0.015392 0.000000 0.000000 0.000000 0.015216 0.000000 0.000000 0.000000 0.006281 0.00000 0.00000 0.00000 Julien, J.-P. Diwanji, D.C. Burton, D.R. Wilson, I.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 64.970 65.720 159.210 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 C6 H12 O6 180.156 beta-D-mannopyranose beta-D-mannose; D-mannose; mannose D-saccharide, beta linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C6 H12 O5 164.156 alpha-L-fucopyranose alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose L-saccharide, alpha linking C6 H12 O6 180.156 beta-D-galactopyranose beta-D-galactose; D-galactose; galactose D-saccharide, beta 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 C3 H8 O3 92.094 GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL non-polymer 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 C6 H12 O6 180.156 alpha-D-mannopyranose alpha-D-mannose; D-mannose; mannose D-saccharide, alpha 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 C11 H19 N O9 309.270 N-acetyl-alpha-neuraminic acid N-acetylneuraminic acid; sialic acid; alpha-sialic acid; O-SIALIC ACID D-saccharide, alpha linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 R C N 75 S C N 76 S C N 77 S C N 78 R C N 79 N C N 80 N O N 81 N O N 82 N O N 83 N O N 84 N O N 85 N O N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N N N 99 R C N 100 N C N 101 N O N 102 N C N 103 N S N 104 N O N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 R C N 113 S C N 114 R C N 115 S C N 116 S C N 117 N C N 118 N O N 119 N O N 120 N O N 121 N O N 122 N O 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 H N 132 N H N 133 N H N 134 N H N 135 R C N 136 R C N 137 S C N 138 R C N 139 R C N 140 N C N 141 N O N 142 N O N 143 N O N 144 N O N 145 N O 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 H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N N N 160 S C N 161 N C N 162 N O N 163 N C N 164 N C N 165 N C N 166 N O N 167 N N N 168 N O N 169 N H N 170 N H 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 N N 180 S C N 181 N C N 182 N O N 183 N C N 184 N C N 185 N C N 186 N O N 187 N O N 188 N O N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N N N 199 N C N 200 N C N 201 N O N 202 N O N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 208 N C N 209 N O N 210 N C N 211 N O N 212 N C N 213 N O N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N N N 223 S C N 224 N C N 225 N O N 226 N C Y 227 N C Y 228 N N Y 229 N C Y 230 N C Y 231 N N N 232 N O N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N H N 242 N H N 243 N O N 244 N H N 245 N H N 246 N N N 247 S C N 248 N C N 249 N O N 250 S C N 251 N C N 252 N C N 253 N C N 254 N O N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N H N 266 N H N 267 N H N 268 N N N 269 S C N 270 N C N 271 N O N 272 N C N 273 N C N 274 N C N 275 N C 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 H 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 N C N 295 N C N 296 N C N 297 N C N 298 N N N 299 N O 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 H N 313 N H N 314 N H N 315 S C N 316 S C N 317 S C N 318 S C N 319 R C N 320 N C N 321 N O N 322 N O N 323 N O N 324 N O N 325 N O N 326 N O 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 H N 335 N H N 336 N H N 337 N H N 338 N H N 339 N N N 340 S C N 341 N C N 342 N O N 343 N C N 344 N C N 345 N S N 346 N C N 347 N O 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 R C N 360 R C N 361 R C N 362 S C N 363 R C N 364 N C N 365 N C N 366 N C N 367 N N N 368 N O N 369 N O N 370 N O N 371 N O N 372 N O N 373 N O N 374 N H N 375 N H N 376 N H N 377 N H N 378 N H N 379 N H N 380 N H N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N H N 387 N H N 388 N H N 389 N N N 390 S C N 391 N C N 392 N O N 393 N C Y 394 N C Y 395 N C Y 396 N C Y 397 N C Y 398 N C Y 399 N C N 400 N O 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 H N 410 N H N 411 N H N 412 N N N 413 S C N 414 N C N 415 N O N 416 N C N 417 N C N 418 N C N 419 N O N 420 N H N 421 N H N 422 N H N 423 N H N 424 N H N 425 N H N 426 N H N 427 N H N 428 N H N 429 N N N 430 S C N 431 N C N 432 N O N 433 N C N 434 N O N 435 N O 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 C N 444 R C N 445 N C N 446 S C N 447 R C N 448 R C N 449 R C N 450 R C N 451 N C N 452 N C N 453 N C N 454 N N N 455 N O N 456 N O N 457 N O N 458 N O N 459 N O N 460 N O N 461 N O N 462 N O N 463 N O N 464 N H N 465 N H N 466 N H N 467 N H N 468 N H N 469 N H N 470 N H N 471 N H N 472 N H N 473 N H N 474 N H N 475 N H 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 N N 484 S C N 485 N C N 486 N O N 487 R C N 488 N O N 489 N C N 490 N O N 491 N H N 492 N H N 493 N H N 494 N H N 495 N H N 496 N H N 497 N H N 498 N H N 499 N H N 500 N N N 501 S C N 502 N C N 503 N O N 504 N C Y 505 N C Y 506 N C Y 507 N C Y 508 N N Y 509 N C Y 510 N C Y 511 N C Y 512 N C Y 513 N C N 514 N O N 515 N H N 516 N H N 517 N H N 518 N H N 519 N H N 520 N H N 521 N H N 522 N H N 523 N H N 524 N H N 525 N H N 526 N H N 527 N N N 528 S C N 529 N C N 530 N O N 531 N C Y 532 N C Y 533 N C Y 534 N C Y 535 N C Y 536 N C Y 537 N C N 538 N O N 539 N O N 540 N H N 541 N H N 542 N H N 543 N H 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 N N 552 S C N 553 N C N 554 N O N 555 N C N 556 N C N 557 N C N 558 N O N 559 N H N 560 N H N 561 N H N 562 N H N 563 N H N 564 N H N 565 N H N 566 N H N 567 N H N 568 N H N 569 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N 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 doub 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 sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N doub N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N doub N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N 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 doub N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N doub 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 sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N doub N 220 N sing N 221 N sing N 222 N sing N 223 N sing Y 224 N sing Y 225 N doub Y 226 N doub N 227 N sing Y 228 N sing N 229 N sing Y 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 doub N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N doub N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N doub N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N 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 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 sing N 330 N sing N 331 N sing N 332 N doub 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 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 doub N 382 N sing N 383 N sing N 384 N sing N 385 N sing Y 386 N doub Y 387 N sing Y 388 N sing N 389 N sing Y 390 N doub N 391 N sing Y 392 N doub N 393 N sing Y 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 N 403 N sing N 404 N doub 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 sing N 416 N sing N 417 N sing N 418 N sing N 419 N sing N 420 N sing N 421 N doub N 422 N sing N 423 N sing N 424 N sing N 425 N sing N 426 N sing N 427 N sing N 428 N sing N 429 N doub 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 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 sing N 456 N sing N 457 N doub 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 sing N 469 N sing N 470 N sing N 471 N sing N 472 N sing N 473 N sing N 474 N doub 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 sing N 485 N sing N 486 N sing N 487 N sing N 488 N sing N 489 N sing N 490 N doub N 491 N sing N 492 N sing N 493 N sing N 494 N sing Y 495 N doub Y 496 N sing Y 497 N sing N 498 N sing Y 499 N doub Y 500 N sing Y 501 N sing N 502 N sing Y 503 N sing Y 504 N doub N 505 N sing Y 506 N doub N 507 N sing Y 508 N sing N 509 N sing N 510 N sing N 511 N sing N 512 N sing N 513 N sing N 514 N sing N 515 N sing N 516 N sing N 517 N sing N 518 N doub N 519 N sing N 520 N sing N 521 N sing N 522 N sing Y 523 N doub Y 524 N sing Y 525 N sing N 526 N sing Y 527 N doub N 528 N sing Y 529 N doub N 530 N sing Y 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 N 539 N sing N 540 N sing N 541 N sing N 542 N doub N 543 N sing N 544 N sing N 545 N sing N 546 N sing N 547 N sing N 548 N sing N 549 N sing N 550 N sing N 551 N sing N 552 N sing N 553 N sing US Plos Pathog. 1553-7366 9 e1003342 e1003342 10.1371/journal.ppat.1003342 23658524 Broadly neutralizing antibody PGT121 allosterically modulates CD4 binding via recognition of the HIV-1 gp120 V3 base and multiple surrounding glycans. 2013 10.2210/pdb4jy4/pdb pdb_00004jy4 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 1 PIXEL 2011-01-18 PSI PILATUS 6M Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees SINGLE WAVELENGTH M x-ray 1 0.979 1.0 BL11-1 SSRL 0.979 SYNCHROTRON SSRL BEAMLINE BL11-1 25169.230 PGT121 heavy chain Fab 1 man polymer 22574.947 PGT121 light chain Fab 1 man polymer 1713.552 N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose 1 man branched 92.094 GLYCEROL 3 syn non-polymer 18.015 water 13 nat water no no QMQLQESGPGLVKPSETLSLTCSVSGASISDSYWSWIRRSPGKGLEWIGYVHKSGDTNYSPSLKSRVNLSLDTSKNQVSL SLVAATAADSGKYYCARTLHGRRIYGIVAFNEWFTYFYMDVWGNGTQVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCL VKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC QMQLQESGPGLVKPSETLSLTCSVSGASISDSYWSWIRRSPGKGLEWIGYVHKSGDTNYSPSLKSRVNLSLDTSKNQVSL SLVAATAADSGKYYCARTLHGRRIYGIVAFNEWFTYFYMDVWGNGTQVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCL VKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC B polypeptide(L) no no SDISVAPGETARISCGEKSLGSRAVQWYQHRAGQAPSLIIYNNQDRPSGIPERFSGSPDSPFGTTATLTITSVEAGDEAD YYCHIWDSRVPTKWVFGGGTTLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVET TTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS SDISVAPGETARISCGEKSLGSRAVQWYQHRAGQAPSLIIYNNQDRPSGIPERFSGSPDSPFGTTATLTITSVEAGDEAD YYCHIWDSRVPTKWVFGGGTTLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVET TTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n 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 human sample 9606 Homo sapiens HEK 293F 9606 Homo sapiens human human sample 9606 Homo sapiens HEK 293F 9606 Homo sapiens 1 3.56 65.45 VAPOR DIFFUSION, SITTING DROP 7.5 0.1 M HEPES, pH 7.5, 30% v/v PEG400, 5% w/v PEG3000, 10% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K 293 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 pdbx_validate_close_contact struct_asym 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 Advisory Atomic model Data collection Derived calculations Structure summary Data collection Database references Refinement description Structure summary 1 0 2013-05-15 1 1 2014-02-05 2 0 2020-07-29 2 1 2023-09-20 _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_struct_assembly_gen.asym_id_list _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.auth_seq_id_2 _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_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession B NAG 302 n C NAG 1 B NAG 303 n C NAG 2 B BMA 304 n C BMA 3 B MAN 305 n C MAN 4 B NAG 306 n C NAG 5 B GAL 307 n C GAL 6 B SIA 308 n C SIA 7 B MAN 309 n C MAN 8 B FUC 310 n C FUC 9 DManpb b-D-mannopyranose b-D-Manp Man LFucpa a-L-fucopyranose a-L-Fucp Fuc DGalpb b-D-galactopyranose b-D-Galp Gal DManpa a-D-mannopyranose a-D-Manp Man DGlcpNAcb N-acetyl-b-D-glucopyranosamine b-D-GlcpNAc GlcNAc DNeup5Aca N-acetyl-a-D-neuraminic acid a-D-Neup5Ac Neu5Ac RCSB Y RCSB 2013-03-29 REL REL oligosaccharide DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1- 