0.017854 0.010308 0.000000 -0.000000 0.020616 0.000000 0.000000 -0.000000 0.008689 0.000000 0.000000 0.000000 Fansa, E.K. Martin-Gago, P. Waldmann, H. Wittinghofer, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.000 90.000 120.000 56.010 56.010 115.090 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 C30 H39 Cl N6 O4 S2 647.251 ~{N}1-[(4-chlorophenyl)methyl]-~{N}1-cyclopentyl-~{N}4-[[2-(methylamino)pyrimidin-4-yl]methyl]-~{N}4-(piperidin-4-ylmethyl)benzene-1,4-disulfonamide non-polymer 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 N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O 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 N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O 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 N N 75 R C N 76 N C N 77 N O N 78 N C N 79 N S N 80 N O N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H Y 88 N C Y 89 N C Y 90 N C Y 91 N N Y 92 N N N 93 N C N 94 N N Y 95 N C N 96 N C N 97 N N N 98 N C N 99 N C N 100 N C N 101 N C N 102 N N N 103 N C N 104 N C N 105 N S N 106 N O N 107 N O Y 108 N C Y 109 N C Y 110 N C Y 111 N C Y 112 N C Y 113 N C N 114 N S N 115 N O N 116 N O N 117 N N N 118 N C N 119 N C N 120 N C N 121 N C N 122 N C N 123 N C Y 124 N C Y 125 N C Y 126 N C Y 127 N C N 128 N CL Y 129 N C Y 130 N C 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 H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H 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 H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N H 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 H N 168 N H N 169 N H N 170 N N N 171 S C N 172 N C N 173 N O N 174 N C N 175 N C N 176 N C N 177 N O N 178 N N N 179 N O 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 H N 188 N H N 189 N H N 190 N N N 191 S C N 192 N C N 193 N O N 194 N C N 195 N C N 196 N C N 197 N O N 198 N O N 199 N O 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 H N 207 N H N 208 N H N 209 N N N 210 N C N 211 N C N 212 N O N 213 N O N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N N N 220 S C N 221 N C N 222 N O N 223 N C Y 224 N C Y 225 N N Y 226 N C Y 227 N C Y 228 N N N 229 N O 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 H N 238 N H N 239 N H N 240 N O N 241 N H N 242 N H N 243 N N N 244 S C N 245 N C N 246 N O N 247 S C N 248 N C N 249 N C N 250 N C N 251 N O 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 H N 263 N H N 264 N H N 265 N N N 266 S C N 267 N C N 268 N O N 269 N C N 270 N C N 271 N C N 272 N C N 273 N O 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 H N 285 N H N 286 N H N 287 N N N 288 S C N 289 N C N 290 N O N 291 N C N 292 N C N 293 N C N 294 N C N 295 N N N 296 N O 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 H N 310 N H N 311 N H N 312 N N N 313 S C N 314 N C N 315 N O N 316 N C N 317 N C N 318 N S N 319 N C N 320 N O 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 H N 330 N H N 331 N H N 332 N N N 333 S C N 334 N C N 335 N O N 336 N C Y 337 N C Y 338 N C Y 339 N C Y 340 N C Y 341 N C Y 