0.023058 -0.008548 0.001602 0.000000 0.023544 -0.009038 0.000000 0.000000 0.020840 0.00000 0.00000 0.00000 Russo Krauss, I. Merlino, A. Mazzarella, L. Sica, F. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 68.97 86.11 69.66 43.369 45.299 51.519 C21 H34 Cl N6 O3 1 453.986 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide PPACK peptide-like 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 Cl -1 35.453 CHLORIDE ION non-polymer C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA 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 K 1 39.098 POTASSIUM ION non-polymer 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 Na 1 22.990 SODIUM ION non-polymer C8 H15 N O6 221.208 2-acetamido-2-deoxy-beta-D-glucopyranose N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE D-saccharide, beta 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 Zn 2 65.409 ZINC ION non-polymer N 1 N N N 2 R C N 3 N C N 4 N O N 5 N C Y 6 N C Y 7 N C Y 8 N C Y 9 N C Y 10 N C Y 11 N C N 12 N N N 13 S C N 14 N C N 15 N O N 16 N C N 17 N C N 18 N C N 19 N N N 20 S C N 21 S C N 22 N O N 23 N C N 24 N C N 25 N C N 26 N N N 27 N C N 28 N N N 29 N N N 30 N C N 31 N CL 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 H N 42 N H N 43 N H 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 N N 67 S C N 68 N C N 69 N O N 70 N C N 71 N O 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 N N 80 S C N 81 N C N 82 N O N 83 N C N 84 N C N 85 N C N 86 N N N 87 N C N 88 N N N 89 N N N 90 N O N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N N N 107 S C N 108 N C N 109 N O N 110 N C N 111 N C N 112 N O N 113 N N N 114 N O N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N N N 124 S C N 125 N C N 126 N O N 127 N C N 128 N C N 129 N O N 130 N O N 131 N O 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 CL N 140 N N N 141 R C N 142 N C N 143 N O N 144 N C N 145 N S N 146 N O 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 O N 155 N P N 156 N O N 157 N O N 158 N O N 159 N C N 160 R C N 161 N O N 162 S C N 163 N O N 164 N C N 165 R C Y 166 N N Y 167 N C Y 168 N N Y 169 N C N 170 N C N 171 N O N 172 N N N 173 N C N 174 N N N 175 N N Y 176 N C 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 H N 188 N H N 189 N H N 190 N H N 191 N O N 192 N P N 193 N O N 194 N O N 195 N O N 196 N C N 197 R C N 198 N O N 199 S C N 200 N O N 201 N C N 202 R C N 203 N N N 204 N C N 205 N O N 206 N N N 207 N C N 208 N O N 209 N C N 210 N C N 211 N C N 212 N H N 213 N H N 214 N H 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 N N 228 S C N 229 N C N 230 N O N 231 N C N 232 N C N 233 N C N 234 N O N 235 N N N 236 N O N 237 N H 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 N N 248 S C N 249 N C N 250 N O N 251 N C N 252 N C N 253 N C N 254 N O N 255 N O N 256 N O 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 H N 266 N N N 267 N C N 268 N C N 269 N O 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 N N 277 S C N 278 N C N 279 N O N 280 N C Y 281 N C Y 282 N N Y 283 N C Y 284 N C Y 285 N N N 286 N O 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 H N 297 N O N 298 N H N 299 N H N 300 N N N 301 S C N 302 N C N 303 N O N 304 S C N 305 N C N 306 N C N 307 N C N 308 N O N 309 N H N 310 N H N 311 N H N 312 N H N 313 N H N 314 N H N 315 N H N 316 N H N 317 N H N 318 N H N 319 N H N 320 N H N 321 N H N 322 N K N 323 N N N 324 S C N 325 N C N 326 N O N 327 N C N 328 N C N 329 N C N 330 N C N 331 N O N 332 N H N 333 N H N 334 N H N 335 N H N 336 N H N 337 N H N 338 N H N 339 N H N 340 N H N 341 N H N 342 N H N 343 N H N 344 N H N 345 N N N 346 S C N 347 N C N 348 N O N 349 N C N 350 N C N 351 N C N 352 N C N 353 N N N 354 N O N 355 N H N 356 N H N 357 N H N 358 N H N 359 N H 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 H N 370 N N N 371 S C N 372 N C N 373 N O N 374 N C N 375 N C N 376 N S N 377 N C 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 H N 387 N H N 388 N H N 389 N H N 390 N NA N 391 R C N 392 R C N 393 R C N 394 S C N 395 R C N 396 N C N 397 N C N 398 N C N 399 N N N 400 N O N 401 N O N 402 N O N 403 N O N 404 N O N 405 N O N 406 N H N 407 N H 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 419 N H N 420 N H N 421 N N N 422 S C N 423 N C N 424 N O N 425 N C Y 426 N C Y 427 N C Y 428 N C Y 429 N C Y 430 N C Y 431 N C N 432 N O N 433 N H N 434 N H N 435 N H N 436 N H N 437 N H N 438 N H N 439 N H N 440 N H N 441 N H N 442 N H N 443 N H N 444 N N N 445 S C N 446 N C N 447 N O N 448 N C N 449 N C N 450 N C N 451 N O N 452 N H N 453 N H N 454 N H N 455 N H N 456 N H N 457 N H N 458 N H N 459 N H N 460 N H N 461 N N N 462 S C N 463 N C N 464 N O N 465 N C N 466 N O N 467 N O N 468 N H N 469 N H N 470 N H N 471 N H N 472 N H N 473 N H N 474 N H N 475 N N N 476 S C N 477 N C N 478 N O N 479 R C N 480 N O N 481 N C N 482 N O N 483 N H N 484 N H N 485 N H N 486 N H N 487 N H N 488 N H N 489 N H N 490 N H N 491 N H N 492 N N N 493 S C N 494 N C N 495 N O N 496 N C Y 497 N C Y 498 N C Y 499 N C Y 500 N N Y 501 N C Y 502 N C Y 503 N C Y 504 N C Y 505 N C N 506 N O N 507 N H N 508 N H N 509 N H N 510 N H N 511 N H N 512 N H N 513 N H N 514 N H N 515 N H N 516 N H N 517 N H N 518 N H N 519 N N N 520 S C N 521 N C N 522 N O N 523 N C Y 524 N C Y 525 N C Y 526 N C Y 527 N C Y 528 N C Y 529 N C N 530 N O N 531 N O N 532 N H N 533 N H N 534 N H N 535 N H N 536 N H N 537 N H N 538 N H N 539 N H N 540 N H N 541 N H N 542 N H N 543 N N N 544 S C N 545 N C N 546 N O N 547 N C N 548 N C N 549 N C N 550 N O N 551 N H N 552 N H N 553 N H N 554 N H N 555 N H N 556 N H N 557 N H N 558 N H N 559 N H N 560 N H N 561 N H N 562 N ZN 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 Y 12 N doub Y 13 N sing Y 14 N sing N 15 N sing Y 16 N doub N 17 N sing Y 18 N doub N 19 N sing Y 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 doub 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 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 sing 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 doub 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 doub 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 doub N 86 N sing 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 sing N 99 N doub 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 doub N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N doub 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 sing N 125 N sing N 126 N sing N 127 N doub N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N doub 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 doub 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 doub 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 Y 172 N sing Y 173 N sing Y 174 N doub N 175 N sing Y 176 N sing N 177 N sing Y 178 N doub N 179 N doub N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N doub N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N doub 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 sing 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 doub N 214 N sing N 215 N sing N 216 N sing N 217 N doub N 218 N sing N 219 N sing N 220 N doub N 221 N sing N 222 N sing N 223 N sing 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 doub 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 doub 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 doub 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 doub 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 doub N 278 N sing N 279 N sing N 280 N sing N 281 N sing Y 282 N sing Y 283 N doub Y 284 N doub N 285 N sing Y 286 N sing N 287 N sing Y 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 doub 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 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 doub 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 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 sing N 340 N sing N 341 N sing N 342 N doub 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 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 sing N 363 N sing N 364 N sing N 365 N sing N 366 N doub 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 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 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 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 sing N 399 N sing N 400 N doub N 401 N sing N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N sing N 407 N sing N 408 N sing N 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 doub N 416 N sing N 417 N sing N 418 N sing N 419 N sing Y 420 N doub Y 421 N sing Y 422 