3 GMML 1.0 Glycam Condensed Sequence WURCS=2.0/6,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a1221m-1a_1-5]/1-1-2-3-1-4-5-3-6/a4-b1_a6-i1_b4-c1_c3-d1_c6-h1_d2-e1_e4-f1_f6-g2 3 PDB2Glycan 1.1.0 WURCS []{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}} 3 PDB-CARE LINUCS C1 O4 NAG NAG 2 1 3 O1 HO4 sing C1 O4 BMA NAG 3 2 3 O1 HO4 sing C1 O3 MAN BMA 4 3 3 O1 HO3 sing C1 O2 NAG MAN 5 4 3 O1 HO2 sing C1 O4 GAL NAG 6 5 3 O1 HO4 sing C2 O6 SIA GAL 7 6 3 O2 HO6 sing C1 O6 MAN BMA 8 3 3 O1 HO6 sing C1 O6 FUC NAG 9 1 3 O1 HO6 sing n n n n n n n n n GOL GLYCEROL HOH water 4JY6 PDB ENTRY 4JY6 PDB experimental model GOL 301 4 GOL GOL 301 B GOL 301 4 GOL GOL 301 A GOL 302 4 GOL GOL 302 A HOH 401 5 HOH HOH 401 B HOH 404 5 HOH HOH 402 B HOH 405 5 HOH HOH 403 B HOH 406 5 HOH HOH 404 B HOH 407 5 HOH HOH 405 B HOH 408 5 HOH HOH 406 B HOH 401 5 HOH HOH 401 A HOH 402 5 HOH HOH 402 A HOH 403 5 HOH HOH 403 A HOH 404 5 HOH HOH 404 A HOH 405 5 HOH HOH 405 A HOH 402 5 HOH HOH 406 A HOH 403 5 HOH HOH 407 A GLN 1 n 1 GLN 1 B MET 2 n 2 MET 2 B GLN 3 n 3 GLN 3 B LEU 4 n 4 LEU 4 B GLN 5 n 5 GLN 5 B GLU 6 n 6 GLU 6 B SER 7 n 7 SER 7 B GLY 8 n 8 GLY 8 B PRO 9 n 9 PRO 9 B GLY 10 n 10 GLY 10 B LEU 11 n 11 LEU 11 B VAL 12 n 12 VAL 12 B LYS 13 n 13 LYS 13 B PRO 14 n 14 PRO 14 B SER 15 n 15 SER 15 B GLU 16 n 16 GLU 16 B THR 17 n 17 THR 17 B LEU 18 n 18 LEU 18 B SER 19 n 19 SER 19 B LEU 20 n 20 LEU 20 B THR 21 n 21 THR 21 B CYS 22 n 22 CYS 22 B SER 23 n 23 SER 23 B VAL 24 n 24 VAL 24 B SER 25 n 25 SER 25 B GLY 26 n 26 GLY 26 B ALA 27 n 27 ALA 27 B SER 28 n 28 SER 28 B ILE 29 n 29 ILE 29 B SER 30 n 30 SER 30 B ASP 31 n 31 ASP 31 B SER 32 n 32 SER 32 B TYR 33 n 33 TYR 33 B TRP 34 n 34 TRP 34 B SER 35 n 35 SER 35 B TRP 36 n 36 TRP 36 B ILE 37 n 37 ILE 37 B ARG 38 n 38 ARG 38 B ARG 39 n 39 ARG 39 B SER 40 n 40 SER 40 B PRO 41 n 41 PRO 41 B GLY 42 n 42 GLY 42 B LYS 43 n 43 LYS 43 B GLY 44 n 44 GLY 44 B LEU 45 n 45 LEU 45 B GLU 46 n 46 GLU 46 B TRP 47 n 47 TRP 47 B ILE 48 n 48 ILE 48 B GLY 49 n 49 GLY 49 B TYR 50 n 50 TYR 50 B VAL 51 n 51 VAL 51 B HIS 52 n 52 HIS 52 B LYS 53 n 53 LYS 53 B SER 54 n 54 SER 54 B GLY 55 n 55 GLY 55 B ASP 56 n 56 ASP 56 B THR 57 n 57 THR 57 B ASN 58 n 58 ASN 58 B TYR 59 n 59 TYR 59 B SER 60 n 60 SER 60 B PRO 61 n 61 PRO 61 B SER 62 n 62 SER 62 B LEU 63 n 63 LEU 63 B LYS 64 n 64 LYS 64 B SER 65 n 65 SER 65 B ARG 66 n 66 ARG 66 B VAL 67 n 67 VAL 67 B ASN 68 n 68 ASN 68 B LEU 69 n 69 LEU 69 B SER 70 n 70 SER 70 B LEU 71 n 71 LEU 71 B ASP 72 n 72 ASP 72 B THR 73 n 73 THR 73 B SER 74 n 74 SER 74 B LYS 75 n 75 LYS 75 B ASN 76 n 76 ASN 76 B GLN 77 n 77 GLN 77 B VAL 78 n 78 VAL 78 B SER 79 n 79 SER 79 B LEU 80 n 80 LEU 80 B SER 81 n 81 SER 81 B LEU 82 n 82 LEU 82 B VAL 82 n 83 A VAL 82 B ALA 82 n 84 B ALA 82 B ALA 82 n 85 C ALA 82 B THR 83 n 86 THR 83 B ALA 84 n 87 ALA 84 B ALA 85 n 88 ALA 85 B ASP 86 n 89 ASP 86 B SER 87 n 90 SER 87 B GLY 88 n 91 GLY 88 B LYS 89 n 92 LYS 89 B TYR 90 n 93 TYR 90 B TYR 91 n 94 TYR 91 B CYS 92 n 95 CYS 92 B ALA 93 n 96 ALA 93 B ARG 94 n 97 ARG 94 B THR 95 n 98 THR 95 B LEU 96 n 99 LEU 96 B HIS 97 n 100 HIS 97 B GLY 98 n 101 GLY 98 B ARG 99 n 102 ARG 99 B ARG 100 n 103 ARG 100 B ILE 100 n 104 A ILE 100 B TYR 100 n 105 B TYR 100 B GLY 100 n 106 C GLY 100 B ILE 100 n 107 D ILE 100 B VAL 100 n 108 E VAL 100 B ALA 100 n 109 F ALA 100 B PHE 100 n 110 G PHE 100 B ASN 100 n 111 H ASN 100 B GLU 100 n 112 I GLU 100 B TRP 100 n 113 J TRP 100 B PHE 100 n 114 K PHE 100 B THR 100 n 115 L THR 100 B TYR 100 n 116 M TYR 100 B PHE 100 n 117 N PHE 100 B TYR 100 n 118 O TYR 100 B MET 100 n 119 P MET 100 B ASP 100 n 120 Q ASP 100 B VAL 100 n 121 R VAL 100 B TRP 101 n 122 TRP 101 B GLY 102 n 123 GLY 102 B ASN 103 n 124 ASN 103 B GLY 104 n 125 GLY 104 B THR 105 n 126 THR 105 B GLN 106 n 127 GLN 106 B VAL 107 n 128 VAL 107 B THR 108 n 129 THR 108 B VAL 109 n 130 VAL 109 B SER 110 n 131 SER 110 B SER 111 n 132 SER 111 B ALA 112 n 133 ALA 112 B SER 113 n 134 SER 113 B THR 114 n 135 THR 114 B LYS 115 n 136 LYS 115 B GLY 116 n 137 GLY 116 B PRO 117 n 138 PRO 117 B SER 118 n 139 SER 118 B VAL 119 n 140 VAL 119 B PHE 120 n 141 PHE 120 B PRO 121 n 142 PRO 121 B LEU 122 n 143 LEU 122 B ALA 123 n 144 ALA 123 B PRO 124 n 145 PRO 124 B SER 125 n 146 SER 125 B SER 126 n 147 SER 126 B LYS 127 n 148 LYS 127 B SER 128 n 149 SER 128 B THR 129 n 150 THR 129 B SER 130 n 151 SER 130 B GLY 131 n 152 GLY 131 B GLY 132 n 153 GLY 132 B THR 133 n 154 THR 133 B ALA 134 n 155 ALA 134 B ALA 135 n 156 ALA 135 B LEU 136 n 157 LEU 136 B GLY 137 n 158 GLY 137 B CYS 138 n 159 CYS 138 B LEU 139 n 160 LEU 139 B VAL 140 n 161 VAL 140 B LYS 141 n 162 LYS 141 B ASP 142 n 163 ASP 142 B TYR 143 n 164 TYR 143 B PHE 144 n 165 PHE 144 B PRO 145 n 166 PRO 145 B GLU 146 n 167 GLU 146 B PRO 147 n 168 PRO 147 B VAL 148 n 169 VAL 148 B THR 149 n 170 THR 149 B VAL 150 n 171 VAL 150 B SER 151 n 172 SER 151 B TRP 152 n 173 TRP 152 B ASN 153 n 174 ASN 153 B SER 154 n 175 SER 154 B GLY 155 n 176 GLY 155 B ALA 156 n 177 ALA 156 B LEU 157 n 178 LEU 157 B THR 158 n 179 THR 158 B SER 159 n 180 SER 159 B GLY 160 n 181 GLY 160 B VAL 161 n 182 VAL 161 B HIS 162 n 183 HIS 162 B THR 163 n 184 THR 163 B PHE 164 n 185 PHE 164 B PRO 165 n 186 PRO 165 B ALA 166 n 187 ALA 166 B VAL 167 n 188 VAL 167 B LEU 168 n 189 LEU 168 B GLN 169 n 190 GLN 169 B SER 170 n 191 SER 170 B SER 171 n 192 SER 171 B GLY 172 n 193 GLY 172 B LEU 173 n 194 LEU 173 B TYR 174 n 195 TYR 174 B SER 175 n 196 SER 175 B LEU 176 n 197 LEU 176 B SER 177 n 198 SER 177 B SER 178 n 199 SER 178 B VAL 179 n 200 VAL 179 B VAL 180 n 201 VAL 180 B THR 181 n 202 THR 181 B VAL 182 n 203 VAL 182 B PRO 183 n 204 PRO 183 B SER 184 n 205 SER 184 B SER 185 n 206 SER 185 B SER 186 n 207 SER 186 B LEU 187 n 208 LEU 187 B GLY 188 n 209 GLY 188 B THR 189 n 210 THR 189 B GLN 190 n 211 GLN 190 B THR 191 n 212 THR 191 B TYR 192 n 213 TYR 192 B ILE 193 n 214 ILE 193 B CYS 194 n 215 CYS 194 B ASN 195 n 216 ASN 195 B VAL 196 n 217 VAL 196 B ASN 197 n 218 ASN 197 B HIS 198 n 219 HIS 198 B LYS 199 n 220 LYS 199 B PRO 200 n 221 PRO 200 B SER 201 n 222 SER 201 B ASN 202 n 223 ASN 202 B THR 203 n 224 THR 203 B LYS 204 n 225 LYS 204 B VAL 205 n 226 VAL 205 B ASP 206 n 227 ASP 206 B LYS 207 n 228 LYS 207 B ARG 208 n 229 ARG 208 B VAL 209 n 230 VAL 209 B GLU 210 n 231 GLU 210 B PRO 211 n 232 PRO 211 B n 233 212 B n 234 213 B n 235 214 B n 1 8 A ASP 9 n 2 ASP 9 A ILE 11 n 3 ILE 11 A SER 12 n 4 SER 12 A VAL 13 n 5 VAL 13 A ALA 14 n 6 ALA 14 A PRO 15 n 7 PRO 15 A GLY 16 n 8 GLY 16 A GLU 17 n 9 GLU 17 A THR 18 n 10 THR 18 A ALA 19 n 11 ALA 19 A ARG 20 n 12 ARG 20 A ILE 21 n 13 ILE 21 A SER 22 n 14 SER 22 A CYS 23 n 15 CYS 23 A GLY 24 n 16 GLY 24 A GLU 25 n 17 GLU 25 A LYS 26 n 18 LYS 26 A SER 27 n 19 SER 27 A LEU 28 n 20 LEU 28 A GLY 29 n 21 GLY 29 A SER 30 n 22 SER 30 A ARG 31 n 23 ARG 31 A ALA 32 n 24 ALA 32 A VAL 33 n 25 VAL 33 A GLN 34 n 26 GLN 34 A TRP 35 n 27 TRP 35 A TYR 36 n 28 TYR 36 A GLN 37 n 29 GLN 37 A HIS 38 n 30 HIS 38 A ARG 39 n 31 ARG 39 A ALA 40 n 32 ALA 40 A GLY 41 n 33 GLY 41 A GLN 42 n 34 GLN 42 A ALA 43 n 35 ALA 43 A PRO 44 n 36 PRO 44 A SER 45 n 37 SER 45 A LEU 46 n 38 LEU 46 A ILE 47 n 39 ILE 47 A ILE 48 n 40 ILE 48 A TYR 49 n 41 TYR 49 A ASN 50 n 42 ASN 50 A ASN 51 n 43 ASN 51 A GLN 52 n 44 GLN 52 A ASP 53 n 45 ASP 53 A ARG 54 n 46 ARG 54 A PRO 55 n 47 PRO 55 A SER 56 n 48 SER 56 A GLY 57 n 49 GLY 57 A ILE 58 n 50 ILE 58 A PRO 59 n 51 PRO 59 A GLU 60 n 52 GLU 60 A ARG 61 n 53 ARG 61 A PHE 62 n 54 PHE 62 A SER 63 n 55 SER 63 A GLY 64 n 56 GLY 64 A SER 65 n 57 SER 65 A PRO 66 n 58 PRO 66 A ASP 67 n 59 ASP 67 A SER 67 n 60 A SER 67 A PRO 67 n 61 B PRO 67 A PHE 67 n 62 C PHE 67 A GLY 68 n 63 GLY 68 A THR 69 n 64 THR 69 A THR 70 n 65 THR 70 A ALA 71 n 66 ALA 71 A THR 72 n 67 THR 72 A LEU 73 n 68 LEU 73 A THR 74 n 69 THR 74 A ILE 75 n 70 ILE 75 A THR 76 n 71 THR 76 A SER 77 n 72 SER 77 A VAL 78 n 73 VAL 78 A GLU 79 n 74 GLU 79 A ALA 80 n 75 ALA 80 A GLY 81 n 76 GLY 81 A ASP 82 n 77 ASP 82 A GLU 83 n 78 GLU 83 A ALA 84 n 79 ALA 84 A ASP 85 n 80 ASP 85 A TYR 86 n 81 TYR 86 A TYR 87 n 82 TYR 87 A CYS 88 n 83 CYS 88 A HIS 89 n 84 HIS 89 A ILE 90 n 85 ILE 90 A TRP 91 n 86 TRP 91 A ASP 92 n 87 ASP 92 A SER 93 n 88 SER 93 A ARG 94 n 89 ARG 94 A VAL 95 n 90 VAL 95 A PRO 95 n 91 A PRO 95 A THR 95 n 92 B THR 95 A LYS 95 n 93 C LYS 95 A TRP 96 n 94 TRP 96 A VAL 97 n 95 VAL 97 A PHE 98 n 96 PHE 98 A GLY 99 n 97 GLY 99 A GLY 100 n 98 GLY 100 A GLY 101 n 99 GLY 101 A THR 102 n 100 THR 102 A THR 103 n 101 THR 103 A LEU 104 n 102 LEU 104 A THR 105 n 103 THR 105 A VAL 106 n 104 VAL 106 A LEU 107 n 105 LEU 107 A GLY 108 n 106 GLY 108 A GLN 109 n 107 GLN 109 A PRO 110 n 108 PRO 110 A LYS 111 n 109 LYS 111 A ALA 112 n 110 ALA 112 A ALA 113 n 111 ALA 113 A PRO 114 n 112 PRO 114 A SER 115 n 113 SER 115 A VAL 116 n 114 VAL 116 A THR 117 n 115 THR 117 A LEU 118 n 116 LEU 118 A PHE 119 n 117 PHE 119 A PRO 120 n 118 PRO 120 A PRO 121 n 119 PRO 121 A SER 122 n 120 SER 122 A SER 123 n 121 SER 123 A GLU 124 n 122 GLU 124 A GLU 125 n 123 GLU 125 A LEU 126 n 124 LEU 126 A GLN 127 n 125 GLN 127 A ALA 128 n 126 ALA 128 A ASN 129 n 127 ASN 129 A LYS 130 n 128 LYS 130 A ALA 131 n 129 ALA 131 A THR 132 n 130 THR 132 A LEU 133 n 131 LEU 133 A VAL 134 n 132 VAL 134 A CYS 135 n 133 CYS 135 A LEU 136 n 134 LEU 136 A ILE 137 n 135 ILE 137 A SER 138 n 136 SER 138 A ASP 139 n 137 ASP 139 A PHE 140 n 138 PHE 140 A TYR 141 n 139 TYR 141 A PRO 142 n 140 PRO 142 A GLY 143 n 141 GLY 143 A ALA 144 n 142 ALA 144 A VAL 145 n 143 VAL 145 A THR 146 n 144 THR 146 A VAL 147 n 145 VAL 147 A ALA 148 n 146 ALA 148 A TRP 149 n 147 TRP 149 A LYS 150 n 148 LYS 150 A ALA 151 n 149 ALA 151 A ASP 152 n 150 ASP 152 A SER 153 n 151 SER 153 A SER 154 n 152 SER 154 A PRO 155 n 153 PRO 155 A VAL 156 n 154 VAL 156 A LYS 157 n 155 LYS 157 A ALA 158 n 156 ALA 158 A GLY 159 n 157 GLY 159 A VAL 160 n 158 VAL 160 A GLU 161 n 159 GLU 161 A THR 162 n 160 THR 162 A THR 163 n 161 THR 163 A THR 164 n 162 THR 164 A PRO 165 n 163 PRO 165 A SER 166 n 164 SER 166 A LYS 167 n 165 LYS 167 A GLN 168 n 166 GLN 168 A SER 169 n 167 SER 169 A ASN 170 n 168 ASN 170 A ASN 171 n 169 ASN 171 A LYS 172 n 170 LYS 172 A TYR 173 n 171 TYR 173 A ALA 174 n 172 ALA 174 A ALA 175 n 173 ALA 175 A SER 176 n 174 SER 176 A SER 177 n 175 SER 177 A TYR 178 n 176 TYR 178 A LEU 179 n 177 LEU 179 A SER 180 n 178 SER 180 A LEU 181 n 179 LEU 181 A THR 182 n 180 THR 182 A PRO 183 n 181 PRO 183 A GLU 184 n 182 GLU 184 A GLN 185 n 183 GLN 185 A TRP 186 n 184 TRP 186 A LYS 187 n 185 LYS 187 A SER 188 n 186 SER 188 A HIS 189 n 187 HIS 189 A LYS 190 n 188 LYS 190 A SER 191 n 189 SER 191 A TYR 192 n 190 TYR 192 A SER 193 n 191 SER 193 A CYS 194 n 192 CYS 194 A GLN 195 n 193 GLN 195 A VAL 196 n 194 VAL 196 A THR 197 n 195 THR 197 A HIS 198 n 196 HIS 198 A GLU 199 n 197 GLU 199 A GLY 200 n 198 GLY 200 A SER 201 n 199 SER 201 A THR 202 n 200 THR 202 A VAL 203 n 201 VAL 203 A GLU 204 n 202 GLU 204 A LYS 205 n 203 LYS 205 A THR 206 n 204 THR 206 A VAL 207 n 205 VAL 207 A ALA 208 n 206 ALA 208 A PRO 209 n 207 PRO 209 A THR 210 n 208 THR 210 A GLU 211 n 209 GLU 211 A n 210 212 A n 211 213 A -0.0718 -0.1952 0.2492 -0.0405 -0.1111 0.3322 0.0625 0.2470 0.1505 -0.3364 -0.0347 -0.0090 -0.1235 0.5454 0.0000 0.5174 0.0849 -0.0175 0.6081 0.0225 0.5925 refined 22.4673 27.0570 30.9696 X-RAY DIFFRACTION 1.1238 -0.3258 -1.2313 0.4456 -0.4499 1.1404 -0.0405 0.2010 0.0648 0.2834 0.0028 -0.0902 0.1903 0.2317 0.0000 0.4520 0.0682 -0.1287 0.3284 -0.0291 0.3387 refined 15.9122 24.9088 39.5005 X-RAY DIFFRACTION -0.0196 0.0703 0.1465 0.2942 -0.2105 -0.0375 -0.0030 0.0345 0.0658 0.0511 0.2133 -0.1883 -0.1186 0.4437 0.0000 0.2262 -0.0051 -0.0239 0.3347 -0.0463 0.2518 refined 13.6153 25.7388 24.1858 X-RAY DIFFRACTION 0.3328 -0.5244 -0.1608 -0.1790 -0.0969 0.3426 -0.0397 -0.1547 -0.0589 -0.1499 0.1434 0.0195 -0.0849 -0.0342 0.0000 0.1795 -0.0028 -0.0069 0.2647 -0.0185 0.2861 refined 6.5299 22.5636 1.1652 X-RAY DIFFRACTION 1.1643 1.2517 0.1025 0.3705 0.5336 0.5874 -0.0913 -0.2313 0.2600 0.0842 -0.0927 0.0415 -0.1054 0.0493 0.0000 0.2766 0.0688 -0.0555 0.4158 -0.0585 0.3833 refined 6.9307 24.9027 3.9451 X-RAY DIFFRACTION 0.0780 0.0274 -0.0820 -0.0605 -0.2286 0.1292 -0.0209 0.2004 0.3137 0.2143 0.0252 0.0432 0.0334 0.0339 -0.0000 0.2735 -0.0305 0.0062 0.4128 -0.0058 0.3868 refined 14.0102 26.4714 -2.3132 X-RAY DIFFRACTION 0.7828 -0.0643 -0.2948 0.6269 0.4861 0.7377 0.0649 0.2056 0.0178 0.2443 -0.0503 0.2614 0.2155 0.0199 -0.0000 0.4368 -0.0097 0.0362 0.2259 -0.0167 0.3137 refined -7.1076 19.7711 36.2569 X-RAY DIFFRACTION 0.0566 0.1448 0.0502 0.2378 0.2359 0.0443 -0.9796 -0.1347 0.7467 -0.2520 0.8183 -0.1325 -0.0153 0.0657 0.0000 0.5263 -0.1467 0.0117 0.2660 0.0749 0.3384 refined 0.0606 29.2974 34.2099 X-RAY DIFFRACTION 1.1311 0.1851 -0.4170 0.3916 0.2887 0.8409 0.0125 -0.0468 -0.0169 0.2946 -0.0442 0.1671 0.1037 -0.1522 -0.0000 0.4623 0.0094 0.0025 0.1689 -0.0109 0.2819 refined -2.3259 28.2502 43.3963 X-RAY DIFFRACTION 0.2877 0.3872 -0.1966 0.2422 0.0710 0.1148 -0.0761 0.2872 -0.1035 0.0792 -0.1493 0.2209 0.0406 0.0119 -0.0000 0.3965 0.0202 -0.1046 0.3331 -0.0159 0.3920 refined -8.5714 20.9467 18.9714 X-RAY DIFFRACTION 1.8860 0.5735 0.3222 0.4958 0.2201 0.4416 -0.0996 -0.1509 -0.1484 0.0049 0.0724 -0.1767 0.0004 0.0162 -0.0000 0.2394 0.0274 0.0288 0.3916 0.0310 0.3273 refined 1.3549 11.0943 2.1968 X-RAY DIFFRACTION 0.1046 0.0635 0.1066 0.5609 0.0326 0.0590 0.0313 0.4560 -0.6904 0.0358 -0.1564 0.0176 0.0845 -0.5245 0.0000 0.2412 -0.0262 -0.0281 0.5165 -0.0449 0.4466 refined -6.2000 8.2031 -2.6826 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 chain 'A' and (resseq 9:26) X-RAY DIFFRACTION 2 chain 'A' and (resseq 27:92) X-RAY DIFFRACTION 3 chain 'A' and (resseq 93:119) X-RAY DIFFRACTION 4 chain 'A' and (resseq 120:151) X-RAY DIFFRACTION 5 chain 'A' and (resseq 152:188) X-RAY DIFFRACTION 6 chain 'A' and (resseq 189:211) X-RAY DIFFRACTION 7 chain 'B' and (resseq 1:39) X-RAY DIFFRACTION 8 chain 'B' and (resseq 40:51) X-RAY DIFFRACTION 9 chain 'B' and (resseq 52:101) X-RAY DIFFRACTION 10 chain 'B' and (resseq 102:117) X-RAY DIFFRACTION 11 chain 'B' and (resseq 118:201) X-RAY DIFFRACTION 12 chain 'B' and (resseq 202:211) author_and_software_defined_assembly PISA 2 dimeric 6320 0 20670 B ASN 103 GLYCOSYLATION SITE A ASN 124 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 N ILE 11 B N ILE 3 A O THR 105 B O THR 103 A O GLY 101 B O GLY 99 A N TYR 86 B N TYR 81 A O ASP 85 B O ASP 80 A N HIS 38 B N HIS 30 A N TRP 35 B N TRP 27 A O ILE 48 B O ILE 40 A N ALA 19 B N ALA 11 A O ILE 75 B O ILE 70 A O THR 74 B O THR 69 A N SER 63 B N SER 55 A N THR 117 B N THR 115 A O LEU 136 B O LEU 134 A N CYS 135 B N CYS 133 A O SER 177 B O SER 175 A O TYR 178 B O TYR 176 A N GLU 161 B N GLU 159 A N THR 117 B N THR 115 A O LEU 136 B O LEU 134 A N CYS 135 B N CYS 133 A O SER 177 B O SER 175 A O ALA 174 B O ALA 172 A N SER 166 B N SER 164 A O SER 154 B O SER 152 A N ALA 151 B N ALA 149 A N THR 146 B N THR 144 A O THR 197 B O THR 195 A N VAL 196 B N VAL 194 A O VAL 203 B O VAL 201 B N SER 7 A N SER 7 B O THR 21 A O THR 21 B N CYS 22 A N CYS 22 B O VAL 78 A O VAL 78 B O GLN 77 A O GLN 77 B N ASP 72 A N ASP 72 B N VAL 12 A N VAL 12 B O THR 108 A O THR 129 B O VAL 107 A O VAL 128 B N GLY 88 A N GLY 91 B O TYR 91 A O TYR 94 B N ILE 37 A N ILE 37 B N ARG 38 A N ARG 38 B O GLU 46 A O GLU 46 B N TYR 50 A N TYR 50 B O ASN 58 A O ASN 58 B N VAL 12 A