342 N C N 343 N O 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 H N 353 N H N 354 N H N 355 N N N 356 S C N 357 N C N 358 N O N 359 N C N 360 N C N 361 N C N 362 N O 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 H N 370 N H N 371 N H N 372 N N N 373 S C N 374 N C N 375 N O N 376 N C N 377 N O N 378 N O N 379 N H N 380 N H N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N N N 387 S C N 388 N C N 389 N O N 390 R C N 391 N O N 392 N C N 393 N O 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 H N 401 N H N 402 N H N 403 N N N 404 S C N 405 N C N 406 N O N 407 N C Y 408 N C Y 409 N C Y 410 N C Y 411 N N Y 412 N C Y 413 N C Y 414 N C Y 415 N C Y 416 N C N 417 N O 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 H N 428 N H N 429 N H N 430 N N N 431 S C N 432 N C N 433 N O N 434 N C Y 435 N C Y 436 N C Y 437 N C Y 438 N C Y 439 N C Y 440 N C N 441 N O N 442 N O 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 H N 452 N H N 453 N H N 454 N N N 455 S C N 456 N C N 457 N O N 458 N C N 459 N C N 460 N C N 461 N O 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 470 N H N 471 N H N 472 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 doub 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 sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub 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 sing N 33 N doub 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 sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub 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 sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub 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 doub 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 Y 84 N doub Y 85 N sing Y 86 N sing N 87 N doub Y 88 N doub N 89 N doub Y 90 N doub N 91 N sing N 92 N sing N 93 N sing N 94 N sing Y 95 N sing N 96 N sing N 97 N sing Y 98 N doub Y 99 N sing N 100 N sing N 101 N sing N 102 N sing Y 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing Y 108 N doub N 109 N sing Y 110 N doub N 111 N sing N 112 N sing Y 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 Y 120 N doub Y 121 N sing N 122 N doub N 123 N doub N 124 N sing N 125 N sing Y 126 N sing Y 127 N doub Y 128 N doub Y 129 N sing 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 sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing 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 sing 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 sing 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 doub N 176 N sing 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 doub N 184 N sing N 185 N sing N 186 N sing N 187 N sing 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 doub N 195 N sing 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 doub N 203 N sing N 204 N sing N 205 N sing 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 doub N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N doub N 222 N sing N 223 N sing N 224 N sing N 225 N sing Y 226 N sing Y 227 N doub Y 228 N doub N 229 