N sing N 423 N sing Y 424 N doub N 425 N sing Y 426 N doub N 427 N sing Y 428 N sing N 429 N sing N 430 N sing N 431 N sing N 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 doub N 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 sing N 451 N sing N 452 N sing N 453 N sing N 454 N sing N 455 N doub N 456 N sing N 457 N sing N 458 N sing N 459 N sing N 460 N sing N 461 N sing N 462 N sing N 463 N sing N 464 N sing N 465 N sing N 466 N sing N 467 N sing N 468 N doub N 469 N sing N 470 N sing N 471 N sing N 472 N sing N 473 N sing N 474 N sing N 475 N sing N 476 N sing N 477 N sing N 478 N sing N 479 N sing N 480 N sing N 481 N sing N 482 N sing N 483 N sing N 484 N doub N 485 N sing N 486 N sing N 487 N sing N 488 N sing Y 489 N doub Y 490 N sing Y 491 N sing N 492 N sing Y 493 N doub Y 494 N sing Y 495 N sing N 496 N sing Y 497 N sing Y 498 N doub N 499 N sing Y 500 N doub N 501 N sing Y 502 N sing N 503 N sing N 504 N sing N 505 N sing N 506 N sing N 507 N sing N 508 N sing N 509 N sing N 510 N sing N 511 N sing N 512 N doub N 513 N sing N 514 N sing N 515 N sing N 516 N sing Y 517 N doub Y 518 N sing Y 519 N sing N 520 N sing Y 521 N doub N 522 N sing Y 523 N doub N 524 N sing Y 525 N sing N 526 N sing N 527 N sing N 528 N sing N 529 N sing N 530 N sing N 531 N sing N 532 N sing N 533 N sing N 534 N sing N 535 N sing N 536 N doub N 537 N sing N 538 N sing N 539 N sing N 540 N sing N 541 N sing N 542 N sing N 543 N sing N 544 N sing N 545 N sing N 546 N sing N 547 N sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 40 8119 8128 10.1093/nar/gks512 22669903 High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity. 2012 UK Nucleic Acids Res. NARHAD 0389 0305-1048 39 7858 7867 10.1093/nar/gkr522 21715374 Thrombin-aptamer recognition: a revealed ambiguity. 2011 US J.Biol.Chem. JBCHA3 0071 0021-9258 268 17651 17654 8102368 The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer. 1993 DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 52 272 282 10.1107/S0907444995013977 15299700 An ambiguous structure of a DNA 15-mer thrombin complex. 1996 10.2210/pdb4dii/pdb pdb_00004dii 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 CCD 2009-12-10 RIGAKU SATURN 944 GRAPHITE SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU 4096.534 Prothrombin 3.4.21.5 Light chain (UNP Residues 328-363) 1 nat polymer 29780.219 Prothrombin 3.4.21.5 Heavy chain (UNP Residues 364-622) 1 nat polymer 4743.051 Thrombin binding aptamer 1 syn polymer 65.409 ZINC ION 2 syn non-polymer 453.986 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide 1 syn non-polymer 221.208 2-acetamido-2-deoxy-beta-D-glucopyranose 1 man non-polymer 22.990 SODIUM ION 1 syn non-polymer 35.453 CHLORIDE ION 2 syn non-polymer 39.098 POTASSIUM ION 1 syn non-polymer 18.015 water 183 nat water Coagulation factor II, Thrombin light chain Coagulation factor II, Thrombin heavy chain no no TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR L polypeptide(L) no no IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFGE IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFGE H polypeptide(L) no no (DG)(DG)(DT)(DT)(DG)(DG)(DT)(DG)(DT)(DG)(DG)(DT)(DT)(DG)(DG) GGTTGGTGTGGTTGG D polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n 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 human sample 9606 Homo sapiens 1 2.29 46.26 VAPOR DIFFUSION, SITTING DROP 7.4 10-15% w/v polyethylene glycol 8000, 0.05 M zinc acetate, 0.1 M sodium cacodylate , pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K 293 chem_comp entity pdbx_chem_comp_identifier pdbx_entity_nonpoly pdbx_struct_conn_angle struct_conn struct_site struct_site_gen chem_comp chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model repository Initial release Carbohydrate remediation repository Remediation Database references Other Data collection Derived calculations Structure summary Data collection Database references Refinement description Structure summary 1 0 2012-07-18 1 1 2012-09-26 1 2 2013-02-27 1 3 2020-07-29 1 4 2023-09-13 _chem_comp.name _chem_comp.type _entity.pdbx_description _pdbx_entity_nonpoly.name _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_role _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession DGlcpNAcb N-acetyl-b-D-glucopyranosamine b-D-GlcpNAc GlcNAc The same complex in the presence of Na+ ion RCSB Y RCSB 2012-01-31 REL REL ZN ZINC ION 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide NAG 2-acetamido-2-deoxy-beta-D-glucopyranose NA SODIUM ION CL CHLORIDE ION K POTASSIUM ION HOH water 32630 Synthetic DNA sample THE INHIBITOR IS COVALENTLY CONNECTED TO ACTIVE_SITE RESIDUES: 1) VIA A HEMIKETAL GROUP TO OG SER 195 IN CHAIN H 2) VIA A METHYLENE GROUP TO NE2 HIS 57 IN CHAIN H 3QLP PDB ENTRY 3QLP AND 1HAO PDB experimental model 1HAO PDB ENTRY 3QLP AND 1HAO PDB experimental model Inhibitor D-Phe-Pro-Arg-CH2Cl Peptide-like ZN 1031 4 ZN ZN 101 L 0G6 1 5 0G6 0G6 301 H NAG 2 6 NAG NAG 302 H NA 417 7 NA NA 303 H ZN 1032 4 ZN ZN 304 H CL 418 8 CL CL 305 H CL 419 8 CL CL 306 H K 416 9 K K 101 D HOH 1047 10 HOH HOH 201 L HOH 1057 10 HOH HOH 202 L HOH 1072 10 HOH HOH 203 L HOH 1118 10 HOH HOH 204 L HOH 1141 10 HOH HOH 205 L HOH 1151 10 HOH HOH 206 L HOH 1154 10 HOH HOH 207 L HOH 1191 10 HOH HOH 208 L HOH 1206 10 HOH HOH 209 L HOH 1185 10 HOH HOH 210 L HOH 1033 10 HOH HOH 401 H HOH 1034 10 HOH HOH 402 H HOH 1035 10 HOH HOH 403 H HOH 1036 10 HOH HOH 404 H HOH 1037 10 HOH HOH 405 H HOH 1038 10 HOH HOH 406 H HOH 1039 10 HOH HOH 407 H HOH 1041 10 HOH HOH 408 H HOH 1042 10 HOH HOH 409 H HOH 1043 10 HOH HOH 410 H HOH 1045 10 HOH HOH 411 H HOH 1046 10 HOH HOH 412 H HOH 1048 10 HOH HOH 413 H HOH 1049 10 HOH HOH 414 H HOH 1050 10 HOH HOH 415 H HOH 1051 10 HOH HOH 416 H HOH 1052 10 HOH HOH 417 H HOH 1053 10 HOH HOH 418 H HOH 1054 10 HOH HOH 419 H HOH 1055 10 HOH HOH 420 H HOH 1056 10 HOH HOH 421 H HOH 1059 10 HOH HOH 422 H HOH 1060 10 HOH HOH 423 H HOH 1061 10 HOH HOH 424 H HOH 1062 10 HOH HOH 425 H HOH 1063 10 HOH HOH 426 H HOH 1064 10 HOH HOH 427 H HOH 1065 10 HOH HOH 428 H HOH 1066 10 HOH HOH 429 H HOH 1067 10 HOH HOH 430 H HOH 1068 10 HOH HOH 431 H HOH 1069 10 HOH HOH 432 H HOH 1070 10 HOH HOH 433 H HOH 1073 10 HOH HOH 434 H HOH 1074 10 HOH HOH 435 H HOH 1075 10 HOH HOH 436 H HOH 1076 10 HOH HOH 437 H HOH 1077 10 HOH HOH 438 H HOH 1078 10 HOH HOH 439 H HOH 1079 10 HOH HOH 440 H HOH 1080 10 HOH HOH 441 H HOH 1081 10 HOH HOH 442 H HOH 1082 10 HOH HOH 443 H HOH 1083 10 HOH HOH 444 H HOH 1084 10 HOH HOH 445 H HOH 1085 10 HOH HOH 446 H HOH 1086 10 HOH HOH 447 H HOH 1087 10 HOH HOH 448 H HOH 1088 10 HOH HOH 449 H HOH 1089 10 HOH HOH 450 H HOH 1091 10 HOH HOH 451 H HOH 1092 10 HOH HOH 452 H HOH 1093 10 HOH HOH 453 H HOH 1094 10 HOH HOH 454 H HOH 1095 10 HOH HOH 455 H HOH 1096 10 HOH HOH 456 H HOH 1097 10 HOH HOH 457 H HOH 1098 10 HOH HOH 458 H HOH 1099 10 HOH HOH 459 H HOH 1100 10 HOH HOH 460 H HOH 1102 10 HOH HOH 461 H HOH 1103 10 HOH HOH 462 H HOH 1104 10 HOH HOH 463 H HOH 1105 10 HOH HOH 464 H HOH 1106 10 HOH HOH 465 H HOH 1108 10 HOH HOH 466 H HOH 1110 10 HOH HOH 467 H HOH 1111 10 HOH HOH 468 H HOH 1112 10 HOH HOH 469 H HOH 1114 10 HOH HOH 470 H HOH 1115 10 HOH HOH 471 H HOH 1116 10 HOH HOH 472 H HOH 1117 10 HOH HOH 473 H HOH 1119 10 HOH HOH 474 H HOH 1120 10 HOH HOH 475 H HOH 1121 10 HOH HOH 476 H HOH 1122 10 HOH HOH 477 H HOH 1123 10 HOH HOH 478 H HOH 1124 10 HOH HOH 479 H HOH 1126 10 HOH HOH 480 H HOH 1127 10 HOH HOH 481 H HOH 1128 10 HOH HOH 482 H HOH 1129 10 HOH HOH 483 H HOH 1130 10 HOH HOH 484 H HOH 1132 10 HOH HOH 485 H HOH 1133 10 HOH HOH 486 H HOH 1134 10 HOH HOH 487 H HOH 1135 10 HOH HOH 488 H HOH 1136 10 HOH HOH 489 H HOH 1140 10 HOH HOH 490 H HOH 1142 10 HOH HOH 491 H HOH 1143 10 HOH HOH 492 H HOH 1144 10 HOH HOH 493 H HOH 1145 10 HOH HOH 494 H HOH 1147 10 HOH HOH 495 H HOH 1148 10 HOH HOH 496 H HOH 1152 10 HOH HOH 497 H HOH 1153 10 HOH HOH 498 H HOH 1155 10 HOH HOH 499 H HOH 1157 10 HOH HOH 500 H HOH 1158 10 HOH HOH 501 H HOH 1159 10 HOH HOH 502 H HOH 1160 10 HOH HOH 503 H HOH 1161 10 HOH HOH 504 H HOH 1162 10 HOH HOH 505 H HOH 1163 10 HOH HOH 506 H HOH 1166 10 HOH HOH 507 H HOH 1167 10 HOH HOH 508 H HOH 1168 10 HOH HOH 509 H HOH 1169 10 HOH HOH 510 H HOH 1170 10 HOH HOH 511 H HOH 1171 10 HOH HOH 512 H HOH 1172 10 HOH HOH 513 H HOH 1174 10 HOH HOH 514 H HOH 1175 10 HOH HOH 515 H HOH 1176 10 HOH HOH 516 H HOH 1178 10 HOH HOH 517 H HOH 1179 10 HOH HOH 518 H HOH 1180 10 HOH HOH 519 H HOH 1181 10 HOH HOH 520 H HOH 1182 10 HOH HOH 521 H HOH 1183 10 HOH HOH 522 H HOH 1184 10 HOH HOH 523 H HOH 1186 10 HOH HOH 524 H HOH 1187 10 HOH HOH 