0.028357 0.000000 0.006201 0.000000 0.016966 0.000000 0.000000 0.000000 0.028091 0.00000 0.00000 0.00000 Komander, D. Deak, M. Alessi, D.R. Van Aalten, D.M.F. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 2 90.00 102.33 90.00 35.264 58.943 36.440 C17 H36 O22 P4 716.350 (2R)-3-{[(S)-{[(2S,3R,5S,6S)-2,6-DIHYDROXY-3,4,5-TRIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-(1-HYDROXY BUTOXY)PROPYL BUTYRATE DIC4-PHOSPHATIDYLINOSITOL(3,4,5)TRISPHOSPHATE non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N O N 2 N C N 3 R C N 4 N O N 5 N C N 6 N O N 7 S P N 8 N O N 9 N O N 10 N O N 11 N C N 12 S C N 13 N O N 14 S C N 15 N O N 16 N P N 17 N O N 18 N O N 19 N O N 20 N C N 21 N O N 22 N P N 23 N O N 24 N O N 25 N O N 26 R C N 27 N O N 28 N P N 29 N O N 30 N O N 31 N O N 32 S C N 33 N O N 34 N C N 35 N O N 36 N C N 37 N C N 38 N C N 39 S C N 40 N O N 41 N C N 42 N C N 43 N C N 44 N H N 45 N H N 46 N H N 47 N H N 48 N H N 49 N H N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N N N 81 S C N 82 N C N 83 N O N 84 N C N 85 N O N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N N N 94 S C N 95 N C N 96 N O N 97 N C N 98 N C N 99 N C N 100 N N N 101 N C N 102 N N N 103 N N N 104 N O N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N N N 121 S C N 122 N C N 123 N O N 124 N C N 125 N C N 126 N O N 127 N N N 128 N O N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N N N 138 S C N 139 N C N 140 N O N 141 N C N 142 N C N 143 N O N 144 N O N 145 N O N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N N N 154 R C N 155 N C N 156 N O N 157 N C N 158 N S N 159 N O N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N N N 168 S C N 169 N C N 170 N O N 171 N C N 172 N C N 173 N C N 174 N O N 175 N N N 176 N O N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N N N 188 S C N 189 N C N 190 N O N 191 N C N 192 N C N 193 N C N 194 N O N 195 N O N 196 N O N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N N N 207 N C N 208 N C N 209 N O N 210 N O N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N N N 217 S C N 218 N C N 219 N O N 220 N C Y 221 N C Y 222 N N Y 223 N C Y 224 N C Y 225 N N N 226 N O N 227 N H N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N O N 238 N H N 239 N H N 240 N N N 241 S C N 242 N C N 243 N O N 244 S C N 245 N C N 246 N C N 247 N C N 248 N O N 249 N H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 N N N 263 S C N 264 N C N 265 N O N 266 N C N 267 N C N 268 N C N 269 N C N 270 N O N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N H N 278 N H N 279 N H N 280 N H N 281 N H N 282 N H N 283 N H N 284 N N N 285 S C N 286 N C N 287 N O N 288 N C N 289 N C N 290 N C N 291 N C N 292 N N N 293 N O N 294 N H N 295 N H N 296 N H N 297 N H N 298 N H N 299 N H N 300 N H N 301 N H N 302 N H N 303 N H N 304 N H N 305 N H N 306 N H N 307 N H N 308 N H N 309 N N N 310 S C N 311 N C N 312 N O N 313 N C N 314 N C N 315 N S N 316 N C N 317 N O N 318 N H N 319 N H N 320 N H N 321 N H N 322 N H N 323 N H N 324 N H N 325 N H N 326 N H N 327 N H N 328 N H N 329 N N N 330 S C N 331 N C N 332 N O N 333 N C Y 334 N C Y 335 N C Y 336 N C Y 337 N C Y 338 N C Y 339 N C N 340 N O N 341 N H N 342 N H N 343 N H N 344 N H N 345 N H N 346 N H N 347 N H N 348 N H N 349 N H N 350 N H N 351 N H N 352 N N N 353 S C N 354 N C N 355 N O N 356 N C N 357 N C N 358 N C N 359 N O N 360 N H N 361 N H N 362 N H N 363 N H N 364 N H N 365 N H N 366 N H N 367 N H N 368 N H N 369 N N N 370 S C N 371 N C N 372 N O N 373 N C N 374 N O N 375 N O N 376 N H N 377 N H N 378 N H N 379 N H N 380 N H N 381 N H N 382 N H N 383 N N N 384 S C N 385 N C N 386 N O N 387 R C N 388 N O N 389 N C N 390 N O N 391 N H N 392 N H N 393 N H N 394 N H N 395 N H N 396 N H N 397 N H N 398 N H N 399 N H N 400 N N N 401 S C N 402 N C N 403 N O N 404 N C Y 405 N C Y 406 N C Y 407 N C Y 408 N N Y 409 N C Y 410 N C Y 411 N C Y 412 N C Y 413 N C N 414 N O N 415 N H N 416 N H N 417 N H N 418 N H N 419 N H N 420 N H N 421 N H N 422 N H N 423 N H N 424 N H N 425 N H N 426 N H N 427 N N N 428 S C N 429 N C N 430 N O N 431 N C Y 432 N C Y 433 N C Y 434 N C Y 435 N C Y 436 N C Y 437 N C N 438 N O N 439 N O N 440 N H N 441 N H N 442 N H N 443 N H N 444 N H N 445 N H N 446 N H N 447 N H N 448 N H N 449 N H N 450 N H N 451 N N N 452 S C N 453 N C N 454 N O N 455 N C N 456 N C N 457 N C N 458 N O N 459 N H N 460 N H N 461 N H N 462 N H N 463 N H N 464 N H N 465 N H N 466 N H N 467 N H N 468 N H N 469 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N doub N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N doub N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N doub N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N doub N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N doub N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N doub N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N doub N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N doub N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N doub N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N doub N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N doub N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N doub N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N doub N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N doub N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N doub N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N doub N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N doub N 215 N sing N 216 N sing N 217 N sing N 218 N sing Y 219 N sing Y 220 N doub Y 221 N doub N 222 N sing Y 223 N sing N 224 N sing Y 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N doub N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N doub N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N doub N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N doub N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N doub N 323 N sing N 324 N sing N 325 N sing N 326 N sing Y 327 N doub Y 328 N sing Y 329 N sing N 330 N sing Y 331 N doub N 332 N sing Y 333 N doub N 334 N sing Y 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N sing N 342 N sing N 343 N sing N 344 N sing N 345 N doub N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N sing N 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N sing N 358 N sing N 359 N sing N 360 N sing N 361 N sing N 362 N doub N 363 N sing N 364 N sing N 365 N sing N 366 N sing N 367 N sing N 368 N sing N 369 N sing N 370 N sing N 371 N sing N 372 N sing N 373 N sing N 374 N sing N 375 N doub N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N sing N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N sing N 390 N sing N 391 N doub N 392 N sing N 393 N sing N 394 N sing N 395 N sing Y 396 N doub Y 397 N sing Y 398 N sing N 399 N sing Y 400 N doub Y 401 N sing Y 402 N sing N 403 N sing Y 404 N sing Y 405 N doub N 406 N sing Y 407 N doub N 408 N sing Y 409 N sing N 410 N sing N 411 N sing N 412 N sing N 413 N sing N 414 N sing N 415 N sing N 416 N sing N 417 N sing N 418 N sing N 419 N doub N 420 N sing N 421 N sing N 422 N sing N 423 N sing Y 424 N doub Y 425 N sing Y 426 N sing N 427 N sing Y 428 N doub N 429 N sing Y 430 N doub N 431 N sing Y 432 N sing N 433 N sing N 434 N sing N 435 N sing N 436 N sing N 437 N sing N 438 N sing N 439 N sing N 440 N sing N 441 N sing N 442 N sing N 443 N doub N 444 N sing N 445 N sing N 446 N sing N 447 N sing N 448 N sing N 449 N sing N 450 N sing N 451 N sing N 452 N sing N 453 N sing N 454 N sing UK Embo J. EMJODG 0897 0261-4189 23 3918 10.1038/SJ.EMBOJ.7600379 15457207 Structural Insights Into the Regulation of Pdk1 by Phosphoinositides and Inositol Phosphates 2004 10.2210/pdb1w1g/pdb pdb_00001w1g 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100.0 1 MIRRORS IMAGE PLATE 2003-09-15 RIGAKU RAXIS 4 SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU MICROMAX-007 17816.186 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 2.7.1.37 PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 409-556 1 man polymer 716.350 (2R)-3-{[(S)-{[(2S,3R,5S,6S)-2,6-DIHYDROXY-3,4,5-TRIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-(1-HYDROXY BUTOXY)PROPYL BUTYRATE 1 syn non-polymer 18.015 water 163 nat water HPDK1 no no GPLGSNIEQYIHDLDSNSFELDLQFSEDEKRLLLEKQAGGNPWHQFVENNLILKMGPVDKRKGLFARRRQLLLTEGPHLY YVDPVNKVLKGEIPWSQELRPEAKNFKTFFVHTPNRTYYLMDPSGNAHKWCRKIQEVWRQRYQSHPDAAVQ GPLGSNIEQYIHDLDSNSFELDLQFSEDEKRLLLEKQAGGNPWHQFVENNLILKMGPVDKRKGLFARRRQLLLTEGPHLY YVDPVNKVLKGEIPWSQELRPEAKNFKTFFVHTPNRTYYLMDPSGNAHKWCRKIQEVWRQRYQSHPDAAVQ A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n HUMAN sample 9606 HOMO SAPIENS 511693 ESCHERICHIA COLI BL21 PGEX 1 2.1 0.41 4.20 25 % PEG 4000, 0.1 M SODIUM ACETATE [PH 4.2], 0.3 M AMMONIUM ACETATE chem_comp chem_comp_atom chem_comp_bond database_2 entity pdbx_database_status pdbx_entity_nonpoly repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Other Structure summary 1 0 2004-11-19 1 1 2011-05-08 1 2 2011-07-13 1 3 2024-05-08 _chem_comp.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _entity.pdbx_description _pdbx_database_status.status_code_sf _pdbx_entity_nonpoly.name HIGH RESOLUTION CRYSTAL STRUCTURE OF THE HUMAN PDK1 CATALYTIC DOMAIN STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH STAUROSPORINE STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH UCN-01 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH LY333531 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-2 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-1 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-3 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-8 CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN BOUND TO INOSITOL (1, 3,4,5)-TETRAKISPHOSPHATE CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. PDBE Y PDBE 2004-06-21 REL REL 4PT (2R)-3-{[(S)-{[(2S,3R,5S,6S)-2,6-DIHYDROXY-3,4,5-TRIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-(1-HYDROXY BUTOXY)PROPYL BUTYRATE HOH water 4PT 1550 2 4PT 4PT 1550 A HOH 2001 3 HOH HOH 2001 A HOH 2002 3 HOH HOH 2002 A HOH 2003 3 HOH HOH 2003 A HOH 2004 3 HOH HOH 2004 A HOH 2005 3 HOH HOH 2005 A HOH 2006 3 HOH HOH 2006 A HOH 2007 3 HOH HOH 2007 A HOH 2008 3 HOH HOH 2008 A HOH 2009 3 HOH HOH 2009 A HOH 2010 3 HOH HOH 2010 A HOH 2011 3 HOH HOH 2011 A HOH 2012 3 HOH HOH 2012 A HOH 2013 3 HOH HOH 2013 A HOH 2014 3 HOH HOH 2014 A HOH 2015 3 HOH HOH 2015 A HOH 2016 3 HOH HOH 2016 A HOH 2017 3 HOH HOH 2017 A HOH 2018 3 HOH HOH 2018 A HOH 2019 3 HOH HOH 2019 A HOH 2020 3 HOH HOH 2020 A HOH 2021 3 HOH HOH 2021 A HOH 2022 3 HOH HOH 2022 A HOH 2023 3 HOH HOH 2023 A HOH 2024 3 HOH HOH 2024 A HOH 2025 3 HOH HOH 2025 A HOH 2026 3 HOH HOH 2026 A HOH 2027 3 HOH HOH 2027 A HOH 2028 3 HOH HOH 2028 A HOH 2029 3 HOH HOH 2029 A HOH 2030 3 HOH HOH 2030 A HOH 2031 3 HOH HOH 2031 A HOH 2032 3 HOH HOH 2032 A HOH 2033 3 HOH HOH 2033 A HOH 2034 3 HOH HOH 2034 A HOH 2035 3 HOH HOH 2035 A HOH 2036 3 HOH HOH 2036 A HOH 2037 3 HOH HOH 2037 A HOH 2038 3 HOH HOH 2038 A HOH 2039 3 HOH HOH 2039 A HOH 2040 3 HOH HOH 2040 A HOH 2041 3 HOH HOH 2041 A HOH 2042 3 HOH HOH 2042 A HOH 2043 3 HOH HOH 2043 A HOH 2044 3 HOH HOH 2044 A HOH 2045 3 HOH HOH 2045 A HOH 2046 3 HOH HOH 2046 A HOH 2047 3 HOH HOH 2047 A HOH 2048 3 HOH HOH 2048 A HOH 2049 3 HOH HOH 2049 A HOH 2050 3 HOH HOH 2050 A HOH 2051 3 HOH HOH 2051 A HOH 2052 3 HOH HOH 2052 A HOH 2053 3 HOH HOH 2053 A HOH 2054 3 HOH HOH 2054 A HOH 2055 3 HOH HOH 2055 A HOH 2056 3 HOH HOH 2056 A HOH 2057 3 HOH HOH 2057 A HOH 2058 3 HOH HOH 2058 A HOH 2059 3 HOH HOH 2059 A HOH 2060 3 HOH HOH 2060 A HOH 2061 3 HOH HOH 