 ? N3A NDP 300 A 1 HETATM 22 C C4A NDP . . . B 2 21.124 8.876 12.75 1 39.79 ? C4A NDP 300 A 1 HETATM 23 O O3 NDP . . . B 2 27.4 7.316 8.669 1 32.87 ? O3 NDP 300 A 1 HETATM 24 P PN NDP . . . B 2 27.998 6.401 7.411 1 35.59 ? PN NDP 300 A 1 HETATM 25 O O1N NDP . . . B 2 27 5.543 6.81 1 33.52 ? O1N NDP 300 A 1 HETATM 26 O O2N NDP . . . B 2 28.877 5.523 8.188 1 36.2 ? O2N NDP 300 A 1 HETATM 27 O O5D NDP . . . B 2 29.029 7.178 6.54 1 34.88 ? O5D NDP 300 A 1 HETATM 28 C C5D NDP . . . B 2 30.08 8.192 6.379 1 35.46 ? C5D NDP 300 A 1 HETATM 29 C C4D NDP . . . B 2 31.009 7.396 5.395 1 35.46 ? C4D NDP 300 A 1 HETATM 30 O O4D NDP . . . B 2 30.371 7.392 4.022 1 35.64 ? O4D NDP 300 A 1 HETATM 31 C C3D NDP . . . B 2 32.395 8.206 5.15 1 35.32 ? C3D NDP 300 A 1 HETATM 32 O O3D NDP . . . B 2 32.959 7 4.616 1 34.84 ? O3D NDP 300 A 1 HETATM 33 C C2D NDP . . . B 2 31.788 9.295 4.251 1 35.55 ? C2D NDP 300 A 1 HETATM 34 O O2D NDP . . . B 2 32.768 10.069 3.628 1 36.5 ? O2D NDP 300 A 1 HETATM 35 C C1D NDP . . . B 2 31.067 8.482 3.194 1 35.52 ? C1D NDP 300 A 1 HETATM 36 N N1N NDP . . . B 2 29.925 9.1 2.377 1 34.63 ? N1N NDP 300 A 1 HETATM 37 C C2N NDP . . . B 2 29.96 8.967 0.908 1 33.42 ? C2N NDP 300 A 1 HETATM 38 C C3N NDP . . . B 2 28.872 9.611 0.241 1 31.68 ? C3N NDP 300 A 1 HETATM 39 C C7N NDP . . . B 2 28.86 9.399 -1.298 1 29.88 ? C7N NDP 300 A 1 HETATM 40 O O7N NDP . . . B 2 28.173 9.724 -2.06 1 27.23 ? O7N NDP 300 A 1 HETATM 41 N N7N NDP . . . B 2 30 8.554 -1.896 1 26.23 ? N7N NDP 300 A 1 HETATM 42 C C4N NDP . . . B 2 27.728 10.377 0.873 1 32.19 ? C4N NDP 300 A 1 HETATM 43 C C5N NDP . . . B 2 27.881 10.384 2.373 1 33.57 ? C5N NDP 300 A 1 HETATM 44 C C6N NDP . . . B 2 28.901 9.8 3.069 1 33.98 ? C6N NDP 300 A 1 HETATM 45 P P2B NDP . . . B 2 24.456 8.732 16.955 1 35.17 ? P2B NDP 300 A 1 HETATM 46 O O1X NDP . . . B 2 25.322 9.862 17.034 1 33.74 ? O1X NDP 300 A 1 HETATM 47 O O2X NDP . . . B 2 25.389 7.656 17.209 1 35.9 ? O2X NDP 300 A 1 HETATM 48 O O3X NDP . . . B 2 23.19 8.79 17.37 1 34.81 ? O3X NDP 300 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #