0.013399 0.007736 0.000000 0.000000 0.015472 0.000000 0.000000 0.000000 0.006383 0.000000 0.000000 0.000000 0000-0002-6471-872X Rondelet, G. 0000-0002-4920-6857 Wouters, J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.000 90.000 120.000 74.630 74.630 156.670 C11 H25 N 171.323 (2~{S})-6-methyl-~{N}-propan-2-yl-heptan-2-amine 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 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 O4 S -2 96.063 SULFATE ION non-polymer 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 C N 5 N C N 6 N C N 7 N C N 8 N C N 9 N C N 10 N C N 11 N C N 12 N C N 13 N H N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N H N 21 N H N 22 N H N 23 N H N 24 N H N 25 N H 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 N N 39 S C N 40 N C N 41 N O N 42 N C N 43 N O 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 N N 52 S C N 53 N C N 54 N O N 55 N C N 56 N C N 57 N C N 58 N N N 59 N C N 60 N N N 61 N N N 62 N O 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 N N 79 S C N 80 N C N 81 N O N 82 N C N 83 N C N 84 N O N 85 N N N 86 N O 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 H N 94 N H N 95 N N N 96 S C N 97 N C N 98 N O N 99 N C N 100 N C N 101 N O N 102 N O N 103 N O N 104 N H 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 N N 112 S C N 113 N C N 114 N O N 115 N C N 116 N C N 117 N C N 118 N O N 119 N N N 120 N O N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N N N 132 S C N 133 N C N 134 N O N 135 N C N 136 N C N 137 N C N 138 N O N 139 N O N 140 N O 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 N N 151 N C N 152 N C N 153 N O N 154 N O N 155 N H N 156 N H N 157 N H N 158 N H N 159 N H N 160 N N N 161 S C N 162 N C N 163 N O N 164 N C Y 165 N C Y 166 N N Y 167 N C Y 168 N C Y 169 N N N 170 N O N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N O N 182 N H N 183 N H N 184 N N N 185 S C N 186 N C N 187 N O N 188 S C N 189 N C N 190 N C N 191 N C N 192 N O N 193 N H N 194 N H N 195 N H N 196 N H 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 S C N 208 N C N 209 N O N 210 N C N 211 N C N 212 N C N 213 N C N 214 N O N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N H N 228 N N N 229 S C N 230 N C N 231 N O N 232 N C N 233 N C N 234 N C N 235 N C N 236 N N N 237 N O N 238 N H N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N H N 251 N H N 252 N H N 253 N N N 254 S C N 255 N C N 256 N O N 257 N C N 258 N C N 259 N S N 260 N C N 261 N O N 262 N H N 263 N H N 264 N H N 265 N H N 266 N H N 267 N H N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N N N 274 S C N 275 N C N 276 N O N 277 N C Y 278 N C Y 279 N C Y 280 N C Y 281 N C Y 282 N C Y 283 N C N 284 N O N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N H N 294 N H N 295 N H N 296 N N N 297 S C N 298 N C N 299 N O N 300 N C N 301 N C N 302 N C N 303 N O 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 