2061 A HOH 2062 3 HOH HOH 2062 A HOH 2063 3 HOH HOH 2063 A HOH 2064 3 HOH HOH 2064 A HOH 2065 3 HOH HOH 2065 A HOH 2066 3 HOH HOH 2066 A HOH 2067 3 HOH HOH 2067 A HOH 2068 3 HOH HOH 2068 A HOH 2069 3 HOH HOH 2069 A HOH 2070 3 HOH HOH 2070 A HOH 2071 3 HOH HOH 2071 A HOH 2072 3 HOH HOH 2072 A HOH 2073 3 HOH HOH 2073 A HOH 2074 3 HOH HOH 2074 A HOH 2075 3 HOH HOH 2075 A HOH 2076 3 HOH HOH 2076 A HOH 2077 3 HOH HOH 2077 A HOH 2078 3 HOH HOH 2078 A HOH 2079 3 HOH HOH 2079 A HOH 2080 3 HOH HOH 2080 A HOH 2081 3 HOH HOH 2081 A HOH 2082 3 HOH HOH 2082 A HOH 2083 3 HOH HOH 2083 A HOH 2084 3 HOH HOH 2084 A HOH 2085 3 HOH HOH 2085 A HOH 2086 3 HOH HOH 2086 A HOH 2087 3 HOH HOH 2087 A HOH 2088 3 HOH HOH 2088 A HOH 2089 3 HOH HOH 2089 A HOH 2090 3 HOH HOH 2090 A HOH 2091 3 HOH HOH 2091 A HOH 2092 3 HOH HOH 2092 A HOH 2093 3 HOH HOH 2093 A HOH 2094 3 HOH HOH 2094 A HOH 2095 3 HOH HOH 2095 A HOH 2096 3 HOH HOH 2096 A HOH 2097 3 HOH HOH 2097 A HOH 2098 3 HOH HOH 2098 A HOH 2099 3 HOH HOH 2099 A HOH 2100 3 HOH HOH 2100 A HOH 2101 3 HOH HOH 2101 A HOH 2102 3 HOH HOH 2102 A HOH 2103 3 HOH HOH 2103 A HOH 2104 3 HOH HOH 2104 A HOH 2105 3 HOH HOH 2105 A HOH 2106 3 HOH HOH 2106 A HOH 2107 3 HOH HOH 2107 A HOH 2108 3 HOH HOH 2108 A HOH 2109 3 HOH HOH 2109 A HOH 2110 3 HOH HOH 2110 A HOH 2111 3 HOH HOH 2111 A HOH 2112 3 HOH HOH 2112 A HOH 2113 3 HOH HOH 2113 A HOH 2114 3 HOH HOH 2114 A HOH 2115 3 HOH HOH 2115 A HOH 2116 3 HOH HOH 2116 A HOH 2117 3 HOH HOH 2117 A HOH 2118 3 HOH HOH 2118 A HOH 2119 3 HOH HOH 2119 A HOH 2120 3 HOH HOH 2120 A HOH 2121 3 HOH HOH 2121 A HOH 2122 3 HOH HOH 2122 A HOH 2123 3 HOH HOH 2123 A HOH 2124 3 HOH HOH 2124 A HOH 2125 3 HOH HOH 2125 A HOH 2126 3 HOH HOH 2126 A HOH 2127 3 HOH HOH 2127 A HOH 2128 3 HOH HOH 2128 A HOH 2129 3 HOH HOH 2129 A HOH 2130 3 HOH HOH 2130 A HOH 2131 3 HOH HOH 2131 A HOH 2132 3 HOH HOH 2132 A HOH 2133 3 HOH HOH 2133 A HOH 2134 3 HOH HOH 2134 A HOH 2135 3 HOH HOH 2135 A HOH 2136 3 HOH HOH 2136 A HOH 2137 3 HOH HOH 2137 A HOH 2138 3 HOH HOH 2138 A HOH 2139 3 HOH HOH 2139 A HOH 2140 3 HOH HOH 2140 A HOH 2141 3 HOH HOH 2141 A HOH 2142 3 HOH HOH 2142 A HOH 2143 3 HOH HOH 2143 A HOH 2144 3 HOH HOH 2144 A HOH 2145 3 HOH HOH 2145 A HOH 2146 3 HOH HOH 2146 A HOH 2147 3 HOH HOH 2147 A HOH 2148 3 HOH HOH 2148 A HOH 2149 3 HOH HOH 2149 A HOH 2150 3 HOH HOH 2150 A HOH 2151 3 HOH HOH 2151 A HOH 2152 3 HOH HOH 2152 A HOH 2153 3 HOH HOH 2153 A HOH 2154 3 HOH HOH 2154 A HOH 2155 3 HOH HOH 2155 A HOH 2156 3 HOH HOH 2156 A HOH 2157 3 HOH HOH 2157 A HOH 2158 3 HOH HOH 2158 A HOH 2159 3 HOH HOH 2159 A HOH 2160 3 HOH HOH 2160 A HOH 2161 3 HOH HOH 2161 A HOH 2162 3 HOH HOH 2162 A HOH 2163 3 HOH HOH 2163 A n 1 406 A PRO 407 n 2 PRO 407 A LEU 408 n 3 LEU 408 A GLY 409 n 4 GLY 409 A SER 410 n 5 SER 410 A ASN 411 n 6 ASN 411 A ILE 412 n 7 ILE 412 A GLU 413 n 8 GLU 413 A GLN 414 n 9 GLN 414 A TYR 415 n 10 TYR 415 A ILE 416 n 11 ILE 416 A HIS 417 