N sing Y 230 N sing N 231 N sing Y 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing 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 doub 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 sing 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 doub 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 sing 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 doub 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 sing 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 doub 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 sing N 323 N sing N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N sing N 329 N doub N 330 N sing N 331 N sing N 332 N sing N 333 N sing Y 334 N doub Y 335 N sing Y 336 N sing N 337 N sing Y 338 N doub N 339 N sing Y 340 N doub N 341 N sing Y 342 N sing N 343 N sing N 344 N sing N 345 N sing 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 doub 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 sing 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 doub N 370 N sing N 371 N sing N 372 N sing N 373 N sing N 374 N sing N 375 N sing 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 doub 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 sing N 392 N sing N 393 N sing N 394 N sing N 395 N sing N 396 N sing N 397 N sing N 398 N doub N 399 N sing N 400 N sing N 401 N sing N 402 N sing Y 403 N doub Y 404 N sing Y 405 N sing N 406 N sing Y 407 N doub Y 408 N sing Y 409 N sing N 410 N sing Y 411 N sing Y 412 N doub N 413 N sing Y 414 N doub N 415 N sing Y 416 N sing N 417 N sing N 418 N sing N 419 N sing N 420 N sing N 421 N sing N 422 N sing N 423 N sing N 424 N sing N 425 N sing N 426 N doub N 427 N sing N 428 N sing N 429 N sing N 430 N sing Y 431 N doub Y 432 N sing Y 433 N sing N 434 N sing Y 435 N doub N 436 N sing Y 437 N doub N 438 N sing Y 439 N sing N 440 N sing N 441 N sing N 442 N sing N 443 N sing 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 doub N 451 N sing N 452 N sing N 453 N sing N 454 N sing N 455 N sing N 456 N sing N 457 N sing N 458 N sing N 459 N sing N 460 N sing N 461 N sing GE Angew. Chem. Int. Ed. Engl. ACIEAY 0179 1521-3773 56 2423 2428 10.1002/anie.201610957 28106325 A PDE6 delta-KRas Inhibitor Chemotype with up to Seven H-Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2. 2017 10.2210/pdb5ml3/pdb pdb_00005ml3 100 1 PIXEL 2014-12-04 DECTRIS PILATUS3 6M SINGLE WAVELENGTH M x-ray 1 0.978 1.0 X10SA SLS 0.978 SYNCHROTRON SLS BEAMLINE X10SA 17309.793 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta 1 man polymer 647.251 ~{N}1-[(4-chlorophenyl)methyl]-~{N}1-cyclopentyl-~{N}4-[[2-(methylamino)pyrimidin-4-yl]methyl]-~{N}4-(piperidin-4-ylmethyl)benzene-1,4-disulfonamide 1 syn non-polymer 18.015 water 180 nat water GMP-PDE delta,Protein p17 no no SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVY FKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVY FKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV B 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 Human sample 1 149 