H N 313 N N N 314 S C N 315 N C N 316 N O N 317 N C N 318 N O N 319 N O 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 S N 328 N O N 329 N O N 330 N O N 331 N O N 332 N N N 333 S C N 334 N C N 335 N O N 336 R C N 337 N O N 338 N C N 339 N O N 340 N H 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 N N 350 S C N 351 N C N 352 N O N 353 N C Y 354 N C Y 355 N C Y 356 N C Y 357 N N Y 358 N C Y 359 N C Y 360 N C Y 361 N C Y 362 N C N 363 N O 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 H N 373 N H N 374 N H N 375 N H N 376 N N N 377 S C N 378 N C N 379 N O N 380 N C Y 381 N C Y 382 N C Y 383 N C Y 384 N C Y 385 N C Y 386 N C N 387 N O N 388 N O N 389 N H N 390 N H 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 N 405 N C N 406 N C N 407 N O N 408 N H N 409 N H N 410 N H N 411 N H N 412 N H N 413 N H N 414 N H N 415 N H N 416 N H N 417 N H N 418 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 sing 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 sing 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 sing N 42 N sing N 43 N doub 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 sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N doub N 56 N sing 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 doub 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 doub 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 doub N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N doub 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 doub N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N doub 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 doub 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 doub 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 doub N 159 N sing N 160 N sing N 161 N sing N 162 N sing Y 163 N sing Y 164 N doub Y 165 N doub N 166 N sing Y 167 N sing N 168 N sing Y 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 sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N doub N 182 N sing N 183 N sing 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 sing 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 sing 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 sing N 222 N sing N 223 N doub N 224 N sing N 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 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 sing N 245 N sing N 246 N sing N 247 N doub 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 sing N 266 N doub N 267 N sing N 268 N sing N 269 N sing N 270 N sing Y 271 N doub Y 272 N sing Y 273 N sing N 274 N sing Y 275 N doub N 276 N sing Y 277 N doub N 278 N sing Y 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 sing N 287 N sing N 288 N sing N 289 N doub 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 doub 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 doub N 314 N doub 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 doub