525 H HOH 1188 10 HOH HOH 526 H HOH 1190 10 HOH HOH 527 H HOH 1194 10 HOH HOH 528 H HOH 1195 10 HOH HOH 529 H HOH 1196 10 HOH HOH 530 H HOH 1197 10 HOH HOH 531 H HOH 1198 10 HOH HOH 532 H HOH 1199 10 HOH HOH 533 H HOH 1200 10 HOH HOH 534 H HOH 1201 10 HOH HOH 535 H HOH 1202 10 HOH HOH 536 H HOH 1203 10 HOH HOH 537 H HOH 1204 10 HOH HOH 538 H HOH 1205 10 HOH HOH 539 H HOH 1208 10 HOH HOH 540 H HOH 1209 10 HOH HOH 541 H HOH 1210 10 HOH HOH 542 H HOH 1211 10 HOH HOH 543 H HOH 1212 10 HOH HOH 544 H HOH 1214 10 HOH HOH 545 H HOH 1215 10 HOH HOH 546 H HOH 1231 10 HOH HOH 547 H HOH 1058 10 HOH HOH 201 D HOH 1101 10 HOH HOH 202 D HOH 1107 10 HOH HOH 203 D HOH 1137 10 HOH HOH 204 D HOH 1138 10 HOH HOH 205 D HOH 1139 10 HOH HOH 206 D HOH 1173 10 HOH HOH 207 D HOH 1177 10 HOH HOH 208 D HOH 1189 10 HOH HOH 209 D HOH 1192 10 HOH HOH 210 D HOH 1193 10 HOH HOH 211 D HOH 1207 10 HOH HOH 212 D HOH 1213 10 HOH HOH 213 D HOH 1216 10 HOH HOH 214 D HOH 1217 10 HOH HOH 215 D HOH 1218 10 HOH HOH 216 D HOH 1219 10 HOH HOH 217 D HOH 1220 10 HOH HOH 218 D HOH 1221 10 HOH HOH 219 D HOH 1222 10 HOH HOH 220 D HOH 1223 10 HOH HOH 221 D HOH 1224 10 HOH HOH 222 D HOH 1225 10 HOH HOH 223 D HOH 1226 10 HOH HOH 224 D HOH 1228 10 HOH HOH 225 D HOH 1230 10 HOH HOH 226 D n 1 -5 L n 2 -4 L n 3 -3 L n 4 -2 L n 5 -1 L n 6 0 L ALA 1 n 7 B ALA 1 L ASP 1 n 8 A ASP 1 L CYS 1 n 9 CYS 1 L GLY 2 n 10 GLY 2 L LEU 3 n 11 LEU 3 L ARG 4 n 12 ARG 4 L PRO 5 n 13 PRO 5 L LEU 6 n 14 LEU 6 L PHE 7 n 15 PHE 7 L GLU 8 n 16 GLU 8 L LYS 9 n 17 LYS 9 L LYS 10 n 18 LYS 10 L SER 11 n 19 SER 11 L LEU 12 n 20 LEU 12 L GLU 13 n 21 GLU 13 L ASP 14 n 22 ASP 14 L LYS 14 n 23 A LYS 14 L THR 14 n 24 B THR 14 L GLU 14 n 25 C GLU 14 L ARG 14 n 26 D ARG 14 L GLU 14 n 27 E GLU 14 L LEU 14 n 28 F LEU 14 L LEU 14 n 29 G LEU 14 L GLU 14 n 30 H GLU 14 L SER 14 n 31 I SER 14 L TYR 14 n 32 J TYR 14 L ILE 14 n 33 K ILE 14 L n 34 15 L n 35 16 L n 36 17 L ILE 16 n 1 ILE 16 H VAL 17 n 2 VAL 17 H GLU 18 n 3 GLU 18 H GLY 19 n 4 GLY 19 H SER 20 n 5 SER 20 H ASP 21 n 6 ASP 21 H ALA 22 n 7 ALA 22 H GLU 23 n 8 GLU 23 H ILE 24 n 9 ILE 24 H GLY 25 n 10 GLY 25 H MET 26 n 11 MET 26 H SER 27 n 12 SER 27 H PRO 28 n 13 PRO 28 H TRP 29 n 14 TRP 29 H GLN 30 n 15 GLN 30 H VAL 31 n 16 VAL 31 H MET 32 n 17 MET 32 H LEU 33 n 18 LEU 33 H PHE 34 n 19 PHE 34 H ARG 35 n 20 ARG 35 H LYS 36 n 21 LYS 36 H SER 36 n 22 A SER 36 H PRO 37 n 23 PRO 37 H GLN 38 n 24 GLN 38 H GLU 39 n 25 GLU 39 H LEU 40 n 26 LEU 40 H LEU 41 n 27 LEU 41 H CYS 42 n 28 CYS 42 H GLY 43 n 29 GLY 43 H ALA 44 n 30 ALA 44 H SER 45 n 31 SER 45 H LEU 46 n 32 LEU 46 H ILE 47 n 33 ILE 47 H SER 48 n 34 SER 48 H ASP 49 n 35 ASP 49 H ARG 50 n 36 ARG 50 H TRP 51 n 37 TRP 51 H VAL 52 n 38 VAL 52 H LEU 53 n 39 LEU 53 H THR 54 n 40 THR 54 H ALA 55 n 41 ALA 55 H ALA 56 n 42 ALA 56 H HIS 57 n 43 HIS 57 H CYS 58 n 44 CYS 58 H LEU 59 n 45 LEU 59 H LEU 60 n 46 LEU 60 H TYR 60 n 47 A TYR 60 H PRO 60 n 48 B PRO 60 H PRO 60 n 49 C PRO 60 H TRP 60 n 50 D TRP 60 H ASP 60 n 51 E ASP 60 H LYS 60 n 52 F LYS 60 H ASN 60 n 53 G ASN 60 H PHE 60 n 54 H PHE 60 H THR 60 n 55 I THR 60 H GLU 61 n 56 GLU 61 H ASN 62 n 57 ASN 62 H ASP 63 n 58 ASP 63 H LEU 64 n 59 LEU 64 H LEU 65 n 60 LEU 65 H VAL 66 n 61 VAL 66 H ARG 67 n 62 ARG 67 H ILE 68 n 63 ILE 68 H GLY 69 n 64 GLY 69 H LYS 70 n 65 LYS 70 H HIS 71 n 66 HIS 71 H SER 72 n 67 SER 72 H ARG 73 n 68 ARG 73 H THR 74 n 69 THR 74 H ARG 75 n 70 ARG 75 H TYR 76 n 71 TYR 76 H GLU 77 n 72 GLU 77 H ARG 77 n 73 A ARG 77 H ASN 78 n 74 ASN 78 H ILE 79 n 75 ILE 79 H GLU 80 n 76 GLU 80 H LYS 81 n 77 LYS 81 H ILE 82 n 78 ILE 82 H SER 83 n 79 SER 83 H MET 84 n 80 MET 84 H LEU 85 n 81 LEU 85 H GLU 86 n 82 GLU 86 H LYS 87 n 83 LYS 87 H ILE 88 n 84 ILE 88 H TYR 89 n 85 TYR 89 H ILE 90 n 86 ILE 90 H HIS 91 n 87 HIS 91 H PRO 92 n 88 PRO 92 H ARG 93 n 89 ARG 93 H TYR 94 n 90 TYR 94 H ASN 95 n 91 ASN 95 H TRP 96 n 92 TRP 96 H ARG 97 n 93 ARG 97 H GLU 97 n 94 A GLU 97 H ASN 98 n 95 ASN 98 H LEU 99 n 96 LEU 99 H ASP 100 n 97 ASP 100 H ARG 101 n 98 ARG 101 H ASP 102 n 99 ASP 102 H ILE 103 n 100 ILE 103 H ALA 104 n 101 ALA 104 H LEU 105 n 102 LEU 105 H MET 106 n 103 MET 106 H LYS 107 n 104 LYS 107 H LEU 108 n 105 LEU 108 H LYS 109 n 106 LYS 109 H LYS 110 n 107 LYS 110 H PRO 111 n 108 PRO 111 H VAL 112 n 109 VAL 112 H ALA 113 n 110 ALA 113 H PHE 114 n 111 