PDE6D, PDED 9606 Homo sapiens 562 Escherichia coli Biological sequence 1 3.02 59.28 VAPOR DIFFUSION 0.2 M NaOAc, 0.1 M Na3Cit, pH 5.5, 10 % PEG 4000 293 chem_comp_atom chem_comp_bond database_2 pdbx_audit_support pdbx_initial_refinement_model repository Initial release Database references Author supporting evidence Data collection Database references Refinement description 1 0 2017-02-01 1 1 2017-02-22 1 2 2024-01-17 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_audit_support.funding_organization Germany SFB SFB 642 Germany European Research Council ERC Grant 268782 N PDBE Y PDBE 2016-12-06 REL REL DL3 ~{N}1-[(4-chlorophenyl)methyl]-~{N}1-cyclopentyl-~{N}4-[[2-(methylamino)pyrimidin-4-yl]methyl]-~{N}4-(piperidin-4-ylmethyl)benzene-1,4-disulfonamide HOH water 3T5G PDB experimental model DRG 1 2 DL3 DL3 201 B HOH 178 3 HOH HOH 301 B HOH 53 3 HOH HOH 302 B HOH 56 3 HOH HOH 303 B HOH 97 3 HOH HOH 304 B HOH 71 3 HOH HOH 305 B HOH 179 3 HOH HOH 306 B HOH 127 3 HOH HOH 307 B HOH 7 3 HOH HOH 308 B HOH 148 3 HOH HOH 309 B HOH 152 3 HOH HOH 310 B HOH 112 3 HOH HOH 311 B HOH 205 3 HOH HOH 312 B HOH 186 3 HOH HOH 313 B HOH 3 3 HOH HOH 314 B HOH 23 3 HOH HOH 315 B HOH 55 3 HOH HOH 316 B HOH 183 3 HOH HOH 317 B HOH 116 3 HOH HOH 318 B HOH 48 3 HOH HOH 319 B HOH 120 3 HOH HOH 320 B HOH 164 3 HOH HOH 321 B HOH 51 3 HOH HOH 322 B HOH 26 3 HOH HOH 323 B HOH 102 3 HOH HOH 324 B HOH 59 3 HOH HOH 325 B HOH 10 3 HOH HOH 326 B HOH 44 3 HOH HOH 327 B HOH 16 3 HOH HOH 328 B HOH 46 3 HOH HOH 329 B HOH 190 3 HOH HOH 330 B HOH 91 3 HOH HOH 331 B HOH 49 3 HOH HOH 332 B HOH 90 3 HOH HOH 333 B HOH 68 3 HOH HOH 334 B HOH 98 3 HOH HOH 335 B HOH 153 3 HOH HOH 336 B HOH 158 3 HOH HOH 337 B HOH 82 3 HOH HOH 338 B HOH 195 3 HOH HOH 339 B HOH 162 3 HOH HOH 340 B HOH 151 3 HOH HOH 341 B HOH 95 3 HOH HOH 342 B HOH 54 3 HOH HOH 343 B HOH 63 3 HOH HOH 344 B HOH 38 3 HOH HOH 345 B HOH 24 3 HOH HOH 346 B HOH 145 3 HOH HOH 347 B HOH 88 3 HOH HOH 348 B HOH 14 3 HOH HOH 349 B HOH 5 3 HOH HOH 350 B HOH 36 3 HOH HOH 351 B HOH 108 3 HOH HOH 352 B HOH 103 3 HOH HOH 353 B HOH 61 3 HOH HOH 354 B HOH 12 3 HOH HOH 355 B HOH 94 3 HOH HOH 356 B HOH 57 3 HOH HOH 357 B HOH 64 3 HOH HOH 358 B HOH 81 3 HOH HOH 359 B HOH 172 3 HOH HOH 360 B HOH 60 3 HOH HOH 361 B HOH 133 3 HOH HOH 362 B HOH 197 3 HOH HOH 363 B HOH 198 3 HOH HOH 364 B HOH 22 3 HOH HOH 365 B HOH 117 3 HOH HOH 366 B HOH 170 3 HOH HOH 367 B HOH 66 3 HOH HOH 368 B HOH 87 3 HOH HOH 369 B HOH 92 3 HOH HOH 370 B HOH 2 3 HOH HOH 371 B HOH 33 3 HOH HOH 372 B HOH 118 3 HOH HOH 373 B HOH 70 3 HOH HOH 374 B HOH 30 3 HOH HOH 375 B HOH 21 3 HOH HOH 376 B HOH 37 3 HOH HOH 377 B HOH 113 3 HOH HOH 378 B HOH 176 3 HOH HOH 379 B HOH 200 3 HOH HOH 380 B HOH 19 3 HOH HOH 381 B HOH 35 3 HOH HOH 382 B HOH 20 3 HOH HOH 383 B HOH 9 3 HOH HOH 384 B HOH 34 3 HOH HOH 385 B HOH 58 3 HOH HOH 386 B HOH 74 3 HOH HOH 387 B HOH 41 3 HOH HOH 388 B HOH 111 3 HOH HOH 389 B HOH 157 3 HOH HOH 390 B HOH 173 3 HOH HOH 391 B HOH 40 3 HOH HOH 392 B HOH 155 3 HOH HOH 393 B HOH 75 3 HOH HOH 394 B HOH 160 3 HOH HOH 395 B HOH 