N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N doub N 340 N sing N 341 N sing N 342 N sing N 343 N sing Y 344 N doub Y 345 N sing Y 346 N sing N 347 N sing Y 348 N doub Y 349 N sing Y 350 N sing N 351 N sing Y 352 N sing Y 353 N doub N 354 N sing Y 355 N doub N 356 N sing Y 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 doub N 368 N sing N 369 N sing N 370 N sing N 371 N sing Y 372 N doub Y 373 N sing Y 374 N sing N 375 N sing Y 376 N doub N 377 N sing Y 378 N doub N 379 N sing Y 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 N 396 N sing N 397 N sing N 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing To Be Published 0353 Targeting PWWP domain of DNA methyltransferase 3B for epigenetic cancer therapy: Identification and structural characterization of new potential protein-protein interaction inhibitors 10.2210/pdb5nv2/pdb pdb_00005nv2 100 1 PIXEL 2015-12-06 DECTRIS PILATUS 6M channel cut monochromator crystal (Si(111)) SINGLE WAVELENGTH M x-ray 1 0.978570 1.0 PROXIMA 1 SOLEIL 0.978570 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 16698.844 DNA (cytosine-5)-methyltransferase 3B 2.1.1.37 2 man polymer 171.323 (2~{S})-6-methyl-~{N}-propan-2-yl-heptan-2-amine 2 syn non-polymer 96.063 SULFATE ION 8 syn non-polymer 18.015 water 104 nat water Dnmt3b,DNA methyltransferase HsaIIIB,M.HsaIIIB no no EADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQ HFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP EADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQ HFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP A,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 n Human sample 1 150 DNMT3B 9606 Homo sapiens 469008 Escherichia coli BL21(DE3) PLASMID Biological sequence pET28-MHL 1 3.77 67.38 VAPOR DIFFUSION, SITTING DROP 0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350 5.7-6.7 298 citation citation_author pdbx_database_proc reflns_shell chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model repository Initial release Data collection Database references Data collection Data collection Database references Refinement description 1 0 2018-05-30 1 1 2019-03-27 1 2 2019-10-16 1 3 2024-01-17 _citation.journal_abbrev _citation_author.name _database_2.pdbx_DOI _database_2.pdbx_database_accession Belgium F.R.S._FNRS_Televie 7.4.532.15.F. N PDBE Y PDBE 2017-05-03 REL REL 9AE (2~{S})-6-methyl-~{N}-propan-2-yl-heptan-2-amine SO4 SULFATE ION HOH water 3QKJ PDB experimental model 10N 2 2 9AE 9AE 401 A SO4 1 3 SO4 SO4 402 A SO4 2 3 SO4 SO4 403 A SO4 4 3 SO4 SO4 404 A SO4 6 3 SO4 SO4 405 A SO4 8 3 SO4 SO4 406 A 10N 1 2 9AE 9AE 401 B SO4 3 3 SO4 SO4 402 B SO4 5 3 SO4 SO4 403 B SO4 7 3 SO4 SO4 404 B HOH 11 4 HOH HOH 501 A HOH 92 4 HOH HOH 502 A HOH 25 4 HOH HOH 503 A HOH 80 4 HOH HOH 504 A HOH 85 4 HOH HOH 505 A HOH 43 4 HOH HOH 506 A HOH 7 4 HOH HOH 507 A HOH 3 4 HOH HOH 508 A HOH 64 4 HOH HOH 509 A HOH 102 4 HOH HOH 