n 12 HIS 417 A ASP 418 n 13 ASP 418 A LEU 419 n 14 LEU 419 A ASP 420 n 15 ASP 420 A SER 421 n 16 SER 421 A ASN 422 n 17 ASN 422 A SER 423 n 18 SER 423 A PHE 424 n 19 PHE 424 A GLU 425 n 20 GLU 425 A LEU 426 n 21 LEU 426 A ASP 427 n 22 ASP 427 A LEU 428 n 23 LEU 428 A GLN 429 n 24 GLN 429 A PHE 430 n 25 PHE 430 A SER 431 n 26 SER 431 A GLU 432 n 27 GLU 432 A ASP 433 n 28 ASP 433 A GLU 434 n 29 GLU 434 A LYS 435 n 30 LYS 435 A ARG 436 n 31 ARG 436 A LEU 437 n 32 LEU 437 A LEU 438 n 33 LEU 438 A LEU 439 n 34 LEU 439 A GLU 440 n 35 GLU 440 A LYS 441 n 36 LYS 441 A GLN 442 n 37 GLN 442 A ALA 443 n 38 ALA 443 A GLY 444 n 39 GLY 444 A GLY 445 n 40 GLY 445 A ASN 446 n 41 ASN 446 A PRO 447 n 42 PRO 447 A TRP 448 n 43 TRP 448 A HIS 449 n 44 HIS 449 A GLN 450 n 45 GLN 450 A PHE 451 n 46 PHE 451 A VAL 452 n 47 VAL 452 A GLU 453 n 48 GLU 453 A ASN 454 n 49 ASN 454 A ASN 455 n 50 ASN 455 A LEU 456 n 51 LEU 456 A ILE 457 n 52 ILE 457 A LEU 458 n 53 LEU 458 A LYS 459 n 54 LYS 459 A MET 460 n 55 MET 460 A GLY 461 n 56 GLY 461 A PRO 462 n 57 PRO 462 A VAL 463 n 58 VAL 463 A ASP 464 n 59 ASP 464 A LYS 465 n 60 LYS 465 A ARG 466 n 61 ARG 466 A LYS 467 n 62 LYS 467 A GLY 468 n 63 GLY 468 A LEU 469 n 64 LEU 469 A PHE 470 n 65 PHE 470 A ALA 471 n 66 ALA 471 A ARG 472 n 67 ARG 472 A ARG 473 n 68 ARG 473 A ARG 474 n 69 ARG 474 A GLN 475 n 70 GLN 475 A LEU 476 n 71 LEU 476 A LEU 477 n 72 LEU 477 A LEU 478 n 73 LEU 478 A THR 479 n 74 THR 479 A GLU 480 n 75 GLU 480 A GLY 481 n 76 GLY 481 A PRO 482 n 77 PRO 482 A HIS 483 n 78 HIS 483 A LEU 484 n 79 LEU 484 A TYR 485 n 80 TYR 485 A TYR 486 n 81 TYR 486 A VAL 487 n 82 VAL 487 A ASP 488 n 83 ASP 488 A PRO 489 n 84 PRO 489 A VAL 490 n 85 VAL 490 A ASN 491 n 86 ASN 491 A LYS 492 n 87 LYS 492 A VAL 493 n 88 VAL 493 A LEU 494 n 89 LEU 494 A LYS 495 n 90 LYS 495 A GLY 496 n 91 GLY 496 A GLU 497 n 92 GLU 497 A ILE 498 n 93 ILE 498 A PRO 499 n 94 PRO 499 A TRP 500 n 95 TRP 500 A SER 501 n 96 SER 501 A GLN 502 n 97 GLN 502 A GLU 503 n 98 GLU 503 A LEU 504 n 99 LEU 504 A ARG 505 n 100 ARG 505 A PRO 506 n 101 PRO 506 A GLU 507 n 102 GLU 507 A ALA 508 n 103 ALA 508 A LYS 509 n 104 LYS 509 A ASN 510 n 105 ASN 510 A PHE 511 n 106 PHE 511 A LYS 512 n 107 LYS 512 A THR 513 n 108 THR 513 A PHE 514 n 109 PHE 514 A PHE 515 n 110 PHE 515 A VAL 516 n 111 VAL 516 A HIS 517 n 112 HIS 517 A THR 518 n 113 THR 518 A PRO 519 n 114 PRO 519 A ASN 520 n 115 ASN 520 A ARG 521 n 116 ARG 521 A THR 522 n 117 THR 522 A TYR 523 n 118 TYR 523 A TYR 524 n 119 TYR 524 A LEU 525 n 120 LEU 525 A MET 526 n 121 MET 526 A ASP 527 n 122 ASP 527 A PRO 528 n 123 PRO 528 A SER 529 n 124 SER 529 A GLY 530 n 125 GLY 530 A ASN 531 n 126 ASN 531 A ALA 532 n 127 ALA 532 A HIS 533 n 128 HIS 533 A LYS 534 n 129 LYS 534 A TRP 535 n 130 TRP 535 A CYS 536 n 131 CYS 536 A ARG 537 n 132 ARG 537 A LYS 538 n 133 LYS 538 A ILE 539 n 134 ILE 539 A GLN 540 n 135 GLN 540 A GLU 541 n 136 GLU 541 