80 3 HOH HOH 396 B HOH 39 3 HOH HOH 397 B HOH 86 3 HOH HOH 398 B HOH 13 3 HOH HOH 399 B HOH 6 3 HOH HOH 400 B HOH 201 3 HOH HOH 401 B HOH 119 3 HOH HOH 402 B HOH 193 3 HOH HOH 403 B HOH 184 3 HOH HOH 404 B HOH 101 3 HOH HOH 405 B HOH 156 3 HOH HOH 406 B HOH 121 3 HOH HOH 407 B HOH 72 3 HOH HOH 408 B HOH 65 3 HOH HOH 409 B HOH 4 3 HOH HOH 410 B HOH 202 3 HOH HOH 411 B HOH 50 3 HOH HOH 412 B HOH 47 3 HOH HOH 413 B HOH 154 3 HOH HOH 414 B HOH 67 3 HOH HOH 415 B HOH 31 3 HOH HOH 416 B HOH 29 3 HOH HOH 417 B HOH 8 3 HOH HOH 418 B HOH 165 3 HOH HOH 419 B HOH 123 3 HOH HOH 420 B HOH 126 3 HOH HOH 421 B HOH 15 3 HOH HOH 422 B HOH 18 3 HOH HOH 423 B HOH 177 3 HOH HOH 424 B HOH 159 3 HOH HOH 425 B HOH 27 3 HOH HOH 426 B HOH 122 3 HOH HOH 427 B HOH 42 3 HOH HOH 428 B HOH 196 3 HOH HOH 429 B HOH 181 3 HOH HOH 430 B HOH 45 3 HOH HOH 431 B HOH 96 3 HOH HOH 432 B HOH 52 3 HOH HOH 433 B HOH 77 3 HOH HOH 434 B HOH 43 3 HOH HOH 435 B HOH 130 3 HOH HOH 436 B HOH 182 3 HOH HOH 437 B HOH 25 3 HOH HOH 438 B HOH 93 3 HOH HOH 439 B HOH 125 3 HOH HOH 440 B HOH 62 3 HOH HOH 441 B HOH 11 3 HOH HOH 442 B HOH 114 3 HOH HOH 443 B HOH 137 3 HOH HOH 444 B HOH 79 3 HOH HOH 445 B HOH 199 3 HOH HOH 446 B HOH 194 3 HOH HOH 447 B HOH 163 3 HOH HOH 448 B HOH 28 3 HOH HOH 449 B HOH 124 3 HOH HOH 450 B HOH 185 3 HOH HOH 451 B HOH 89 3 HOH HOH 452 B HOH 189 3 HOH HOH 453 B HOH 84 3 HOH HOH 454 B HOH 106 3 HOH HOH 455 B HOH 73 3 HOH HOH 456 B HOH 131 3 HOH HOH 457 B HOH 168 3 HOH HOH 458 B HOH 76 3 HOH HOH 459 B HOH 188 3 HOH HOH 460 B HOH 110 3 HOH HOH 461 B HOH 167 3 HOH HOH 462 B HOH 132 3 HOH HOH 463 B HOH 69 3 HOH HOH 464 B HOH 150 3 HOH HOH 465 B HOH 128 3 HOH HOH 466 B HOH 85 3 HOH HOH 467 B HOH 203 3 HOH HOH 468 B HOH 109 3 HOH HOH 469 B HOH 147 3 HOH HOH 470 B HOH 99 3 HOH HOH 471 B HOH 192 3 HOH HOH 472 B HOH 129 3 HOH HOH 473 B HOH 191 3 HOH HOH 474 B HOH 161 3 HOH HOH 475 B HOH 169 3 HOH HOH 476 B HOH 180 3 HOH HOH 477 B HOH 166 3 HOH HOH 478 B HOH 204 3 HOH HOH 479 B HOH 115 3 HOH HOH 480 B SER 2 n 1 SER 2 B ALA 3 n 2 ALA 3 B LYS 4 n 3 LYS 4 B ASP 5 n 4 ASP 5 B GLU 6 n 5 GLU 6 B ARG 7 n 6 ARG 7 B ALA 8 n 7 ALA 8 B ARG 9 n 8 ARG 9 B GLU 10 n 9 GLU 10 B ILE 11 n 10 ILE 11 B LEU 12 n 11 LEU 12 B ARG 13 n 12 ARG 13 B GLY 14 n 13 GLY 14 B PHE 15 n 14 PHE 15 B LYS 16 n 15 LYS 16 B LEU 17 n 16 LEU 17 B ASN 18 n 17 ASN 18 B TRP 19 n 18 TRP 19 B MET 20 n 19 MET 20 B ASN 21 n 20 ASN 21 B LEU 22 n 21 LEU 22 B ARG 23 n 22 ARG 23 B ASP 24 n 23 ASP 24 B ALA 25 n 24 ALA 25 B ALA 26 n 25 GLU 26 B THR 27 n 26 THR 27 B GLY 28 n 27 GLY 28 B LYS 29 n 28 LYS 29 B ILE 30 n 29 ILE 30 B LEU 31 n 30 LEU 31 B TRP 32 n 31 TRP 32 B GLN 33 n 32 GLN 33 B GLY 34 n 33 GLY 34 B THR 35 n 34 THR 35 B GLU 36 n 35 GLU 36 B ASP 37 n 36 ASP 37 B LEU 38 n 37 LEU 38 B SER 39 n 38 SER 39 B VAL 40 n 39 VAL 40 B PRO 41 n 40 PRO 41 B GLY 42 n 41 GLY 42 B VAL 43 n 42 VAL 43 B GLU 44 n 43 GLU 44 B HIS 45 n 44 HIS 45 B GLU 46 n 45 GLU 46 B ALA 47 n 46 ALA 47 B ARG 48 n 47 ARG 48 B VAL 49 n 48 VAL 49 B PRO 50 n 49 PRO 50 B LYS 51 n 50 LYS 51 B LYS 52 n 51 LYS 52 B ILE 53 