510 A HOH 12 4 HOH HOH 511 A HOH 14 4 HOH HOH 512 A HOH 53 4 HOH HOH 513 A HOH 26 4 HOH HOH 514 A HOH 35 4 HOH HOH 515 A HOH 59 4 HOH HOH 516 A HOH 50 4 HOH HOH 517 A HOH 2 4 HOH HOH 518 A HOH 21 4 HOH HOH 519 A HOH 24 4 HOH HOH 520 A HOH 17 4 HOH HOH 521 A HOH 33 4 HOH HOH 522 A HOH 45 4 HOH HOH 523 A HOH 30 4 HOH HOH 524 A HOH 70 4 HOH HOH 525 A HOH 9 4 HOH HOH 526 A HOH 4 4 HOH HOH 527 A HOH 76 4 HOH HOH 528 A HOH 81 4 HOH HOH 529 A HOH 39 4 HOH HOH 530 A HOH 46 4 HOH HOH 531 A HOH 15 4 HOH HOH 532 A HOH 78 4 HOH HOH 533 A HOH 36 4 HOH HOH 534 A HOH 16 4 HOH HOH 535 A HOH 5 4 HOH HOH 536 A HOH 95 4 HOH HOH 537 A HOH 69 4 HOH HOH 538 A HOH 63 4 HOH HOH 539 A HOH 57 4 HOH HOH 540 A HOH 44 4 HOH HOH 541 A HOH 23 4 HOH HOH 542 A HOH 84 4 HOH HOH 543 A HOH 8 4 HOH HOH 544 A HOH 71 4 HOH HOH 545 A HOH 74 4 HOH HOH 546 A HOH 37 4 HOH HOH 547 A HOH 10 4 HOH HOH 548 A HOH 97 4 HOH HOH 549 A HOH 93 4 HOH HOH 550 A HOH 104 4 HOH HOH 551 A HOH 22 4 HOH HOH 552 A HOH 55 4 HOH HOH 553 A HOH 72 4 HOH HOH 554 A HOH 101 4 HOH HOH 555 A HOH 90 4 HOH HOH 556 A HOH 73 4 HOH HOH 557 A HOH 13 4 HOH HOH 558 A HOH 94 4 HOH HOH 559 A HOH 62 4 HOH HOH 560 A HOH 54 4 HOH HOH 561 A HOH 75 4 HOH HOH 562 A HOH 77 4 HOH HOH 563 A HOH 100 4 HOH HOH 564 A HOH 41 4 HOH HOH 565 A HOH 83 4 HOH HOH 566 A HOH 103 4 HOH HOH 567 A HOH 49 4 HOH HOH 568 A HOH 105 4 HOH HOH 569 A HOH 31 4 HOH HOH 501 B HOH 28 4 HOH HOH 502 B HOH 87 4 HOH HOH 503 B HOH 61 4 HOH HOH 504 B HOH 42 4 HOH HOH 505 B HOH 98 4 HOH HOH 506 B HOH 82 4 HOH HOH 507 B HOH 20 4 HOH HOH 508 B HOH 47 4 HOH HOH 509 B HOH 91 4 HOH HOH 510 B HOH 99 4 HOH HOH 511 B HOH 48 4 HOH HOH 512 B HOH 51 4 HOH HOH 513 B HOH 58 4 HOH HOH 514 B HOH 86 4 HOH HOH 515 B HOH 79 4 HOH HOH 516 B HOH 60 4 HOH HOH 517 B HOH 34 4 HOH HOH 518 B HOH 66 4 HOH HOH 519 B HOH 32 4 HOH HOH 520 B HOH 27 4 HOH HOH 521 B HOH 67 4 HOH HOH 522 B HOH 88 4 HOH HOH 523 B HOH 18 4 HOH HOH 524 B HOH 38 4 HOH HOH 525 B HOH 68 4 HOH HOH 526 B HOH 106 4 HOH HOH 527 B HOH 56 4 HOH HOH 528 B HOH 19 4 HOH HOH 529 B HOH 40 4 HOH HOH 530 B HOH 96 4 HOH HOH 531 B HOH 29 4 HOH HOH 532 B HOH 52 4 HOH HOH 533 B HOH 89 4 HOH HOH 534 B HOH 65 4 HOH HOH 535 B n 1 206 A n 2 207 A n 3 208 A n 4 209 A n 5 210 A n 6 211 A n 7 212 A n 8 213 A n 9 214 A SER 215 n 10 SER 215 A GLU 216 n 11 GLU 216 A TYR 217 n 12 TYR 217 A GLN 218 n 13 GLN 218 A ASP 219 n 14 ASP 219 A GLY 220 n 15 GLY 220 A LYS 221 n 16 LYS 221 A GLU 222 n 17 GLU 222 A PHE 223 n 18 PHE 223 A GLY 224 n 19 GLY 224 A ILE 225 n 20 ILE 225 A GLY 226 n 21 GLY 226 A ASP 227 n 22 ASP 227 A LEU 228 n 23 LEU 228 A VAL 229 n 24 VAL 229 A TRP 230 n 25 TRP 230 A GLY 231 n 26 GLY 231 A LYS 232 n 27 LYS 232 A ILE 233 n 28 ILE 233 A LYS 234 n 29 LYS 234 A GLY 235 n 30 GLY 235 A PHE 236 n 31 PHE 236 A SER 237 n 32 SER 237 A TRP 238 n 33 TRP 238 A TRP 239 n 34 TRP 239 A PRO 240 n 35 PRO 240 A ALA 241 n 36 ALA 241 A MET 242 n 37 MET 242 A VAL 243 n 