PHE 114 H SER 115 n 112 SER 115 H ASP 116 n 113 ASP 116 H TYR 117 n 114 TYR 117 H ILE 118 n 115 ILE 118 H HIS 119 n 116 HIS 119 H PRO 120 n 117 PRO 120 H VAL 121 n 118 VAL 121 H CYS 122 n 119 CYS 122 H LEU 123 n 120 LEU 123 H PRO 124 n 121 PRO 124 H ASP 125 n 122 ASP 125 H ARG 126 n 123 ARG 126 H GLU 127 n 124 GLU 127 H THR 128 n 125 THR 128 H ALA 129 n 126 ALA 129 H ALA 129 n 127 A ALA 129 H SER 129 n 128 B SER 129 H LEU 129 n 129 C LEU 129 H LEU 130 n 130 LEU 130 H GLN 131 n 131 GLN 131 H ALA 132 n 132 ALA 132 H GLY 133 n 133 GLY 133 H TYR 134 n 134 TYR 134 H LYS 135 n 135 LYS 135 H GLY 136 n 136 GLY 136 H ARG 137 n 137 ARG 137 H VAL 138 n 138 VAL 138 H THR 139 n 139 THR 139 H GLY 140 n 140 GLY 140 H TRP 141 n 141 TRP 141 H GLY 142 n 142 GLY 142 H ASN 143 n 143 ASN 143 H LEU 144 n 144 LEU 144 H LYS 145 n 145 LYS 145 H GLU 146 n 146 GLU 146 H THR 147 n 147 THR 147 H n 148 A 147 H n 149 B 147 H n 150 C 147 H n 151 D 147 H n 152 E 147 H n 153 F 147 H n 154 G 147 H n 155 H 147 H GLN 151 n 156 GLN 151 H PRO 152 n 157 PRO 152 H SER 153 n 158 SER 153 H VAL 154 n 159 VAL 154 H LEU 155 n 160 LEU 155 H GLN 156 n 161 GLN 156 H VAL 157 n 162 VAL 157 H VAL 158 n 163 VAL 158 H ASN 159 n 164 ASN 159 H LEU 160 n 165 LEU 160 H PRO 161 n 166 PRO 161 H ILE 162 n 167 ILE 162 H VAL 163 n 168 VAL 163 H GLU 164 n 169 GLU 164 H ARG 165 n 170 ARG 165 H PRO 166 n 171 PRO 166 H VAL 167 n 172 VAL 167 H CYS 168 n 173 CYS 168 H LYS 169 n 174 LYS 169 H ASP 170 n 175 ASP 170 H SER 171 n 176 SER 171 H THR 172 n 177 THR 172 H ARG 173 n 178 ARG 173 H ILE 174 n 179 ILE 174 H ARG 175 n 180 ARG 175 H ILE 176 n 181 ILE 176 H THR 177 n 182 THR 177 H ASP 178 n 183 ASP 178 H ASN 179 n 184 ASN 179 H MET 180 n 185 MET 180 H PHE 181 n 186 PHE 181 H CYS 182 n 187 CYS 182 H ALA 183 n 188 ALA 183 H GLY 184 n 189 GLY 184 H TYR 184 n 190 A TYR 184 H LYS 185 n 191 LYS 185 H PRO 186 n 192 PRO 186 H ASP 186 n 193 A ASP 186 H GLU 186 n 194 B GLU 186 H GLY 186 n 195 C GLY 186 H LYS 186 n 196 D LYS 186 H ARG 187 n 197 ARG 187 H GLY 188 n 198 GLY 188 H ASP 189 n 199 ASP 189 H ALA 190 n 200 ALA 190 H CYS 191 n 201 CYS 191 H GLU 192 n 202 GLU 192 H GLY 193 n 203 GLY 193 H ASP 194 n 204 ASP 194 H SER 195 n 205 SER 195 H GLY 196 n 206 GLY 196 H GLY 197 n 207 GLY 197 H PRO 198 n 208 PRO 198 H PHE 199 n 209 PHE 199 H VAL 200 n 210 VAL 200 H MET 201 n 211 MET 201 H LYS 202 n 212 LYS 202 H SER 203 n 213 SER 203 H PRO 204 n 214 PRO 204 H PHE 204 n 215 A PHE 204 H ASN 204 n 216 B ASN 204 H ASN 205 n 217 ASN 205 H ARG 206 n 218 ARG 206 H TRP 207 n 219 TRP 207 H TYR 208 n 220 TYR 208 H GLN 209 n 221 GLN 209 H MET 210 n 222 MET 210 H GLY 211 n 223 GLY 211 H ILE 212 n 224 ILE 212 H VAL 213 n 225 VAL 213 H SER 214 n 226 SER 214 H TRP 215 n 227 TRP 215 H GLY 216 n 228 GLY 216 H GLU 217 n 229 GLU 217 H GLY 219 n 230 GLY 219 H CYS 220 n 231 CYS 220 H ASP 221 n 232 A ASP 221 H ARG 221 n 233 ARG 221 H ASP 222 n 234 ASP 222 H GLY 223 n 235 GLY 223 H LYS 224 n 236 LYS 224 H TYR 225 n 237 TYR 225 H GLY 226 n 238 GLY 226 H PHE 227 n 239 PHE 227 H TYR 228 n 240 TYR 228 H THR 229 n 241 THR 229 H HIS 230 n 242 HIS 230 H VAL 231 n 243 VAL 231 H PHE 232 n 244 PHE 232 H ARG 233 n 245 ARG 233 H LEU 234 n 246 LEU 234 H LYS 235 n 247 LYS 235 H LYS 236 n 248 LYS 236 H TRP 237 n 249 TRP 237 H ILE 238 n 250 ILE 238 H GLN 239 n 251 GLN 239 H LYS 240 n 252 LYS 240 H VAL 241 n 253 VAL 241 H ILE 242 n 254 ILE 242 H ASP 243 n 255 ASP 243 H GLN 244 n 256 GLN 244 H PHE 245 n 257 PHE 245 H GLY 246 n 258 GLY 246 H n 259 247 H DG 1 n 1 DG 1 D DG 2 n 2 DG 2 D DT 3 n 3 DT 3 D DT 4 n 4 DT 4 D DG 5 n 5 DG 5 D DG 6 n 6 DG 6 D DT 7 n 7 DT 7 D DG 8 n 8 DG 8 D DT 9 n 9 DT 9 D DG 10 n 10 DG 10 D DG 11 n 11 DG 11 D DT 12 n 12 DT 12 D DT 13 n 13 DT 13 D DG 14 n 14 DG 14 D DG 15 n 15 DG 15 D author_and_software_defined_assembly PISA 3 trimeric 3280 -14 14870 A L ASP 1 A OD1 ASP 8 1_555 L ZN 101 D ZN ZN 1_555 H HIS 119 B NE2 HIS 116 1_555 112.0 E H ASP 60 B OD1 ASP 51 1_555 H ZN 304 H ZN ZN 1_555 E H ASP 60 B OD2 ASP 51 1_555 55.0 H ARG 221 B O ARG 233 1_555 H NA 303 G NA NA 1_555 H LYS 224 B O LYS 236 1_555 84.6 H ARG 221 B O ARG 233 1_555 H NA 303 G NA NA 1_555 H HOH 418 M O HOH 1_555 107.2 H LYS 224 B O LYS 236 1_555 H NA 303 G NA NA 1_555 H HOH 418 M O HOH 1_555 145.8 H ARG 221 B O ARG 233 1_555 H NA 303 G NA NA 