0.017926 0.000000 0.000000 -0.000000 0.013427 0.000000 0.000000 -0.000000 0.008136 0.000000 0.000000 0.000000 Wang, J. Zajonc, D.M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.000 90.000 90.000 55.785 74.479 122.917 C40 H79 N O9 718.057 N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexadecanamide non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking 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 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 C N 2 N 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 C N 14 N C N 15 R C N 16 N O N 17 S C N 18 N O N 19 S C N 20 N C N 21 N O N 22 S C N 23 N O N 24 R C N 25 N C N 26 N O N 27 R C N 28 N O N 29 S C N 30 N O N 31 R C N 32 N O N 33 N N N 34 N C N 35 N O N 36 N C N 37 N C N 38 N C N 39 N C N 40 N C N 41 N C N 42 N C N 43 N C N 44 N C N 45 N C N 46 N C N 47 N C N 48 N C N 49 N C N 50 N C N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H 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 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 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 H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H 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 N N 131 S C N 132 N C N 133 N O N 134 N C N 135 N O 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 N N 144 S C N 145 N C N 146 N O N 147 N C N 148 N C N 149 N C N 150 N N N 151 N C N 152 N N N 153 N N 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 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 O N 177 N N N 178 N O N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N N N 188 S C N 189 N C N 190 N O N 191 N C N 192 N C N 193 N O N 194 N O N 195 N O 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 N N 204 R C N 205 N C N 206 N O N 207 N C N 208 N S N 209 N O N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N N N 218 S C N 219 N C N 220 N O N 221 N C N 222 N C N 223 N C N 224 N O N 225 N N N 226 N O N 227 N H N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N N N 238 S C N 239 N C N 240 N O N 241 N C N 242 N C N 243 N C N 244 N O N 245 N O N 246 N O 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 H N 254 N H N 255 N H N 256 N N N 257 N C N 258 N C N 259 N O N 260 N O 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 S C N 268 N C N 269 N O N 270 N C Y 271 N C Y 272 N N Y 273 N C Y 274 N C Y 275 N N N 276 N O 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 O N 288 N H N 289 N H N 290 N N N 291 S C N 292 N C N 293 N O N 294 S C N 295 N C N 296 N C N 297 N C N 298 N O 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 C 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 H N 333 N H N 334 N N N 335 S C N 336 N C N 337 N O N 338 N C N 339 N C N 340 N C N 341 N C N 342 N N 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 H N 356 N H N 357 N H N 358 N H N 359 N N N 360 S C N 361 N C N 362 N O N 363 N C N 364 N C N 365 N S N 366 N C N 367 N O 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 H N 377 N H N 378 N H N 379 R C N 380 R C N 381 R C N 382 S C N 383 R C N 384 N C N 385 N C N 386 N C N 387 N N N 388 N O N 389 N O N 390 N O N 391 N O N 392 N O 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 H N 404 N H N 405 N H N 406 N H N 407 N H N 408 N H N 409 N N N 410 S C N 411 N C N 412 N O N 413 N C Y 414 N C Y 415 N C Y 416 N C Y 417 N C Y 418 N C Y 419 N C N 420 N O 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 H N 431 N H N 432 N N N 433 S C N 434 N C N 435 N O N 436 N C N 437 N C N 438 N C N 439 N O N 440 N H N 441 N H N 442 N H N 443 N H N 444 N H N 445 N H N 446 N H N 447 N H N 448 N H N 449 N N N 450 S C N 451 N C N 452 N O N 453 N C N 454 N O N 455 N O N 456 N H N 457 N H N 458 N H N 459 N H N 460 N H N 461 N H N 462 N H N 463 N S N 464 N O N 465 N O N 466 N O N 467 N O N 468 N N N 469 S C N 470 N C N 471 N O N 472 R C N 473 N O N 474 N C N 475 N O N 476 N H N 477 N H N 478 N H N 479 N H N 480 N H N 481 N H N 482 N H N 483 N H N 484 N H N 485 N N N 486 S C N 487 N C N 488 N O N 489 N C Y 490 N C Y 491 N C Y 492 N C Y 493 N N Y 494 N C Y 495 N C Y 496 N C Y 497 N C Y 498 N C N 499 N O N 500 N H N 501 N H N 502 N H N 503 N H N 504 N H N 505 N H N 506 N H N 507 N H N 508 N H N 509 N H N 510 N H N 511 N H N 512 N N N 513 S C N 514 N C N 515 N O N 516 N C Y 517 N C Y 518 N C Y 519 N C Y 520 N C Y 521 N C Y 522 N C N 523 N O N 524 N O N 525 N H N 526 N H N 527 N H N 528 N H N 529 N H N 530 N H N 531 N H N 532 N H N 533 N H N 534 N H N 535 N H N 536 N N N 537 S C N 538 N C N 539 N O N 540 N C N 541 N C N 542 N C N 543 N O N 544 N H N 545 N H N 546 N H N 547 N H N 548 N H N 549 N H N 550 N H N 551 N H N 552 N H N 553 N H N 554 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 doub 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 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 sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N 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 sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N 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 sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N doub 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 doub 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 doub 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 doub N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N doub N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N 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 doub N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N doub N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N doub N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N doub N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N doub N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N doub 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 doub 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 doub N 265 N sing N 266 N sing N 267 N sing N 268 N sing Y 269 N sing Y 270 N doub Y 271 N doub N 272 N sing Y 273 N sing N 274 N sing Y 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 sing N 287 N doub 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 doub N 309 N sing N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N 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 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 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 sing N 353 N doub 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 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 doub 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 sing N 401 N sing N 402 N doub N 403 N sing N 404 N sing N 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 doub N 412 N sing Y 413 N doub N 414 N sing Y 415 N sing N 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 doub N 426 N sing N 427 N sing N 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 sing N 439 N sing N 440 N sing N 441 N sing N 442 N doub 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 doub 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 doub 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 sing 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 doub N 476 N sing N 477 N sing N 478 N sing N 479 N sing Y 480 N doub Y 481 N sing Y 482 N sing N 483 N sing Y 484 N doub Y 485 N sing Y 486 N sing N 487 N sing Y 488 N sing Y 489 N doub N 490 N sing Y 491 N doub N 492 N sing Y 493 N sing N 494 N sing N 495 N sing N 496 N sing N 497 N sing N 498 N sing N 499 N sing N 500 N sing N 501 N sing N 502 N sing N 503 N doub N 504 N sing N 505 N sing N 506 N sing N 507 N sing Y 508 N doub Y 509 N sing Y 510 N sing N 511 N sing Y 512 N doub N 513 N sing Y 514 N doub N 515 N sing Y 516 N sing N 517 N sing N 518 N sing N 519 N sing N 520 N sing N 521 N sing N 522 N sing N 523 N sing N 524 N sing N 525 N sing N 526 N sing N 527 N doub 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 sing N 537 N sing N 538 N sing US Plos One 1932-6203 7 e47989 e47989 10.1371/journal.pone.0047989 23110152 Crystal Structures of Bovine CD1d Reveal Altered αGalCer Presentation and a Restricted A' Pocket Unable to Bind Long-Chain Glycolipids. 2012 10.2210/pdb4f7e/pdb pdb_00004f7e 100 1 Rh coated flat mirror PIXEL 2012-02-03 DECTRIS PILATUS 6M Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees SINGLE WAVELENGTH M x-ray 1 1.0 1.0 108859 0.059 1.57 2.150 40.000 28064 96.10 3.90 BL11-1 SSRL 1.0 SYNCHROTRON SSRL BEAMLINE BL11-1 32460.561 CD1D antigen, d polypeptide UNP residues 129-405 1 man polymer 11653.148 Beta-2-microglobulin UNP residues 21-118 1 man polymer 424.401 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose 1 man branched 718.057 N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexadecanamide 1 syn non-polymer 221.208 2-acetamido-2-deoxy-beta-D-glucopyranose 1 man non-polymer 96.063 SULFATE ION 1 syn non-polymer 18.015 water 26 nat water T cell surface glycoprotein CD1d antigen Lactollin no no SPAPQTPFSFQGLQISSFANRSWTRTDGLAWLGELQPYTWRNESDTIRFLKPWSRGTFSDQQWEQLQHTLLVYRSSFTRD IWEFVEKLHVEYPLEIQIATGCELLPRNISESFLRAAFQGRDVLSFQGMSWVSAPDAPPFIQEVIKVLNQNQGTKETVHW LLHDIWPELVRGVLQTGKSELEKQVKPEAWLSSGPSPGPGRLLLVCHVSGFYPKPVRVMWMRGEQEEPGTRQGDVMPNAD STWYLRVTLDVAAGEVAGLSCQVKHSSLGDQDIILYWHHHHHH SPAPQTPFSFQGLQISSFANRSWTRTDGLAWLGELQPYTWRNESDTIRFLKPWSRGTFSDQQWEQLQHTLLVYRSSFTRD IWEFVEKLHVEYPLEIQIATGCELLPRNISESFLRAAFQGRDVLSFQGMSWVSAPDAPPFIQEVIKVLNQNQGTKETVHW LLHDIWPELVRGVLQTGKSELEKQVKPEAWLSSGPSPGPGRLLLVCHVSGFYPKPVRVMWMRGEQEEPGTRQGDVMPNAD STWYLRVTLDVAAGEVAGLSCQVKHSSLGDQDIILYWHHHHHH A polypeptide(L) no no IQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSFSKDWSFYLLSHAEFTPNSKDQYSCR VKHVTLEQPRIVKWDRDL IQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSFSKDWSFYLLSHAEFTPNSKDQYSCR VKHVTLEQPRIVKWDRDL 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 n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n bovine fall armyworm sample CD1D 9913 Bos taurus 7108 Spodoptera frugiperda SF9 baculovirus pBACpHp10 bovine fall armyworm sample B2M 9913 Bos taurus 7108 Spodoptera frugiperda SF9 baculovirus pBACpHp10 1 2.90 57.54 VAPOR DIFFUSION, SITTING DROP 20% PEG4000, 200 mM potassium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K 295 atom_site chem_comp entity pdbx_branch_scheme pdbx_chem_comp_identifier pdbx_entity_branch pdbx_entity_branch_descriptor pdbx_entity_branch_link pdbx_entity_branch_list pdbx_entity_nonpoly pdbx_nonpoly_scheme pdbx_struct_assembly_gen struct_asym struct_conn struct_ref_seq_dif 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 Atomic model Data collection Database references Derived calculations Structure summary Data collection Database references Refinement description Structure summary 1 0 2012-11-14 2 0 2020-07-29 2 1 2023-09-13 _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.label_asym_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_entity_id _atom_site.type_symbol _chem_comp.name _chem_comp.type _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_struct_assembly_gen.asym_id_list _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _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_seq_id _struct_conn.ptnr2_label_asym_id _struct_ref_seq_dif.details _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession A NAG 500 n C NAG 1 A NAG 501 n C NAG 2 DGlcpNAcb N-acetyl-b-D-glucopyranosamine b-D-GlcpNAc GlcNAc Structure of a highly potent short-chain galactosyl ceramide agonist bound to CD1d The crystal structure of human CD1d with and without alpha-Galactosylceramide RCSB Y RCSB 2012-05-15 REL REL 0.045 2.853 88.00 3.80 0.046 2.992 96.40 3.90 0.054 2.954 98.80 4.20 0.060 2.567 97.10 3.90 0.066 1.814 98.70 4.20 0.074 1.416 99.10 4.30 0.090 1.167 99.20 4.20 0.113 1.232 97.20 3.80 0.132 0.874 99.40 4.00 0.158 0.788 99.40 4.10 0.198 0.837 98.20 3.90 0.206 0.739 97.50 3.80 0.253 1.008 91.70 3.40 0.255 0.807 91.10 3.20 0.317 0.703 89.80 3.30 oligosaccharide DGlcpNAcb1-4DGlcpNAcb1- 3 GMML 1.0 Glycam Condensed Sequence WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1 3 PDB2Glycan 1.1.0 WURCS []{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}} 3 PDB-CARE LINUCS C1 O4 NAG NAG 2 1 3 O1 HO4 sing n n 0SH N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexadecanamide NAG 2-acetamido-2-deoxy-beta-D-glucopyranose SO4 SULFATE ION HOH water 3L9R PDB ENTRY 3L9R PDB experimental model AGH 282 4 0SH 0SH 301 A NAG 502 5 NAG NAG 304 A SO4 1 6 SO4 SO4 101 B HOH 3 7 HOH HOH 401 A HOH 4 7 HOH HOH 402 A HOH 5 7 HOH HOH 403 A HOH 9 7 HOH HOH 404 A HOH 12 7 HOH HOH 405 A HOH 13 7 HOH HOH 406 A HOH 14 7 HOH HOH 407 A HOH 18 7 HOH HOH 408 A HOH 23 7 HOH HOH 409 A HOH 38 7 HOH HOH 410 A HOH 45 7 HOH HOH 411 A HOH 66 7 HOH HOH 412 A HOH 185 7 HOH HOH 413 A HOH 186 7 HOH HOH 414 A HOH 189 7 HOH HOH 415 A HOH 190 7 HOH HOH 416 A HOH 191 7 HOH HOH 417 A HOH 192 7 HOH HOH 418 A HOH 193 7 HOH HOH 419 A HOH 1 7 HOH HOH 201 B HOH 8 7 HOH HOH 202 B HOH 25 7 HOH HOH 203 B HOH 26 7 HOH HOH 204 B HOH 55 7 HOH HOH 205 B HOH 176 7 HOH HOH 206 B HOH 184 7 HOH HOH 207 B n 1 1 A n 2 2 A n 3 3 A n 4 4 A n 5 5 A n 6 6 A n 7 7 A PHE 8 n 8 PHE 8 A SER 9 n 9 SER 9 A PHE 10 n 10 PHE 10 A GLN 11 n 11 GLN 11 A GLY 12 n 12 GLY 12 A LEU 13 n 13 LEU 13 A GLN 14 n 14 GLN 14 A ILE 15 n 15 ILE 15 A SER 16 n 16 SER 16 A SER 17 n 17 SER 17 A PHE 18 n 18 PHE 18 A ALA 19 n 19 ALA 19 A ASN 20 n 20 ASN 20 A ARG 21 n 21 ARG 21 A SER 22 n 22 SER 22 A TRP 23 n 23 TRP 23 A THR 24 n 24 THR 24 A ARG 25 n 25 ARG 25 A THR 26 n 26 THR 26 A ASP 27 n 27 ASP 27 A GLY 28 n 28 GLY 28 A LEU 29 n 29 LEU 29 A ALA 30 n 30 ALA 30 A TRP 31 n 31 TRP 31 A LEU 32 n 32 LEU 32 A GLY 33 n 33 GLY 33 A GLU 34 n 34 GLU 34 A LEU 35 n 35 LEU 35 A GLN 36 n 36 GLN 36 A PRO 37 n 37 PRO 37 A TYR 38 n 38 TYR 38 A THR 39 n 39 THR 39 A TRP 40 n 40 TRP 40 A ARG 41 n 41 ARG 41 A ASN 42 n 42 ASN 42 A GLU 43 n 43 GLU 43 A SER 44 n 44 SER 44 A ASP 45 n 45 ASP 45 A THR 46 n 46 THR 46 A ILE 47 n 47 ILE 47 A ARG 48 n 48 ARG 48 A PHE 49 n 49 PHE 49 A LEU 50 n 50 LEU 50 A LYS 51 n 51 LYS 51 A PRO 52 n 52 PRO 52 A TRP 53 n 53 TRP 53 A SER 54 n 54 SER 54 A ARG 55 n 55 ARG 55 A GLY 56 n 56 GLY 56 A THR 57 n 57 THR 57 A PHE 58 n 58 PHE 58 A SER 59 n 59 SER 59 A ASP 60 n 60 ASP 60 A GLN 61 n 61 GLN 61 A GLN 62 n 62 GLN 62 A TRP 63 n 63 TRP 63 A GLU 64 n 64 GLU 64 A GLN 65 n 65 GLN 65 A LEU 66 n 66 LEU 66 A GLN 67 n 67 GLN 67 A HIS 68 n 68 HIS 68 A THR 69 n 69 THR 69 A LEU 70 n 70 LEU 70 A LEU 71 n 71 LEU 71 A VAL 72 n 72 VAL 72 A TYR 73 n 73 TYR 73 A ARG 74 n 74 ARG 74 A SER 75 n 75 SER 75 A SER 76 n 76 SER 76 A PHE 77 n 77 PHE 77 A THR 78 n 78 THR 78 A ARG 79 n 79 ARG 79 A ASP 80 n 80 ASP 80 A ILE 81 n 81 ILE 81 A TRP 82 n 82 TRP 82 A GLU 83 n 83 GLU 83 A PHE 84 n 84 PHE 84 A VAL 85 n 85 VAL 85 A GLU 86 n 86 GLU 86 A LYS 87 n 87 LYS 87 A LEU 88 n 88 LEU 88 A HIS 89 n 89 HIS 89 A VAL 90 n 90 VAL 90 A GLU 91 n 91 GLU 91 A TYR 92 n 92 TYR 92 A PRO 93 n 93 PRO 93 A LEU 94 n 94 LEU 94 A GLU 95 n 95 GLU 95 A ILE 96 n 96 ILE 96 A GLN 97 n 97 GLN 97 A ILE 98 n 98 ILE 98 A ALA 99 n 99 ALA 99 A THR 100 n 100 THR 100 A GLY 101 n 101 GLY 101 A CYS 102 n 102 CYS 102 A GLU 103 n 103 GLU 103 A LEU 104 n 104 LEU 104 A LEU 105 n 105 LEU 105 A PRO 106 n 106 PRO 106 A ARG 107 n 107 ARG 107 A ASN 108 n 108 ASN 108 A ILE 109 n 109 ILE 109 A SER 110 n 110 SER 110 A GLU 111 n 111 GLU 111 A SER 112 n 112 SER 112 A PHE 113 n 113 PHE 113 A LEU 114 n 114 LEU 114 A ARG 115 n 115 ARG 115 A ALA 116 n 116 ALA 116 A ALA 117 n 117 ALA 117 A PHE 118 n 118 PHE 118 A GLN 119 n 119 GLN 119 A GLY 120 n 120 GLY 120 A ARG 121 n 121 ARG 121 A ASP 122 n 122 ASP 122 A VAL 123 n 123 VAL 123 A LEU 124 n 124 LEU 124 A SER 125 n 125 SER 125 A PHE 126 n 126 PHE 126 A GLN 127 n 127 GLN 127 A GLY 128 n 128 GLY 128 A MET 129 n 129 MET 129 A SER 130 n 130 SER 130 A TRP 131 n 131 TRP 131 A VAL 132 n 132 VAL 132 A SER 133 n 133 SER 133 A ALA 134 n 134 ALA 134 A PRO 135 n 135 PRO 135 A ASP 136 n 136 ASP 136 A ALA 137 n 137 ALA 137 A PRO 138 n 138 PRO 138 A PRO 139 n 139 PRO 139 A PHE 140 n 140 PHE 140 A ILE 141 n 141 ILE 141 A GLN 142 n 142 GLN 142 A GLU 143 n 143 GLU 143 A VAL 144 n 144 VAL 144 A ILE 145 n 145 ILE 145 A LYS 146 n 146 LYS 146 A VAL 147 n 147 VAL 147 A LEU 148 n 148 LEU 148 A ASN 149 n 149 ASN 149 A GLN 150 n 150 GLN 150 A ASN 151 n 151 ASN 151 A GLN 152 n 152 GLN 152 A GLY 153 n 153 GLY 153 A THR 154 n 154 THR 154 A LYS 155 n 155 LYS 155 A GLU 156 n 156 GLU 156 A THR 157 n 157 THR 157 A VAL 158 n 158 VAL 158 A HIS 159 n 159 HIS 159 A TRP 160 n 160 TRP 160 A LEU 161 n 161 LEU 161 A LEU 162 n 162 LEU 162 A HIS 163 n 163 HIS 163 A ASP 164 n 164 ASP 164 A ILE 165 n 165 ILE 165 A TRP 166 n 166 TRP 166 A PRO 167 n 167 PRO 167 A GLU 168 n 168 GLU 168 A LEU 169 n 169 LEU 169 A VAL 170 n 170 VAL 170 A ARG 171 n 171 ARG 171 A GLY 172 n 172 GLY 172 A VAL 173 n 173 VAL 173 A LEU 174 n 174 LEU 174 A GLN 175 n 175 GLN 175 A THR 176 n 176 THR 176 A GLY 177 n 177 GLY 177 A LYS 178 n 178 LYS 178 A SER 179 n 179 SER 179 A GLU 180 n 180 GLU 180 A LEU 181 n 181 LEU 181 A GLU 182 n 182 GLU 182 A LYS 183 n 183 LYS 183 A GLN 184 n 184 GLN 184 A VAL 185 n 185 VAL 185 A LYS 186 n 186 LYS 186 A PRO 187 n 187 PRO 187 A GLU 188 n 188 GLU 188 A ALA 189 n 189 ALA 189 A TRP 190 n 190 TRP 190 A LEU 191 n 191 LEU 191 A SER 192 n 192 SER 192 A SER 193 n 193 SER 193 A GLY 194 n 194 GLY 194 A PRO 195 n 195 PRO 195 A SER 196 n 196 SER 196 A PRO 197 n 197 PRO 197 A GLY 198 n 198 GLY 198 A PRO 199 n 199 PRO 199 A GLY 200 n 200 GLY 200 A ARG 201 n 201 ARG 201 A LEU 202 n 202 LEU 202 A LEU 203 n 203 LEU 203 A LEU 204 n 204 LEU 204 A VAL 205 n 205 VAL 205 A CYS 206 n 206 CYS 206 A HIS 207 n 207 HIS 207 A VAL 208 n 208 VAL 208 A SER 209 n 209 SER 209 A GLY 210 n 210 GLY 210 A PHE 211 n 211 PHE 211 A TYR 212 n 212 TYR 212 A PRO 213 n 213 PRO 213 A LYS 214 n 214 LYS 214 A PRO 215 n 215 PRO 215 A VAL 216 n 216 VAL 216 A ARG 217 n 217 ARG 217 A VAL 218 n 218 VAL 218 A MET 219 n 219 MET 219 A TRP 220 n 220 TRP 220 A MET 221 n 221 MET 221 A ARG 222 n 222 ARG 222 A GLY 223 n 223 GLY 223 A GLU 224 n 224 GLU 224 A GLN 225 n 225 GLN 225 A GLU 226 n 226 GLU 226 A GLU 227 n 227 GLU 227 A PRO 228 n 228 PRO 228 A GLY 229 n 229 GLY 229 A THR 230 n 230 THR 230 A ARG 231 n 231 ARG 231 A GLN 232 n 232 GLN 232 A GLY 233 n 233 GLY 233 A ASP 234 n 234 ASP 234 A VAL 235 n 235 VAL 235 A MET 236 n 236 MET 236 A PRO 237 n 237 PRO 237 A ASN 238 n 238 ASN 238 A ALA 239 n 239 ALA 239 A ASP 240 n 240 ASP 240 A SER 241 n 241 SER 241 A THR 242 n 242 THR 242 A TRP 243 n 243 TRP 243 A TYR 244 n 244 TYR 244 A LEU 245 n 245 LEU 245 A ARG 246 n 246 ARG 246 A VAL 247 n 247 VAL 247 A THR 248 n 248 THR 248 A LEU 249 n 249 LEU 249 A ASP 250 n 250 ASP 250 A VAL 251 n 251 VAL 251 A ALA 252 n 252 ALA 252 A ALA 253 n 253 ALA 253 A GLY 254 n 254 GLY 254 A GLU 255 n 255 GLU 255 A VAL 256 n 256 VAL 256 A ALA 257 n 257 ALA 257 A GLY 258 n 258 GLY 258 A LEU 259 n 259 LEU 259 A SER 260 n 260 SER 260 A CYS 261 n 261 CYS 261 A GLN 262 n 262 GLN 262 A VAL 263 n 263 VAL 263 A LYS 264 n 264 LYS 264 A HIS 265 n 265 HIS 265 A SER 266 n 266 SER 266 A SER 267 n 267 SER 267 A LEU 268 n 268 LEU 268 A GLY 269 n 269 GLY 269 A ASP 270 n 270 ASP 270 A GLN 271 n 271 GLN 271 A ASP 272 n 272 ASP 272 A ILE 273 n 273 ILE 273 A ILE 274 n 274 ILE 274 A LEU 275 n 275 LEU 275 A TYR 276 n 276 TYR 276 A TRP 277 n 277 TRP 277 A HIS 278 n 278 HIS 278 A n 279 279 A n 280 280 A n 281 281 A n 282 282 A n 283 283 A ILE 1 n 1 ILE 1 B GLN 2 n 2 GLN 2 B ARG 3 n 3 ARG 3 B PRO 4 n 4 PRO 4 B PRO 5 n 5 PRO 5 B LYS 6 n 6 LYS 6 B ILE 7 n 7 ILE 7 B GLN 8 n 8 GLN 8 B VAL 9 n 9 VAL 9 B TYR 10 n 10 TYR 10 B SER 11 n 11 SER 11 B ARG 12 n 12 ARG 12 B HIS 13 n 13 HIS 13 B PRO 14 n 14 PRO 14 B PRO 15 n 15 PRO 15 B GLU 16 n 16 GLU 16 B ASP 17 n 17 ASP 17 B GLY 18 n 18 GLY 18 B LYS 19 n 19 LYS 19 B PRO 20 n 20 PRO 20 B ASN 21 n 21 ASN 21 B TYR 22 n 22 TYR 22 B LEU 23 n 23 LEU 23 B ASN 24 n 24 ASN 24 B CYS 25 n 25 CYS 25 B TYR 26 n 26 TYR 26 B VAL 27 n 27 VAL 27 B TYR 28 n 28 TYR 28 B GLY 29 n 29 GLY 29 B PHE 30 n 30 PHE 30 B HIS 31 n 31 HIS 31 B PRO 32 n 32 PRO 32 B PRO 33 n 33 PRO 33 B GLN 34 n 34 GLN 34 B ILE 35 n 35 ILE 35 B GLU 36 n 36 GLU 36 B ILE 37 n 37 ILE 37 B ASP 38 n 38 ASP 38 B LEU 39 n 39 LEU 39 B LEU 40 n 40 LEU 40 B LYS 41 n 41 LYS 41 B ASN 42 n 42 ASN 42 B GLY 43 n 43 GLY 43 B GLU 44 n 44 GLU 44 B LYS 45 n 45 LYS 45 B ILE 46 n 46 ILE 46 B LYS 47 n 47 LYS 47 B SER 48 n 48 SER 48 B GLU 49 n 49 GLU 49 B GLN 50 n 50 GLN 50 B SER 51 n 51 SER 51 B ASP 52 n 52 ASP 52 B LEU 53 n 53 LEU 53 B SER 54 n 54 SER 54 B PHE 55 n 55 PHE 55 B SER 56 n 56 SER 56 B LYS 57 n 57 LYS 57 B ASP 58 n 58 ASP 58 B TRP 59 n 59 TRP 59 B SER 60 n 60 SER 60 B PHE 61 n 61 PHE 61 B TYR 62 n 62 TYR 62 B LEU 63 n 63 LEU 63 B LEU 64 n 64 LEU 64 B SER 65 n 65 SER 65 B HIS 66 n 66 HIS 66 B ALA 67 n 67 ALA 67 B GLU 68 n 68 GLU 68 B PHE 69 n 69 PHE 69 B THR 70 n 70 THR 70 B PRO 71 n 71 PRO 71 B ASN 72 n 72 ASN 72 B SER 73 n 73 SER 73 B LYS 74 n 74 LYS 74 B ASP 75 n 75 ASP 75 B GLN 76 n 76 GLN 76 B TYR 77 n 77 TYR 77 B SER 78 n 78 SER 78 B CYS 79 n 79 CYS 79 B ARG 80 n 80 ARG 80 B VAL 81 n 81 VAL 81 B LYS 82 n 82 LYS 82 B HIS 83 n 83 HIS 83 B VAL 84 n 84 VAL 84 B THR 85 n 85 THR 85 B LEU 86 n 86 LEU 86 B GLU 87 n 87 GLU 87 B GLN 88 n 88 GLN 88 B PRO 89 n 89 PRO 89 B ARG 90 n 90 ARG 90 B ILE 91 n 91 ILE 91 B VAL 92 n 92 VAL 92 B LYS 93 n 93 LYS 93 B TRP 94 n 94 TRP 94 B ASP 95 n 95 ASP 95 B ARG 96 n 96 ARG 96 B ASP 97 n 97 ASP 97 B LEU 98 n 98 LEU 98 B author_and_software_defined_assembly PISA 2 dimeric 3760 -18 18570 A ASN 20 GLYCOSYLATION SITE A ASN 20 ASN A ASN 42 GLYCOSYLATION SITE A ASN 42 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 A O ARG 48 A O ARG 48 A N THR 39 A N THR 39 A O TRP 40 A O TRP 40 A N GLY 28 A N GLY 28 A O ASP 27 A O ASP 27 A N ILE 15 A N ILE 15 A N GLY 12 A N GLY 12 A O THR 100 A O THR 100 A N GLN 97 A N GLN 97 A O ALA 117 A O ALA 117 A N ALA 116 A N ALA 116 A O LEU 124 A O LEU 124 A N GLN 127 A N GLN 127 A O SER 130 A O SER 130 A N TRP 190 A N TRP 190 A O HIS 207 A O HIS 207 A N GLY 210 A N GLY 210 A O TRP 243 A O TRP 243 A O THR 248 A O THR 248 A N ARG 231 A N ARG 231 A N TRP 190 A N TRP 190 A O HIS 207 A O HIS 207 A N GLY 210 A N GLY 210 A O TRP 243 A O TRP 243 A O TYR 244 A O TYR 244 A N MET 236 A N MET 236 A O GLN 225 A O GLN 225 A N ARG 222 A N ARG 222 A N ARG 217 A N ARG 217 A O LYS 264 A O LYS 264 A N VAL 263 A N VAL 263 A O ILE 273 A O ILE 273 B N GLN 8 B N GLN 8 B O TYR 26 B O TYR 26 B N LEU 23 B N LEU 23 B O ALA 67 B O ALA 67 B O HIS 66 B O HIS 66 B N GLU 49 B N GLU 49 B N GLN 8 B N GLN 8 B O TYR 26 B O TYR 26 B N LEU 23 B N LEU 23 B O ALA 67 B O ALA 67 B O TYR 62 B O TYR 62 B N SER 54 B N SER 54 B O GLU 44 B O GLU 44 B N LYS 41 B N LYS 41 B N ASP 38 B N ASP 38 B O ARG 80 B O ARG 80 B N VAL 81 B N VAL 81 B O ARG 90 B O ARG 90 1 A CG GLU 86 A CG GLU 86 1 Y 1 A CD GLU 86 A CD GLU 86 1 Y 1 A OE1 GLU 86 A OE1 GLU 86 1 Y 1 A OE2 GLU 86 A OE2 GLU 86 1 Y 1 A CG LYS 87 A CG LYS 87 1 Y 1 A CD LYS 87 A CD LYS 87 1 Y 1 A CE LYS 87 A CE LYS 87 1 Y 1 A NZ LYS 87 A NZ LYS 87 1 Y 1 A CG ARG 107 A CG ARG 107 1 Y 1 A CD ARG 107 A CD ARG 107 1 Y 1 A NE ARG 107 A NE ARG 107 1 Y 1 A CZ ARG 107 A CZ ARG 107 1 Y 1 A NH1 ARG 107 A NH1 ARG 107 1 Y 1 A NH2 ARG 107 A NH2 ARG 107 1 Y 1 A CG1 ILE 109 A CG1 ILE 109 1 Y 1 A CG2 ILE 109 A CG2 ILE 109 1 Y 1 A CD1 ILE 109 A CD1 ILE 109 1 Y 1 A CG ASP 136 A CG ASP 136 1 Y 1 A OD1 ASP 136 A OD1 ASP 136 1 Y 1 A OD2 ASP 136 A OD2 ASP 136 1 Y 1 A CG GLN 142 A CG GLN 142 1 Y 1 A CD GLN 142 A CD GLN 142 1 Y 1 A OE1 GLN 142 A OE1 GLN 142 1 Y 1 A NE2 GLN 142 A NE2 GLN 142 1 Y 1 A CG LYS 146 A CG LYS 146 1 Y 1 A CD LYS 146 A CD LYS 146 1 Y 1 A CE LYS 146 A CE LYS 146 1 Y 1 A NZ LYS 146 A NZ LYS 146 1 Y 1 A CG ARG 171 A CG ARG 171 1 Y 1 A CD ARG 171 A CD ARG 171 1 Y 1 A NE ARG 171 A NE ARG 171 1 Y 1 A CZ ARG 171 A CZ ARG 171 1 Y 1 A NH1 ARG 171 A NH1 ARG 171 1 Y 1 A NH2 ARG 171 A NH2 ARG 171 1 Y 1 A CG GLU 224 A CG GLU 224 1 Y 1 A CD GLU 224 A CD GLU 224 1 Y 1 A OE1 GLU 224 A OE1 GLU 224 1 Y 1 A OE2 GLU 224 A OE2 GLU 224 1 Y 1 A CG GLN 225 A CG GLN 225 1 Y 1 A CD GLN 225 A CD GLN 225 1 Y 1 A OE1 GLN 225 A OE1 GLN 225 1 Y 1 A NE2 GLN 225 A NE2 GLN 225 1 Y 1 A CG ASP 270 A CG ASP 270 1 Y 1 A OD1 ASP 270 A OD1 ASP 270 1 Y 1 A OD2 ASP 270 A OD2 ASP 270 1 Y 1 B CG LYS 19 B CG LYS 19 1 Y 1 B CD LYS 19 B CD LYS 19 1 Y 1 B CE LYS 19 B CE LYS 19 1 Y 1 B NZ LYS 19 B NZ LYS 19 1 Y 1 B CG GLU 44 B CG GLU 44 1 Y 1 B CD GLU 44 B CD GLU 44 1 Y 1 B OE1 GLU 44 B OE1 GLU 44 1 Y 1 B OE2 GLU 44 B OE2 GLU 44 1 Y 1 B CG LYS 45 B CG LYS 45 1 Y 1 B CD LYS 45 B CD LYS 45 1 Y 1 B CE LYS 45 B CE LYS 45 1 Y 1 B NZ LYS 45 B NZ LYS 45 1 Y 1 B CG LYS 57 B CG LYS 57 1 Y 1 B CD LYS 57 B CD LYS 57 1 Y 1 B CE LYS 57 B CE LYS 57 1 Y 1 B NZ LYS 57 B NZ LYS 57 1 Y 1 B CG LYS 74 B CG LYS 74 1 Y 1 B CD LYS 74 B CD LYS 74 1 Y 1 B CE LYS 74 B CE LYS 74 1 Y 1 B NZ LYS 74 B NZ LYS 74 1 Y 1 B CG LYS 82 B CG LYS 82 1 Y 1 B CD LYS 82 B CD LYS 82 1 Y 1 B CE LYS 82 B CE LYS 82 1 Y 1 B NZ LYS 82 B NZ LYS 82 1 Y 1 B CG GLU 87 B CG GLU 87 1 Y 1 B CD GLU 87 B CD GLU 87 1 Y 1 B OE1 GLU 87 B OE1 GLU 87 1 Y 1 B OE2 GLU 87 B OE2 GLU 87 1 Y 1 A SER 1 A SER 1 1 Y 1 A PRO 2 A PRO 2 1 Y 1 A ALA 3 A ALA 3 1 Y 1 A PRO 4 A PRO 4 1 Y 1 A GLN 5 A GLN 5 1 Y 1 A THR 6 A THR 6 1 Y 1 A PRO 7 A PRO 7 1 Y 1 A HIS 279 A HIS 279 1 Y 1 A HIS 280 A HIS 280 1 Y 1 A HIS 281 A HIS 281 1 Y 1 A HIS 282 A HIS 282 1 Y 1 A HIS 283 A HIS 283 1 Y 1 A ASN 20 -114.62 -129.43 1 A LEU 88 -150.04 11.77 1 A GLU 91 -63.38 -179.93 1 A PRO 106 -54.16 171.01 1 A ARG 107 63.95 -100.83 1 A VAL 123 -138.07 -40.64 1 A MET 129 -140.28 -6.09 1 A PRO 138 -43.22 150.59 1 B HIS 31 176.70 125.33 1 B TRP 59 79.80 -0.62 132.440 61.7012 30.290 0.0700 -0.0000 -0.0000 -0.0500 0.0000 -0.0300 0.9490 0.9180 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY 0.2763 0.2211 0.2233 0.2233 2.400 35.9 804 20132 4.0 97.31 0.2878 0.2328 1.000 1.000 0.7586 9.7390 0.2180 0.3582 0.2704 RANDOM 1 THROUGHOUT 0.0 MOLECULAR REPLACEMENT 0.3580 0.2700 0.8000 0.8000 1.2000 PDB ENTRY 3L9R MAXIMUM LIKELIHOOD MASK 2.400 35.9 26 3070 97 0 2947 0.011 0.022 3140 1.400 1.965 4282 6.161 5.000 367 35.365 23.611 144 16.911 15.000 466 21.572 15.000 19 