38 VAL 243 A VAL 244 n 39 VAL 244 A SER 245 n 40 SER 245 A TRP 246 n 41 TRP 246 A LYS 247 n 42 LYS 247 A ALA 248 n 43 ALA 248 A THR 249 n 44 THR 249 A SER 250 n 45 SER 250 A LYS 251 n 46 LYS 251 A ARG 252 n 47 ARG 252 A GLN 253 n 48 GLN 253 A ALA 254 n 49 ALA 254 A MET 255 n 50 MET 255 A SER 256 n 51 SER 256 A GLY 257 n 52 GLY 257 A MET 258 n 53 MET 258 A ARG 259 n 54 ARG 259 A TRP 260 n 55 TRP 260 A VAL 261 n 56 VAL 261 A GLN 262 n 57 GLN 262 A TRP 263 n 58 TRP 263 A PHE 264 n 59 PHE 264 A GLY 265 n 60 GLY 265 A ASP 266 n 61 ASP 266 A GLY 267 n 62 GLY 267 A LYS 268 n 63 LYS 268 A PHE 269 n 64 PHE 269 A SER 270 n 65 SER 270 A GLU 271 n 66 GLU 271 A VAL 272 n 67 VAL 272 A SER 273 n 68 SER 273 A ALA 274 n 69 ALA 274 A ASP 275 n 70 ASP 275 A LYS 276 n 71 LYS 276 A LEU 277 n 72 LEU 277 A VAL 278 n 73 VAL 278 A ALA 279 n 74 ALA 279 A LEU 280 n 75 LEU 280 A GLY 281 n 76 GLY 281 A LEU 282 n 77 LEU 282 A PHE 283 n 78 PHE 283 A SER 284 n 79 SER 284 A GLN 285 n 80 GLN 285 A HIS 286 n 81 HIS 286 A PHE 287 n 82 PHE 287 A ASN 288 n 83 ASN 288 A LEU 289 n 84 LEU 289 A ALA 290 n 85 ALA 290 A THR 291 n 86 THR 291 A PHE 292 n 87 PHE 292 A ASN 293 n 88 ASN 293 A LYS 294 n 89 LYS 294 A LEU 295 n 90 LEU 295 A VAL 296 n 91 VAL 296 A SER 297 n 92 SER 297 A TYR 298 n 93 TYR 298 A ARG 299 n 94 ARG 299 A LYS 300 n 95 LYS 300 A ALA 301 n 96 ALA 301 A MET 302 n 97 MET 302 A TYR 303 n 98 TYR 303 A HIS 304 n 99 HIS 304 A ALA 305 n 100 ALA 305 A LEU 306 n 101 LEU 306 A GLU 307 n 102 GLU 307 A LYS 308 n 103 LYS 308 A ALA 309 n 104 ALA 309 A ARG 310 n 105 ARG 310 A VAL 311 n 106 VAL 311 A ARG 312 n 107 ARG 312 A ALA 313 n 108 ALA 313 A GLY 314 n 109 GLY 314 A LYS 315 n 110 LYS 315 A THR 316 n 111 THR 316 A PHE 317 n 112 PHE 317 A PRO 318 n 113 PRO 318 A SER 319 n 114 SER 319 A n 115 320 A n 116 321 A n 117 322 A n 118 323 A SER 324 n 119 SER 324 A LEU 325 n 120 LEU 325 A GLU 326 n 121 GLU 326 A ASP 327 n 122 ASP 327 A GLN 328 n 123 GLN 328 A LEU 329 n 124 LEU 329 A LYS 330 n 125 LYS 330 A PRO 331 n 126 PRO 331 A MET 332 n 127 MET 332 A LEU 333 n 128 LEU 333 A GLU 334 n 129 GLU 334 A TRP 335 n 130 TRP 335 A ALA 336 n 131 ALA 336 A HIS 337 n 132 HIS 337 A GLY 338 n 133 GLY 338 A GLY 339 n 134 GLY 339 A PHE 340 n 135 PHE 340 A LYS 341 n 136 LYS 341 A PRO 342 n 137 PRO 342 A THR 343 n 138 THR 343 A GLY 344 n 139 GLY 344 A ILE 345 n 140 ILE 345 A GLU 346 n 141 GLU 346 A GLY 347 n 142 GLY 347 A LEU 348 n 143 LEU 348 A LYS 349 n 144 LYS 349 A PRO 350 n 145 PRO 350 A ASN 351 n 146 ASN 351 A n 147 352 A n 148 353 A n 149 354 A n 150 355 A n 1 206 B n 2 207 B n 3 208 B n 4 209 B n 5 210 B n 6 211 B n 7 212 B n 8 213 B n 9 214 B SER 215 n 10 SER 215 B GLU 216 n 11 GLU 216 B TYR 217 n 12 TYR 217 B GLN 218 n 13 GLN 218 B ASP 219 n 14 ASP 219 B GLY 220 n 15 GLY 220 B LYS 221 n 16 LYS 221 B GLU 222 n 17 GLU 222 B PHE 223 n 18 PHE 223 B GLY 224 n 19 GLY 224 B ILE 225 n 20 ILE 225 B GLY 226 n 21 GLY 226 B ASP 