1_555 H HOH 464 M O HOH 1_555 135.0 H LYS 224 B O LYS 236 1_555 H NA 303 G NA NA 1_555 H HOH 464 M O HOH 1_555 65.0 H HOH 418 M O HOH 1_555 H NA 303 G NA NA 1_555 H HOH 464 M O HOH 1_555 85.6 D DG 1 C O6 DG 1 1_555 D K 101 K K K 1_555 D DG 2 C O6 DG 2 1_555 68.2 D DG 1 C O6 DG 1 1_555 D K 101 K K K 1_555 D DG 5 C O6 DG 5 1_555 116.6 D DG 2 C O6 DG 2 1_555 D K 101 K K K 1_555 D DG 5 C O6 DG 5 1_555 65.3 D DG 1 C O6 DG 1 1_555 D K 101 K K K 1_555 D DG 6 C O6 DG 6 1_555 76.1 D DG 2 C O6 DG 2 1_555 D K 101 K K K 1_555 D DG 6 C O6 DG 6 1_555 100.3 D DG 5 C O6 DG 5 1_555 D K 101 K K K 1_555 D DG 6 C O6 DG 6 1_555 72.6 D DG 1 C O6 DG 1 1_555 D K 101 K K K 1_555 D DG 10 C O6 DG 10 1_555 118.7 D DG 2 C O6 DG 2 1_555 D K 101 K K K 1_555 D DG 10 C O6 DG 10 1_555 164.5 D DG 5 C O6 DG 5 1_555 D K 101 K K K 1_555 D DG 10 C O6 DG 10 1_555 99.8 D DG 6 C O6 DG 6 1_555 D K 101 K K K 1_555 D DG 10 C O6 DG 10 1_555 69.8 D DG 1 C O6 DG 1 1_555 D K 101 K K K 1_555 D DG 11 C O6 DG 11 1_555 165.9 D DG 2 C O6 DG 2 1_555 D K 101 K K K 1_555 D DG 11 C O6 DG 11 1_555 108.9 D DG 5 C O6 DG 5 1_555 D K 101 K K K 1_555 D DG 11 C O6 DG 11 1_555 72.2 D DG 6 C O6 DG 6 1_555 D K 101 K K K 1_555 D DG 11 C O6 DG 11 1_555 117.8 D DG 10 C O6 DG 10 1_555 D K 101 K K K 1_555 D DG 11 C O6 DG 11 1_555 67.9 D DG 1 C O6 DG 1 1_555 D K 101 K K K 1_555 D DG 14 C O6 DG 14 1_555 100.6 D DG 2 C O6 DG 2 1_555 D K 101 K K K 1_555 D DG 14 C O6 DG 14 1_555 66.7 D DG 5 C O6 DG 5 1_555 D K 101 K K K 1_555 D DG 14 C O6 DG 14 1_555 98.1 D DG 6 C O6 DG 6 1_555 D K 101 K K K 1_555 D DG 14 C O6 DG 14 1_555 166.7 D DG 10 C O6 DG 10 1_555 D K 101 K K K 1_555 D DG 14 C O6 DG 14 1_555 122.1 D DG 11 C O6 DG 11 1_555 D K 101 K K K 1_555 D DG 14 C O6 DG 14 1_555 66.3 D DG 1 C O6 DG 1 1_555 D K 101 K K K 1_555 D DG 15 C O6 DG 15 1_555 75.3 D DG 2 C O6 DG 2 1_555 D K 101 K K K 1_555 D DG 15 C O6 DG 15 1_555 123.1 D DG 5 C O6 DG 5 1_555 D K 101 K K K 1_555 D DG 15 C O6 DG 15 1_555 168.1 D DG 6 C O6 DG 6 1_555 D K 101 K K K 1_555 D DG 15 C O6 DG 15 1_555 111.5 D DG 10 C O6 DG 10 1_555 D K 101 K K K 1_555 D DG 15 C O6 DG 15 1_555 72.3 D DG 11 C O6 DG 11 1_555 D K 101 K K K 1_555 D DG 15 C O6 DG 15 1_555 96.4 D DG 14 C O6 DG 14 1_555 D K 101 K K K 1_555 D DG 15 C O6 DG 15 1_555 79.5 G H ASN 60 GLYCOSYLATION SITE B ASN 53 ASN 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 H N SER 20 B N SER 5 H O VAL 157 B O VAL 162 H O LEU 160 B O LEU 165 H N GLY 136 B N GLY 136 H N ARG 137 B N ARG 137 H O VAL 200 B O VAL 210 H N MET 201 B N MET 211 H O TYR 208 B O TYR 220 H N TRP 215 B N TRP 227 H O PHE 227 B O PHE 239 H O TYR 228 B O TYR 240 H N PHE 181 B N PHE 186 H N ARG 35 B N ARG 20 H O GLU 39 B O GLU 25 H N SER 45 B N SER 31 H O LEU 53 B O LEU 39 H N VAL 52 B N VAL 38 H O MET 106 B O MET 103 H O LEU 105 B O LEU 102 H N TYR 89 B N TYR 85 H O SER 83 B O SER 79 H N VAL 66 B N VAL 61 H O LEU 65 B O LEU 60 H N PHE 34 B N PHE 19 A H N TYR 60 B N TYR 47 F H O LYS 60 B O LYS 52 1 L THR -5 A THR 1 1 Y 1 L PHE -4 A PHE 2 1 Y 1 L GLY -3 A GLY 3 1 Y 1 L SER -2 A SER 4 1 Y 1 L GLY -1 A GLY 5 1 Y 1 L GLU 0 A GLU 6 1 Y 1 L ASP 15 A ASP 34 1 Y 1 L GLY 16 A GLY 35 1 Y 1 L ARG 17 A ARG 36 1 Y A 1 H TRP 147 B TRP 148 1 Y B 1 H THR 147 B THR 149 1 Y C 1 H ALA 147 B ALA 150 1 Y D 1 H ASN 147 B ASN 151 1 Y E 1 H VAL 147 B VAL 152 1 Y F 1 H GLY 147 B GLY 153 1 Y G 1 H LYS 147 B LYS 154 1 Y H 1 H GLY 147 B GLY 155 1 Y 1 H GLU 247 B GLU 259 1 Y 1 D D O O HOH HOH 207 217 2.17 1 H H OG O2 SER 0G6 195 301 2.19 1 3.40 0.50 120.30 123.70 H H H NE CZ NH1 ARG ARG ARG 75 75 75 N 1 -3.28 0.50 120.30 117.02 H H H NE CZ NH2 ARG ARG ARG 126 126 126 N 1 L PHE 7 -126.09 -82.04 A 1 H TYR 60 -159.37 85.01 G 1 H ASN 60 -162.50 83.36 1 H ASN 98 -143.12 17.85 1 H PRO 186 -26.44 -22.44 A 1 H ASP 186 -163.68 34.42 B 1 H GLU 186 -66.04 17.62 0.226 0.174 0.195 0.195 2.05 50.00 18499 21478 19447 RANDOM 1 0.00 0.00 MOLECULAR REPLACEMENT PDB ENTRY 3QLP AND 1HAO Engh & Huber 2.05 50.00 183 2795 50 315 2247 2.05 50.00 4DII 20850 20850 0.000 0.000 1 94.5 2.05 2.12 1 84.5 data collection CrystalClear phasing PHASES refinement CNS data reduction HKL-2000 data scaling HKL-2000 X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of potassium ions 1 N N 2 N N 3 N N 4 N N 5 N N 6 N N 7 N N 4 N N 8 N N 8 N N 9 N N 10 N N 10 N N 10 N N 