A VAL 542 n 137 VAL 542 A TRP 543 n 138 TRP 543 A ARG 544 n 139 ARG 544 A GLN 545 n 140 GLN 545 A ARG 546 n 141 ARG 546 A TYR 547 n 142 TYR 547 A GLN 548 n 143 GLN 548 A SER 549 n 144 SER 549 A HIS 550 n 145 HIS 550 A n 146 551 A n 147 552 A n 148 553 A n 149 554 A n 150 555 A n 151 556 A 0.1679 0.1263 -0.1429 1.4071 -0.5604 0.4956 -0.0012 -0.0141 0.0265 -0.0763 0.0301 -0.0092 0.0443 -0.0069 -0.0288 -0.0377 -0.0001 -0.0004 0.0133 -0.0049 -0.0088 refined 10.5388 27.1746 24.0723 X-RAY DIFFRACTION 0.4742 0.2713 -0.2195 1.4621 -0.8330 0.4845 0.0278 0.0203 0.0334 -0.0906 0.0671 0.0777 0.0498 0.0051 -0.0950 -0.0232 -0.0101 -0.0146 -0.0096 -0.0199 -0.0304 refined 9.5684 26.7739 22.8190 X-RAY DIFFRACTION A 414 A 466 X-RAY DIFFRACTION 1 A 472 A 487 X-RAY DIFFRACTION 1 A 494 A 543 X-RAY DIFFRACTION 1 A 408 A 413 X-RAY DIFFRACTION 2 A 466 A 471 X-RAY DIFFRACTION 2 A 544 A 549 X-RAY DIFFRACTION 2 A 488 A 493 X-RAY DIFFRACTION 2 author_and_software_defined_assembly PQS 1 monomeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N LEU 419 A N LEU 14 A O SER 423 A O SER 18 A N LEU 426 A N LEU 21 A O LEU 458 A O LEU 53 A N LYS 467 A N LYS 62 A O PHE 470 A O PHE 65 A N THR 479 A N THR 74 A O HIS 483 A O HIS 78 A N ASP 488 A N ASP 83 A O VAL 493 A O VAL 88 A N LEU 419 A N LEU 14 A O SER 423 A O SER 18 A N LEU 426 A N LEU 21 A O LEU 458 A O LEU 53 A N ARG 466 A N ARG 61 A O TYR 524 A O TYR 119 A N LEU 525 A N LEU 120 A O PHE 514 A O PHE 109 A N HIS 517 A N HIS 112 A O ARG 505 A O ARG 100 1 A CG LEU 408 A CG LEU 3 1 Y 1 A CD1 LEU 408 A CD1 LEU 3 1 Y 1 A CD2 LEU 408 A CD2 LEU 3 1 Y 1 A CG GLU 503 A CG GLU 98 1 Y 1 A CD GLU 503 A CD GLU 98 1 Y 1 A OE1 GLU 503 A OE1 GLU 98 1 Y 1 A OE2 GLU 503 A OE2 GLU 98 1 Y 1 A CG LYS 509 A CG LYS 104 1 Y 1 A CD LYS 509 A CD LYS 104 1 Y 1 A CE LYS 509 A CE LYS 104 1 Y 1 A NZ LYS 509 A NZ LYS 104 1 Y 1 A CA HIS 550 A CA HIS 145 1 Y 1 A C HIS 550 A C HIS 145 1 Y 1 A O HIS 550 A O HIS 145 1 Y 1 A CB HIS 550 A CB HIS 145 1 Y 1 A CG HIS 550 A CG HIS 145 1 Y 1 A ND1 HIS 550 A ND1 HIS 145 1 Y 1 A CD2 HIS 550 A CD2 HIS 145 1 Y 1 A CE1 HIS 550 A CE1 HIS 145 1 Y 1 A NE2 HIS 550 A NE2 HIS 145 1 Y 1 A C0L 4PT 1550 B C0L 4PT 1 1 N 1 A O0M 4PT 1550 B O0M 4PT 1 1 N 1 A C0N 4PT 1550 B C0N 4PT 1 1 N 1 A C0P 4PT 1550 B C0P 4PT 1 1 N 1 A C0Q 4PT 1550 B C0Q 4PT 1 1 N 1 A C0G 4PT 1550 B C0G 4PT 1 1 N 1 A O0H 4PT 1550 B O0H 4PT 1 1 N 1 A C0I 4PT 1550 B C0I 4PT 1 1 N 1 A C0J 4PT 1550 B C0J 4PT 1 1 N 1 A C0K 4PT 1550 B C0K 4PT 1 1 N 1 A GLY 406 A GLY 1 1 Y 1 A PRO 551 A PRO 146 1 Y 1 A ASP 552 A ASP 147 1 Y 1 A ALA 553 A ALA 148 1 Y 1 A ALA 554 A ALA 149 1 Y 1 A VAL 555 A VAL 150 1 Y 1 A GLN 556 A GLN 151 1 Y 1 A A NE2 O GLN HOH 429 2041 2.13 1 7.53 0.90 118.30 125.83 A A A CB CG OD2 ASP ASP ASP 464 464 464 N 1 A A O O HOH HOH 2025 2108 2.09 1_555 1_556 1 A A O O HOH HOH 2104 2147 2.17 1_555 1_554 1 A ASN 411 39.46 64.84 1 A PHE 470 -121.79 -137.16 1 A ASN 510 -160.56 -154.91 1 A GLN 548 -119.56 -163.18 1 A SER 549 67.85 151.93 26.94 1.58000 0.00000 0.06000 -0.83000 0.00000 -0.73000 0.972 0.956 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIDE CHAINS OF SOME DISORDERED RESIDUES WERE REFINED EITHER WITH THE OCCUPANCY SET TO 0.02, OR THE RESIDUE WAS MUTATED TO ALA. THE ACYL-CHAINS OF THE LIGAND WERE NOT MODELLED DUE TO DISORDER. 