227 n 22 ASP 227 B LEU 228 n 23 LEU 228 B VAL 229 n 24 VAL 229 B TRP 230 n 25 TRP 230 B GLY 231 n 26 GLY 231 B LYS 232 n 27 LYS 232 B ILE 233 n 28 ILE 233 B LYS 234 n 29 LYS 234 B GLY 235 n 30 GLY 235 B PHE 236 n 31 PHE 236 B SER 237 n 32 SER 237 B TRP 238 n 33 TRP 238 B TRP 239 n 34 TRP 239 B PRO 240 n 35 PRO 240 B ALA 241 n 36 ALA 241 B MET 242 n 37 MET 242 B VAL 243 n 38 VAL 243 B VAL 244 n 39 VAL 244 B SER 245 n 40 SER 245 B TRP 246 n 41 TRP 246 B LYS 247 n 42 LYS 247 B ALA 248 n 43 ALA 248 B THR 249 n 44 THR 249 B SER 250 n 45 SER 250 B LYS 251 n 46 LYS 251 B ARG 252 n 47 ARG 252 B GLN 253 n 48 GLN 253 B ALA 254 n 49 ALA 254 B MET 255 n 50 MET 255 B SER 256 n 51 SER 256 B GLY 257 n 52 GLY 257 B MET 258 n 53 MET 258 B ARG 259 n 54 ARG 259 B TRP 260 n 55 TRP 260 B VAL 261 n 56 VAL 261 B GLN 262 n 57 GLN 262 B TRP 263 n 58 TRP 263 B PHE 264 n 59 PHE 264 B GLY 265 n 60 GLY 265 B ASP 266 n 61 ASP 266 B GLY 267 n 62 GLY 267 B LYS 268 n 63 LYS 268 B PHE 269 n 64 PHE 269 B SER 270 n 65 SER 270 B GLU 271 n 66 GLU 271 B VAL 272 n 67 VAL 272 B SER 273 n 68 SER 273 B ALA 274 n 69 ALA 274 B ASP 275 n 70 ASP 275 B LYS 276 n 71 LYS 276 B LEU 277 n 72 LEU 277 B VAL 278 n 73 VAL 278 B ALA 279 n 74 ALA 279 B LEU 280 n 75 LEU 280 B GLY 281 n 76 GLY 281 B LEU 282 n 77 LEU 282 B PHE 283 n 78 PHE 283 B SER 284 n 79 SER 284 B GLN 285 n 80 GLN 285 B HIS 286 n 81 HIS 286 B PHE 287 n 82 PHE 287 B ASN 288 n 83 ASN 288 B LEU 289 n 84 LEU 289 B ALA 290 n 85 ALA 290 B THR 291 n 86 THR 291 B PHE 292 n 87 PHE 292 B ASN 293 n 88 ASN 293 B LYS 294 n 89 LYS 294 B LEU 295 n 90 LEU 295 B VAL 296 n 91 VAL 296 B SER 297 n 92 SER 297 B TYR 298 n 93 TYR 298 B ARG 299 n 94 ARG 299 B LYS 300 n 95 LYS 300 B ALA 301 n 96 ALA 301 B MET 302 n 97 MET 302 B TYR 303 n 98 TYR 303 B HIS 304 n 99 HIS 304 B ALA 305 n 100 ALA 305 B LEU 306 n 101 LEU 306 B GLU 307 n 102 GLU 307 B LYS 308 n 103 LYS 308 B ALA 309 n 104 ALA 309 B ARG 310 n 105 ARG 310 B VAL 311 n 106 VAL 311 B ARG 312 n 107 ARG 312 B ALA 313 n 108 ALA 313 B GLY 314 n 109 GLY 314 B LYS 315 n 110 LYS 315 B THR 316 n 111 THR 316 B PHE 317 n 112 PHE 317 B PRO 318 n 113 PRO 318 B SER 319 n 114 SER 319 B n 115 320 B n 116 321 B n 117 322 B n 118 323 B SER 324 n 119 SER 324 B LEU 325 n 120 LEU 325 B GLU 326 n 121 GLU 326 B ASP 327 n 122 ASP 327 B GLN 328 n 123 GLN 328 B LEU 329 n 124 LEU 329 B LYS 330 n 125 LYS 330 B PRO 331 n 126 PRO 331 B MET 332 n 127 MET 332 B LEU 333 n 128 LEU 333 B GLU 334 n 129 GLU 334 B TRP 335 n 130 TRP 335 B ALA 336 n 131 ALA 336 B HIS 337 n 132 HIS 337 B GLY 338 n 133 GLY 338 B GLY 339 n 134 GLY 339 B PHE 340 n 135 PHE 340 B LYS 341 n 136 LYS 341 B PRO 342 n 137 PRO 342 B THR 343 n 138 THR 343 B GLY 344 n 139 GLY 344 B ILE 345 n 140 ILE 345 B GLU 346 n 141 GLU 346 B GLY 347 n 142 GLY 347 B LEU 348 n 143 LEU 348 B LYS 349 n 144 LYS 349 B PRO 350 n 145 PRO 350 B ASN 351 n 146 ASN 351 B n 147 352 B n 148 353 B n 149 354 B n 150 