n 52 ILE 53 B LEU 54 n 53 LEU 54 B LYS 55 n 54 LYS 55 B CYS 56 n 55 CYS 56 B LYS 57 n 56 LYS 57 B ALA 58 n 57 ALA 58 B VAL 59 n 58 VAL 59 B SER 60 n 59 SER 60 B ARG 61 n 60 ARG 61 B GLU 62 n 61 GLU 62 B LEU 63 n 62 LEU 63 B ASN 64 n 63 ASN 64 B PHE 65 n 64 PHE 65 B SER 66 n 65 SER 66 B SER 67 n 66 SER 67 B THR 68 n 67 THR 68 B GLU 69 n 68 GLU 69 B GLN 70 n 69 GLN 70 B MET 71 n 70 MET 71 B GLU 72 n 71 GLU 72 B LYS 73 n 72 LYS 73 B PHE 74 n 73 PHE 74 B ARG 75 n 74 ARG 75 B LEU 76 n 75 LEU 76 B GLU 77 n 76 GLU 77 B GLN 78 n 77 GLN 78 B LYS 79 n 78 LYS 79 B VAL 80 n 79 VAL 80 B TYR 81 n 80 TYR 81 B PHE 82 n 81 PHE 82 B LYS 83 n 82 LYS 83 B GLY 84 n 83 GLY 84 B GLN 85 n 84 GLN 85 B CYS 86 n 85 CYS 86 B LEU 87 n 86 LEU 87 B GLU 88 n 87 GLU 88 B GLU 89 n 88 GLU 89 B TRP 90 n 89 TRP 90 B PHE 91 n 90 PHE 91 B PHE 92 n 91 PHE 92 B GLU 93 n 92 GLU 93 B PHE 94 n 93 PHE 94 B GLY 95 n 94 GLY 95 B PHE 96 n 95 PHE 96 B VAL 97 n 96 VAL 97 B ILE 98 n 97 ILE 98 B PRO 99 n 98 PRO 99 B ASN 100 n 99 ASN 100 B SER 101 n 100 SER 101 B THR 102 n 101 THR 102 B ASN 103 n 102 ASN 103 B THR 104 n 103 THR 104 B TRP 105 n 104 TRP 105 B GLN 106 n 105 GLN 106 B SER 107 n 106 SER 107 B LEU 108 n 107 LEU 108 B ILE 109 n 108 ILE 109 B GLU 110 n 109 GLU 110 B ALA 111 n 110 ALA 111 B ALA 112 n 111 ALA 112 B PRO 113 n 112 PRO 113 B GLU 114 n 113 GLU 114 B SER 115 n 114 SER 115 B GLN 116 n 115 GLN 116 B MET 117 n 116 MET 117 B MET 118 n 117 MET 118 B PRO 119 n 118 PRO 119 B ALA 120 n 119 ALA 120 B SER 121 n 120 SER 121 B VAL 122 n 121 VAL 122 B LEU 123 n 122 LEU 123 B THR 124 n 123 THR 124 B GLY 125 n 124 GLY 125 B ASN 126 n 125 ASN 126 B VAL 127 n 126 VAL 127 B ILE 128 n 127 ILE 128 B ILE 129 n 128 ILE 129 B GLU 130 n 129 GLU 130 B THR 131 n 130 THR 131 B LYS 132 n 131 LYS 132 B PHE 133 n 132 PHE 133 B PHE 134 n 133 PHE 134 B ASP 135 n 134 ASP 135 B ASP 136 n 135 ASP 136 B ASP 137 n 136 ASP 137 B LEU 138 n 137 LEU 138 B LEU 139 n 138 LEU 139 B VAL 140 n 139 VAL 140 B SER 141 n 140 SER 141 B THR 142 n 141 THR 142 B SER 143 n 142 SER 143 B ARG 144 n 143 ARG 144 B VAL 145 n 144 VAL 145 B ARG 146 n 145 ARG 146 B LEU 147 n 146 LEU 147 B PHE 148 n 147 PHE 148 B TYR 149 n 148 TYR 149 B VAL 150 n 149 VAL 150 B author_and_software_defined_assembly PISA 1 monomeric 0 0 8100 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 B O LEU 31 A O LEU 30 B N LEU 22 A N LEU 21 B N TRP 19 A N TRP 18 B O ASN 64 A O ASN 63 B N VAL 59 A N VAL 58 B O ILE 109 A O ILE 108 B N VAL 49 A N VAL 48 B O PHE 148 A O PHE 147 B O VAL 140 A O VAL 139 B N PHE 133 A N PHE 132 B O ILE 128 A O ILE 127 B N TYR 81 A N TYR 80 B N VAL 80 A N VAL 79 B O LEU 87 A O LEU 86 1 B CG GLU 10 A CG GLU 9 1 Y 1 B CD GLU 10 A CD GLU 9 1 Y 1 B OE1 GLU 10 A OE1 GLU 9 1 Y 1 B OE2 GLU 10 A OE2 GLU 9 1 Y 1 B CG GLU 26 A CG GLU 25 1 Y 1 B CD GLU 26 A CD GLU 25 1 Y 1 B OE1 GLU 26 A OE1 GLU 25 1 Y 1 B OE2 GLU 26 A OE2 GLU 25 1 Y 1 B CG GLU 36 A CG GLU 35 1 Y 1 B CD GLU 36 A CD GLU 35 1 Y 1 B OE1 GLU 36 A OE1 GLU 35 1 Y 1 B OE2 GLU 36 A OE2 GLU 35 1 Y 1 B CG GLU 72 A CG GLU 71 1 Y 1 B CD GLU 