0.236 0.182 0.183 1.45 25.00 545 25241 2.100 99.7 4.471 0.073 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.089 0.081 0.80 0.80 1.20 PDK1PH INSP4 MODEL MAXIMUM LIKELIHOOD BABINET MODEL WITH MASK 1.45 25.00 163 1390 33 0 1194 0.016 0.022 1273 0.002 0.020 1115 1.703 1.961 1731 0.860 3.001 2588 6.622 5.000 142 34.693 23.731 67 13.710 15.000 219 17.708 15.000 10 0.109 0.200 184 0.008 0.020 1363 0.001 0.020 263 0.221 0.200 267 0.200 0.200 1116 0.181 0.200 613 0.107 0.200 672 0.159 0.200 117 0.166 0.200 8 0.240 0.200 39 0.274 0.200 17 1.727 1.500 746 0.745 1.500 287 2.305 2.000 1168 3.614 3.000 612 4.923 4.500 563 0.3080 0.3390 1.49 44 1834 20 100.00 1.450 30.000 1W1G 25810 2.000 0.05000 1 8.8000 2.900 99.7 0.37000 1.45 1.50 2.500 1 2.70 100.0 refinement REFMAC 5.2.0003 data reduction CrystalClear data scaling d*TREK phasing CNS Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to DiC4-phosphatidylinositol (3,4,5)-trisphosphate 1 N N 2 N N 3 N N A ASN 411 A ASN 6 HELX_P A GLN 414 A GLN 9 5 1 4 A SER 431 A SER 26 HELX_P A ASN 446 A ASN 41 1 2 16 A TRP 448 A TRP 43 HELX_P A VAL 452 A VAL 47 5 3 5 A ASN 531 A ASN 126 HELX_P A GLN 548 A GLN 143 1 4 18 TRANSFERASE TRANSFERASE, PDK1, PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1, PKB, PLECKSTRIN HOMOLOGY DOMAIN, INOSITOL PHOSPHATE, PHOSPHOINOSITIDE, SIGNAL TRANSDUCTION, PI3-KINASE, PIP3 SERINE/THREONINE PROTEIN KINASE A GLY 481 A GLY 76 1 A PRO 482 A PRO 77 -0.22 1W1G PDB 1 1W1G PDPK_HUMAN UNP 1 O15530 406 408 1W1G 406 408 1W1G A 1 1 3 409 556 1W1G 409 556 O15530 A 2 4 151 6 6 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A ILE 416 A ILE 11 A ASP 420 A ASP 15 A SER 423 A SER 18 A LEU 426 A LEU 21 A ILE 457 A ILE 52 A LYS 467 A LYS 62 A PHE 470 A PHE 65 A THR 479 A THR 74 A HIS 483 A HIS 78 A ASP 488 A ASP 83 A VAL 493 A VAL 88 A ILE 498 A ILE 93 A ILE 416 A ILE 11 A ASP 420 A ASP 15 A SER 423 A SER 18 A LEU 426 A LEU 21 A ILE 457 A ILE 52 A LYS 467 A LYS 62 A ARG 521 A ARG 116 A MET 526 A MET 121 A THR 513 A THR 108 A THR 518 A THR 113 A ARG 505 A ARG 100 A ALA 508 A ALA 103 BINDING SITE FOR RESIDUE 4PT A1550 Software 14 A HIS 417 A HIS 12 14 1_555 A LEU 419 A LEU 14 14 1_555 A LYS 465 A LYS 60 14 1_555 A LYS 467 A LYS 62 14 1_555 A ARG 472 A ARG 67 14 1_555 A ARG 474 A ARG 69 14 1_555 A TYR 486 A TYR 81 14 1_555 A LYS 495 A LYS 90 14 1_555 A ARG 521 A ARG 116 14 1_555 A HOH 2029 C HOH 14 1_555 A HOH 2084 C HOH 14 1_555 A HOH 2155 C HOH 14 1_555 A HOH 2156 C HOH 14 1_555 A HOH 2157 C HOH 14 1_555 4 P 1 21 1