1:1 protein-DNA aptamer complex L PHE 7 A PHE 15 HELX_P L SER 11 A SER 19 5 1 5 L THR 14 A THR 24 HELX_P L TYR 14 A TYR 32 1 2 9 B J H ALA 55 B ALA 41 HELX_P H LEU 59 B LEU 45 1 3 5 H PRO 60 B PRO 48 HELX_P H ASP 60 B ASP 51 5 4 4 B E H THR 60 B THR 55 HELX_P H ASN 62 B ASN 57 5 5 3 I H ASP 125 B ASP 122 HELX_P H LEU 130 B LEU 130 1 6 9 H GLU 164 B GLU 169 HELX_P H SER 171 B SER 176 1 7 8 H LEU 234 B LEU 246 HELX_P H GLY 246 B GLY 258 1 8 13 disulf 2.073 L CYS 1 A SG CYS 9 1_555 H CYS 122 B SG CYS 119 1_555 disulf 2.044 H CYS 42 B SG CYS 28 1_555 H CYS 58 B SG CYS 44 1_555 disulf 2.031 H CYS 168 B SG CYS 173 1_555 H CYS 182 B SG CYS 187 1_555 disulf 2.038 H CYS 191 B SG CYS 201 1_555 H CYS 220 B SG CYS 231 1_555 covale 1.395 one H HIS 57 B NE2 HIS 43 1_555 H 0G6 301 E C3 0G6 1_555 covale 1.447 one G N-Glycosylation H ASN 60 B ND2 ASN 53 1_555 H NAG 302 F C1 NAG 1_555 covale 1.360 none H SER 195 B OG SER 205 1_555 H 0G6 301 E C2 0G6 1_555 metalc 1.920 A L ASP 1 A OD1 ASP 8 1_555 L ZN 101 D ZN ZN 1_555 metalc 2.179 L ZN 101 D ZN ZN 1_555 H HIS 119 B NE2 HIS 116 1_555 metalc 2.208 E H ASP 60 B OD1 ASP 51 1_555 H ZN 304 H ZN ZN 1_555 metalc 2.587 E H ASP 60 B OD2 ASP 51 1_555 H ZN 304 H ZN ZN 1_555 metalc 2.541 H ARG 221 B O ARG 233 1_555 H NA 303 G NA NA 1_555 metalc 2.676 H LYS 224 B O LYS 236 1_555 H NA 303 G NA NA 1_555 metalc 2.542 H NA 303 G NA NA 1_555 H HOH 418 M O HOH 1_555 metalc 2.599 H NA 303 G NA NA 1_555 H HOH 464 M O HOH 1_555 metalc 2.689 D DG 1 C O6 DG 1 1_555 D K 101 K K K 1_555 metalc 2.951 D DG 2 C O6 DG 2 1_555 D K 101 K K K 1_555 metalc 2.726 D DG 5 C O6 DG 5 1_555 D K 101 K K K 1_555 metalc 2.924 D DG 6 C O6 DG 6 1_555 D K 101 K K K 1_555 metalc 2.901 D DG 10 C O6 DG 10 1_555 D K 101 K K K 1_555 metalc 2.820 D DG 11 C O6 DG 11 1_555 D K 101 K K K 1_555 metalc 2.714 D DG 14 C O6 DG 14 1_555 D K 101 K K K 1_555 metalc 2.807 D DG 15 C O6 DG 15 1_555 D K 101 K K K 1_555 hydrog TYPE_6_PAIR D DG 1 C N1 DG 1 1_555 D DG 6 C O6 DG 6 1_555 hydrog TYPE_6_PAIR D DG 1 C N2 DG 1 1_555 D DG 6 C N7 DG 6 1_555 hydrog TYPE_6_PAIR D DG 1 C N7 DG 1 1_555 D DG 15 C N2 DG 15 1_555 hydrog TYPE_6_PAIR D DG 1 C O6 DG 1 1_555 D DG 15 C N1 DG 15 1_555 hydrog TYPE_6_PAIR D DG 2 C N7 DG 2 1_555 D DG 5 C N2 DG 5 1_555 hydrog TYPE_6_PAIR D DG 2 C O6 DG 2 1_555 D DG 5 C N1 DG 5 1_555 hydrog TYPE_6_PAIR D DG 2 C N1 DG 2 1_555 D DG 14 C O6 DG 14 1_555 hydrog TYPE_6_PAIR D DG 2 C N2 DG 2 1_555 D DG 14 C N7 DG 14 1_555 hydrog TYPE_6_PAIR D DG 5 C N7 DG 5 1_555 D DG 11 C N2 DG 11 1_555 hydrog TYPE_6_PAIR D DG 5 C O6 DG 5 1_555 D DG 11 C N1 DG 11 1_555 hydrog TYPE_6_PAIR D DG 6 C N1 DG 6 1_555 D DG 10 C O6 DG 10 1_555 hydrog TYPE_6_PAIR D DG 6 C N2 DG 6 1_555 D DG 10 C N7 DG 10 1_555 hydrog TYPE_6_PAIR D DG 10 C N1 DG 10 1_555 D DG 15 C O6 DG 15 1_555 hydrog TYPE_6_PAIR D DG 10 C N2 DG 10 1_555 D DG 15 C N7 DG 15 1_555 hydrog TYPE_6_PAIR D DG 11 C N7 DG 11 1_555 D DG 14 C N2 DG 14 1_555 hydrog TYPE_6_PAIR D DG 11 C O6 DG 11 1_555 D DG 14 C N1 DG 14 1_555 hydrog DT-DG MISPAIR D DT 13 C O2 DT 13 1_555 D DG 14 C N1 DG 14 1_555 HYDROLASE/HYDROLASE INHIBITOR/DNA protein-DNA complex, serine protease, blood coagulation, aptamer, hydrolase-hydrolase inhibitor-DNA complex, serine protease fold, DNA aptamer, blood, G-quadruplex H SER 36 B SER 22 A 1 H PRO 37 B PRO 23 0.10 THRB_HUMAN UNP 1 328 P00734 TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR THRB_HUMAN UNP 2 364 P00734 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFGE 4DII PDB 3 1 4DII GGTTGGTGTGGTTGG 328 363 4DII -5 17 P00734 L 1 1 36 364 622 4DII 16 247 P00734 H 2 1 259 1 15 4DII 1 15 4DII D 3 1 15 7 7 2 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel H SER 20 B SER 5 H ASP 21 B ASP 6 H GLN 156 B GLN 161 H PRO 161 B PRO 166 H LYS 135 B LYS 135 H GLY 140 B GLY 140 H PRO 198 B PRO 208 H LYS 202 B LYS 212 H TRP 207 B TRP 219 H TRP 215 B TRP 227 H GLY 226 B GLY 238 H HIS 230 B HIS 242 H MET 180 B MET 185 H ALA 183 B ALA 188 H GLN 30 B GLN 15 H ARG 35 B ARG 20 H GLU 39 B GLU 25 H LEU 46 B LEU 32 H TRP 51 B TRP 37 H THR 54 B THR 40 H ALA 104 B ALA 101 H LEU 108 B LEU 105 H LYS 81 B LYS 77 H ILE 90 B ILE 86 H LEU 64 B LEU 59 H ILE 68 B ILE 63 H GLN 30 B GLN 15 H ARG 35 B ARG 20 H LEU 60 B LEU 46 H TYR 60 B TYR 47 A H LYS 60 B LYS 52 H ASN 60 B ASN 53 F G 1 P 1