0.088 0.200 462 0.007 0.021 2401 0.3900 0.4010 2.462 55 1277 1332 1332 20 98.52 45.6 2.4 40 4F7E 20240 20240 0 0 0.067 1 35 4.1 97.4 0.199 2.4 2.46 4.9 1901 1 4.1 98.2 phasing Randy J. Read cimr-phaser@lists.cam.ac.uk http://www-structmed.cimr.cam.ac.uk/phaser/ PHASER program refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program data extraction PDB deposit@deposit.rcsb.org April 22, 2011 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.11 data collection HKL-2000 data reduction HKL-2000 data scaling HKL-2000 Crystal structure of bovine CD1d with bound C16:0-alpha-galactosyl ceramide 1 N N 2 N N 3 N N 4 N N 5 N N 6 N N 7 N N 7 N N A SER 59 A SER 59 HELX_P A LYS 87 A LYS 87 1 1 29 A PHE 140 A PHE 140 HELX_P A ASN 149 A ASN 149 1 2 10 A ASN 151 A ASN 151 HELX_P A ASP 164 A ASP 164 1 3 14 A ASP 164 A ASP 164 HELX_P A GLY 177 A GLY 177 1 4 14 A GLY 177 A GLY 177 HELX_P A GLU 182 A GLU 182 1 5 6 A GLY 254 A GLY 254 HELX_P A ALA 257 A ALA 257 5 6 4 disulf 2.050 A CYS 206 A SG CYS 206 1_555 A CYS 261 A SG CYS 261 1_555 disulf 2.058 B CYS 25 B SG CYS 25 1_555 B CYS 79 B SG CYS 79 1_555 covale 1.447 one N-Glycosylation A ASN 20 A ND2 ASN 20 1_555 C NAG 1 C C1 NAG 1_555 covale 1.449 one N-Glycosylation A ASN 42 A ND2 ASN 42 1_555 A NAG 304 E C1 NAG 1_555 covale 1.448 both C NAG 1 C O4 NAG 1_555 C NAG 2 C C1 NAG 1_555 IMMUNE SYSTEM protein-glycolipid complex, MHC-fold, Ig-fold, antigen presentation, TCR, membrane, IMMUNE SYSTEM A TYR 92 A TYR 92 1 A PRO 93 A PRO 93 -10.36 A TYR 212 A TYR 212 1 A PRO 213 A PRO 213 -5.26 B HIS 31 B HIS 31 1 B PRO 32 B PRO 32 5.50 A1L565_BOVIN UNP 1 129 A1L565 SPAPQTPFSFQGLQISSFANRSWTRTDGLAWLGELQPYTWRNESDTIRFLKPWSRGTFSDQQWEQLQHTLLVYRSSFTRD IWEFVEKLHVEYPLEIQIATGCELLPRNISESFLRAAFQGRDVLSFQGMSWVSAPDAPPFIQEVIKVLNQNQGTKETVHW LLHDIWPELVRGVLQTGKSELEKQVKPEAWLSSGPSPGPGRLLLVCHVSGFYPKPVRVMWMRGEQEEPGTRQGDVMPNAD STWYLRVTLDVAAGEVAGLSCQVKHSSLGDQDIILYW B2MG_BOVIN UNP 2 21 P01888 IQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSFSKDWSFYLLSHAEFTPNSKDQYSCR VKHVTLEQPRIVKWDRDL 129 405 4F7E 1 277 A1L565 A 1 1 277 21 118 4F7E 1 98 P01888 B 2 1 98 1 expression tag HIS 278 4F7E A A1L565 UNP 278 1 expression tag HIS 279 4F7E A A1L565 UNP 279 1 expression tag HIS 280 4F7E A A1L565 UNP 280 1 expression tag HIS 281 4F7E A A1L565 UNP 281 1 expression tag HIS 282 4F7E A A1L565 UNP 282 1 expression tag HIS 283 4F7E A A1L565 UNP 283 8 4 4 4 4 4 4 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 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A ARG 48 A ARG 48 A PHE 49 A PHE 49 A LEU 35 A LEU 35 A TRP 40 A TRP 40 A THR 24 A THR 24 A LEU 32 A LEU 32 A PHE 10 A PHE 10 A PHE 18 A PHE 18 A LEU 94 A LEU 94 A LEU 104 A LEU 104 A SER 110 A SER 110 A PHE 118 A PHE 118 A ARG 121 A ARG 121 A GLN 127 A GLN 127 A SER 130 A SER 130 A SER 133 A SER 133 A GLU 188 A GLU 188 A SER 193 A SER 193 A ARG 201 A ARG 201 A PHE 211 A PHE 211 A TRP 243 A TRP 243 A ALA 252 A ALA 252 A ARG 231 A ARG 231 A GLN 232 A GLN 232 A GLU 188 A GLU 188 A SER 193 A SER 193 A ARG 201 A ARG 201 A PHE 211 A PHE 211 A TRP 243 A TRP 243 A ALA 252 A ALA 252 A MET 236 A MET 236 A PRO 237 A PRO 237 A GLN 225 A GLN 225 A GLU 226 A GLU 226 A VAL 216 A VAL 216 A ARG 222 A ARG 222 A LEU 259 A LEU 259 A HIS 265 A HIS 265 A ILE 273 A ILE 273 A TYR 276 A TYR 276 B LYS 6 B LYS 6 B SER 11 B SER 11 B ASN 21 B ASN 21 B PHE 30 B PHE 30 B PHE 61 B PHE 61 B PHE 69 B PHE 69 B GLU 49 B GLU 49 B GLN 50 B GLN 50 B LYS 6 B LYS 6 B SER 11 B SER 11 B ASN 21 B ASN 21 B PHE 30 B PHE 30 B PHE 61 B PHE 61 B PHE 69 B PHE 69 B SER 54 B SER 54 B PHE 55 B PHE 55 B GLU 44 B GLU 44 B LYS 45 B LYS 45 B GLU 36 B GLU 36 B LYS 41 B LYS 41 B TYR 77 B TYR 77 B LYS 82 B LYS 82 B ARG 90 B ARG 90 B LYS 93 B LYS 93 19 P 21 21 21