72 A CD GLU 71 1 Y 1 B OE1 GLU 72 A OE1 GLU 71 1 Y 1 B OE2 GLU 72 A OE2 GLU 71 1 Y 1 B CG GLN 106 A CG GLN 105 1 Y 1 B CD GLN 106 A CD GLN 105 1 Y 1 B OE1 GLN 106 A OE1 GLN 105 1 Y 1 B NE2 GLN 106 A NE2 GLN 105 1 Y 1 B CG GLU 114 A CG GLU 113 1 Y 1 B CD GLU 114 A CD GLU 113 1 Y 1 B OE1 GLU 114 A OE1 GLU 113 1 Y 1 B OE2 GLU 114 A OE2 GLU 113 1 Y 1 B B C N ARG VAL 144 145 1.16 1 -16.95 2.20 117.20 100.25 B B B CA C N PHE PHE PHE 133 133 134 Y 1 15.04 1.60 122.70 137.74 B B B O C N PHE PHE PHE 133 133 134 Y 1 B B C N ARG VAL 144 145 -0.180 0.023 1.336 1.156 Y 1 B GLU 114 -97.74 41.85 1 B ASP 136 59.74 -114.79 61.310 20.7880 10.340 0.3600 0.3600 -0.0000 0.3600 -0.0000 -1.1800 0.9650 0.9570 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY 0.2034 0.1891 0.1898 1.4000 44.7000 2098 39854 5.0000 99.9600 0.9080 0.0360 RANDOM 1 THROUGHOUT 0.000 MOLECULAR REPLACEMENT 0.0560 0.0560 0.8000 0.8000 1.2000 3T5G 1.4000 44.7000 180 1416 21.73 33.46 43 0 1193 149 0.011 0.020 1320 0.003 0.020 1276 1.665 1.985 1792 0.998 3.013 2934 6.039 5.000 159 39.260 22.951 61 11.861 15.000 235 16.345 15.000 12 0.127 0.200 195 0.006 0.020 1460 0.001 0.020 328 0.2830 0.0000 0.2670 1.4360 153 2902 3055 20 99.9700 1.4 44.700 5ML3 39854 0.075 1 16.5 9.6 100 0.64 1.4 1.5 3.4 1 9.4 100 data scaling XSCALE refinement REFMAC 5.7.0032 data extraction PDB_EXTRACT 3.22 data reduction XDS phasing MOLREP N The crystal structure of PDE6D in complex to Deltasonamide1 1 N N 2 N N 3 N N B SER 2 A SER 1 HELX_P B GLY 14 A GLY 13 1 AA1 13 B LYS 52 A LYS 51 HELX_P B CYS 56 A CYS 55 5 AA2 5 B PRO 119 A PRO 118 HELX_P B THR 124 A THR 123 1 AA3 6 LIPID BINDING PROTEIN Prenyl binding protein, farnesylated KRas, plasma membrane, Arl2, Lipid binding protein B PRO 113 A PRO 112 1 B GLU 114 A GLU 113 -27.43 PDE6D_HUMAN UNP 1 2 O43924 SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVY FKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 2 150 5ML3 2 150 O43924 B 1 1 149 4 5 anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel B ILE 30 A ILE 29 B GLY 34 A GLY 33 B PHE 15 A PHE 14 B ASP 24 A ASP 23 B ALA 58 A ALA 57 B SER 67 A SER 66 B SER 101 A SER 100 B GLU 110 A GLU 109 B GLU 44 A GLU 43 B PRO 50 A PRO 49 B LEU 138 A LEU 137 B VAL 150 A VAL 149 B VAL 127 A VAL 126 B ASP 135 A ASP 134 B MET 71 A MET 70 B PHE 82 A PHE 81 B GLN 85 A GLN 84 B VAL 97 A VAL 96 binding site for residue DL3 B 201 B DL3 201 Software 23 B LEU 17 A LEU 16 23 1_555 B MET 20 A MET 19 23 1_555 B LEU 22 A LEU 21 23 1_555 B TRP 32 A TRP 31 23 1_555 B VAL 49 A VAL 48 23 1_555 B ILE 53 A ILE 52 23 1_555 B LEU 54 A LEU 53 23 1_555 B CYS 56 A CYS 55 23 1_555 B LYS 57 A LYS 56 23 1_555 B VAL 59 A VAL 58 23 1_555 B ARG 61 A ARG 60 23 1_555 B GLN 78 A GLN 77 23 1_555 B GLU 88 A GLU 87 23 1_555 B TRP 90 A TRP 89 23 1_555 B ILE 109 A ILE 108 23 1_555 B MET 117 A MET 116 23 1_555 B THR 131 A THR 130 23 1_555 B PHE 133 A PHE 132 23 1_555 B LEU 147 A LEU 146 23 1_555 B TYR 149 A TYR 148 23 1_555 B HOH 341 C HOH 23 1_555 B HOH 399 C HOH 23 1_555 B HOH 430 C HOH 23 1_555 154 P 32 2 1