355 B software_defined_assembly PISA 2 dimeric none 2320 -101 14190 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 O VAL 272 A O VAL 67 A N ARG 259 A N ARG 54 A O TRP 260 A O TRP 55 A N VAL 244 A N VAL 39 A O TRP 239 A O TRP 34 A N GLY 231 A N GLY 26 A N TRP 230 A N TRP 25 A O VAL 278 A O VAL 73 B O VAL 272 B O VAL 67 B N ARG 259 B N ARG 54 B O GLN 262 B O GLN 57 B N MET 242 B N MET 37 B O TRP 239 B O TRP 34 B N GLY 231 B N GLY 26 B N TRP 230 B N TRP 25 B O VAL 278 B O VAL 73 1 B SO4 404 L SO4 1 A HOH 548 M HOH 1 A GLU 206 A GLU 1 1 Y 1 A ALA 207 A ALA 2 1 Y 1 A ASP 208 A ASP 3 1 Y 1 A SER 209 A SER 4 1 Y 1 A GLY 210 A GLY 5 1 Y 1 A ASP 211 A ASP 6 1 Y 1 A GLY 212 A GLY 7 1 Y 1 A ASP 213 A ASP 8 1 Y 1 A SER 214 A SER 9 1 Y 1 A SER 320 A SER 115 1 Y 1 A PRO 321 A PRO 116 1 Y 1 A GLY 322 A GLY 117 1 Y 1 A ASP 323 A ASP 118 1 Y 1 A ASN 352 A ASN 147 1 Y 1 A THR 353 A THR 148 1 Y 1 A GLN 354 A GLN 149 1 Y 1 A PRO 355 A PRO 150 1 Y 1 B GLU 206 B GLU 1 1 Y 1 B ALA 207 B ALA 2 1 Y 1 B ASP 208 B ASP 3 1 Y 1 B SER 209 B SER 4 1 Y 1 B GLY 210 B GLY 5 1 Y 1 B ASP 211 B ASP 6 1 Y 1 B GLY 212 B GLY 7 1 Y 1 B ASP 213 B ASP 8 1 Y 1 B SER 214 B SER 9 1 Y 1 B SER 320 B SER 115 1 Y 1 B PRO 321 B PRO 116 1 Y 1 B GLY 322 B GLY 117 1 Y 1 B ASP 323 B ASP 118 1 Y 1 B ASN 352 B ASN 147 1 Y 1 B THR 353 B THR 148 1 Y 1 B GLN 354 B GLN 149 1 Y 1 B PRO 355 B PRO 150 1 Y 1 A GLN 218 -106.53 68.41 1 A PHE 223 82.46 126.62 1 A LYS 251 -125.46 -96.40 1 B GLN 218 -100.48 77.53 1 B PHE 223 84.35 128.21 1 B LEU 325 -60.06 -73.68 100.680 50.7000 25.350 0.2405 0.2013 0.2032 2.0290 40.6200 1674 33471 5.0000 99.8700 0.2900 1 FREE R-VALUE 1.390 MOLECULAR REPLACEMENT 27.4000 0.9000 1.1100 3QKJ 2.0290 40.6200 104 2296 66.19 50.76 64 0 2128 266 0.008 2263 1.102 3047 0.081 297 0.005 370 13.776 800 0.3900 0.0000 0.3705 2.0883 136 2581 2717 12 99.0000 0.3305 0.0000 0.3085 2.1557 137 2607 2744 12 100.0000 0.3237 0.0000 0.2804 2.2328 137 2604 2741 12 100.0000 0.3018 0.0000 0.2469 2.3222 138 2628 2766 12 100.0000 0.2958 0.0000 0.2343 2.4278 137 2603 2740 12 100.0000 0.2466 0.0000 0.2333 2.5558 138 2619 2757 12 100.0000 0.2711 0.0000 0.2198 2.7159 139 2642 2781 12 100.0000 0.2683 0.0000 0.2229 2.9256 139 2636 2775 12 100.0000 0.2904 0.0000 0.2284 3.2199 141 2671 2812 12 100.0000 0.2583 0.0000 0.1950 3.6855 140 2660 2800 12 100.0000 0.1837 0.0000 0.1651 4.6423 142 2714 2856 12 100.0000 0.2164 0.0000 0.1809 40.6284 150 2832 2982 12 100.0000 50.720 2.029 40.620 5NV2 33473 1.0 0.042 1 26.76 9.8 99.9 0.87 2.03 2.15 2.38 5331 0.54 1 9.9 99.2 data scaling XSCALE refinement PHENIX 1.8.1_1168 data extraction PDB_EXTRACT 3.22 data reduction XDS phasing PHASER N Human DNMT3B PWWP domain in complex with N-isopropyl-1,5-dimethylhexylamine (Metron S) 1 N N 1 N N 2 N N 3 N N 3 N N 3 N N 3 N N 3 N N 2 N N 3 N N 3 N N 3 N N 4 N N 4 N N A SER 245 A SER 40 HELX_P A THR 249 A THR 44 5 AA1 5 A ASN 288 A ASN 83 HELX_P A LEU 295 A LEU 90 1 AA2 8 A LEU 295 A LEU 90 HELX_P A GLY 314 A GLY 109 1 AA3 20 A LEU 325 A LEU 120 HELX_P A GLY 338 A GLY 133 1 AA4 14 A GLY 344 A GLY 139 HELX_P A LYS 349 A LYS 144 5 AA5 6 B SER 245 B SER 40 HELX_P B THR 249 B THR 44 5 AA6 5 B LEU 282 B LEU 77 HELX_P B PHE 287 B PHE 82 1 AA7 6 B ASN 288 B ASN 83 HELX_P B LEU 295 B LEU 90 1 AA8 8 B LEU 295 B LEU 90 HELX_P B GLY 314 B GLY 109 1 AA9 20 B LEU 325 B LEU 120 HELX_P B GLY 338 B GLY 133 1 AB1 14 B THR 343 B THR 138 HELX_P B LYS 349 B LYS 144 5 AB2 7 TRANSFERASE DNMT3B PWWP DOMAIN, HISTONE BINDING, BETA BARREL, LIGAND, TRANSFERASE A LYS 341 A LYS 136 1 A PRO 342 A PRO 137 4.98 B LYS 341 B LYS 136 1 B PRO 342 B PRO 137 6.04 DNM3B_HUMAN UNP 1 206 Q9UBC3 EADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQ HFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP 206 355 5NV2 206 355 Q9UBC3 A 1 1 150 206 355 5NV2 206 355 Q9UBC3 B 1 1 150 5 5 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A PHE 269 A PHE 64 A SER 273 A SER 68 A MET 258 A MET 53 A TRP 263 A TRP 58 A TRP 239 A TRP 34 A VAL 244 A VAL 39 A LEU 228 A LEU 23 A GLY 231 A GLY 26 A LEU 277 A LEU 72 A ALA 279 A ALA 74 B PHE 269 B PHE 64 B SER 273 B SER 68 B MET 258 B MET 53 B TRP 263 B TRP 58 B TRP 238 B TRP 33 B VAL 244 B VAL 39 B LEU 228 B LEU 23 B LYS 232 B LYS 27 B LEU 277 B LEU 72 B ALA 279 B ALA 74 binding site for residue 9AE A 401 A 9AE 401 Software 4 binding site for residue SO4 A 402 A SO4 402 Software 3 binding site for residue SO4 A 403 A SO4 403 Software 2 binding site for residue SO4 A 404 A SO4 404 Software 5 binding site for residue SO4 A 405 A SO4 405 Software 3 binding site for residue SO4 A 406 A SO4 406 Software 3 binding site for residue 9AE B 401 B 9AE 401 Software 6 binding site for residue SO4 B 402 B SO4 402 Software 4 binding site for residue SO4 B 403 B SO4 403 Software 3 binding site for residue SO4 B 404 B SO4 404 Software 4 A ILE 233 A ILE 28 4 1_555 A TRP 239 A TRP 34 4 1_555 A ASP 266 A ASP 61 4 1_555 A HOH 508 M HOH 4 1_555 A LYS 308 A LYS 103 3 1_555 A ARG 312 A ARG 107 3 1_555 A ASN 351 A ASN 146 3 1_555 A ARG 310 A ARG 105 2 1_555 B LYS 234 B LYS 29 2 4_545 A LYS 251 A LYS 46 5 1_555 A ARG 252 A ARG 47 5 1_555 A HOH 524 M HOH 5 1_555 A HOH 529 M HOH 5 1_555 B HIS 304 B HIS 99 5 1_555 A LYS 232 A LYS 27 3 1_555 A LYS 234 A LYS 29 3 1_555 A GLY 235 A GLY 30 3 1_555 A LYS 251 A LYS 46 3 1_555 A ARG 252 A ARG 47 3 1_555 B GLY 265 B GLY 60 3 1_555 B ILE 233 B ILE 28 6 1_555 B PHE 236 B PHE 31 6 1_555 B TRP 239 B TRP 34 6 1_555 B TRP 263 B TRP 58 6 1_555 B ASP 266 B ASP 61 6 1_555 B SER 297 B SER 92 6 1_555 A ASP 275 A ASP 70 4 1_555 B LYS 308 B LYS 103 4 1_555 B ARG 312 B ARG 107 4 1_555 B ASN 351 B ASN 146 4 1_555 B LYS 251 B LYS 46 3 1_555 B ARG 252 B ARG 47 3 1_555 B HOH 502 N HOH 3 1_555 B LYS 232 B LYS 27 4 1_555 B LYS 232 B LYS 27 4 5_555 B TRP 238 B TRP 33 4 5_555 B TRP 238 B TRP 33 4 1_555 154 P 32 2 1