N VAL 12 B O THR 108 A O THR 129 B O VAL 107 A O VAL 128 B N GLY 88 A N GLY 91 B N LEU 96 A N LEU 99 O B O TYR 100 A O TYR 118 B N LEU 122 A N LEU 143 B O GLY 137 A O GLY 158 B N VAL 140 A N VAL 161 B O LEU 176 A O LEU 197 B O VAL 179 A O VAL 200 B N HIS 162 A N HIS 183 B N LEU 122 A N LEU 143 B O GLY 137 A O GLY 158 B N VAL 140 A N VAL 161 B O LEU 176 A O LEU 197 B O SER 175 A O SER 196 B N VAL 167 A N VAL 188 B N THR 149 A N THR 170 B O ASN 197 A O ASN 218 B N HIS 198 A N HIS 219 B O THR 203 A O THR 224 1 B LYS 212 A LYS 233 1 Y 1 B SER 213 A SER 234 1 Y 1 B CYS 214 A CYS 235 1 Y 1 A SER 8 B SER 1 1 Y 1 A CYS 212 B CYS 210 1 Y 1 A SER 213 B SER 211 1 Y 1 C C O6 O6 GAL SIA 6 7 2.02 1 B C ND2 C2 ASN NAG 103 1 2.17 1 9.48 1.50 119.30 128.78 B B B C N CA ALA PRO PRO 123 124 124 Y 1 B SER 15 84.56 -19.02 G 1 B PHE 100 -69.64 12.11 1 B PRO 124 -37.71 136.02 1 B PHE 144 -172.55 140.11 1 A LEU 28 -103.88 -65.96 1 A ASN 51 67.56 -50.55 1 A LEU 107 -68.93 74.85 1 A ASP 152 48.24 -109.52 -3.3525 0.0000 -0.0000 10.1945 -0.0000 -6.8420 0.2341 0.1894 0.1917 2.800 19.915 870 17491 17353 5.01 99.89 0.76 1 0.00 MOLECULAR REPLACEMENT 21.65 0.73 1.00 PDB ENTRY 4JY6 ML FLAT BULK SOLVENT MODEL 20.370 0.357 2.800 19.915 13 3466 134 0 3319 0.010 3550 1.443 4851 23.928 1299 0.201 571 0.006 597 0.3495 0.2727 2.9749 148 2681 100.00 0.2665 0.2341 3.2037 151 2674 100.00 0.2895 0.2011 3.5245 136 2726 100.00 0.2405 0.1960 4.0308 139 2748 100.00 0.1910 0.1497 5.0646 155 2760 100.00 0.2030 0.1754 19.9151 141 2894 100.00 2.8 40 4JY4 17491 17409 0 0 0.088 1 19.8 7.2 99.5 2.8 2.9 3.5 0.484 1 7.4 99.9 data collection Blu-Ice phasing PHASER refinement PHENIX (phenix.refine: 1.7.2_869) data reduction XDS data scaling XDS Crystal structure of human Fab PGT121, a broadly reactive and potent HIV-1 neutralizing antibody 1 N N 2 N N 3 N N 4 N N 4 N N 4 N N 5 N N 5 N N B SER 28 A SER 28 HELX_P B SER 32 A SER 32 5 4 5 B SER 60 A SER 60 HELX_P B SER 65 A SER 65 1 5 6 B THR 83 A THR 86 HELX_P B SER 87 A SER 90 5 6 5 B ILE 100 A ILE 107 HELX_P B ASN 100 A ASN 111 5 7 5 D H B SER 154 A SER 175 HELX_P B ALA 156 A ALA 177 5 8 3 B SER 185 A SER 206 HELX_P B GLY 188 A GLY 209 5 9 4 B LYS 199 A LYS 220 HELX_P B ASN 202 A ASN 223 5 10 4 A GLU 79 B GLU 74 HELX_P A GLU 83 B GLU 78 5 1 5 A SER 122 B SER 120 HELX_P A ALA 128 B ALA 126 1 2 7 A THR 182 B THR 180 HELX_P A HIS 189 B HIS 187 1 3 8 disulf 2.062 B CYS 22 A SG CYS 22 1_555 B CYS 92 A SG CYS 95 1_555 disulf 2.021 B CYS 138 A SG CYS 159 1_555 B CYS 194 A SG CYS 215 1_555 disulf 2.041 A CYS 23 B SG CYS 15 1_555 A CYS 88 B SG CYS 83 1_555 disulf 2.022 A CYS 135 B SG CYS 133 1_555 A CYS 194 B SG CYS 192 1_555 covale 1.431 one N-Glycosylation B ASN 103 A ND2 ASN 124 1_555 C NAG 1 C C1 NAG 1_555 covale 1.439 both C NAG 1 C O4 NAG 1_555 C NAG 2 C C1 NAG 1_555 covale 1.444 both C NAG 1 C O6 NAG 1_555 C FUC 9 C C1 FUC 1_555 covale 1.431 both C NAG 2 C O4 NAG 1_555 C BMA 3 C C1 BMA 1_555 covale 1.430 both C BMA 3 C O3 BMA 1_555 C MAN 4 C C1 MAN 1_555 covale 1.452 both C BMA 3 C O6 BMA 1_555 C MAN 8 C C1 MAN 1_555 covale 1.423 both C MAN 4 C O2 MAN 1_555 C NAG 5 C C1 NAG 1_555 covale 1.424 both C NAG 5 C O4 NAG 1_555 C GAL 6 C C1 GAL 1_555 covale 1.456 both C GAL 6 C O6 GAL 1_555 C SIA 7 C C2 SIA 1_555 IMMUNE SYSTEM Broadly neutralizing antibody against HIV-1, HIV-1 Env gp120 subunit, IMMUNE SYSTEM B PHE 144 A PHE 165 1 B PRO 145 A PRO 166 -4.56 B GLU 146 A GLU 167 1 B PRO 147 A PRO 168 2.85 A SER 67 B SER 60 A B 1 A PRO 67 B PRO 61 -0.85 A TYR 141 B TYR 139 1 A PRO 142 B PRO 140 1.84 4JY4 PDB 2 1 4JY4 SDISVAPGETARISCGEKSLGSRAVQWYQHRAGQAPSLIIYNNQDRPSGIPERFSGSPDSPFGTTATLTITSVEAGDEAD YYCHIWDSRVPTKWVFGGGTTLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVET TTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS 4JY4 PDB 1 1 4JY4 QMQLQESGPGLVKPSETLSLTCSVSGASISDSYWSWIRRSPGKGLEWIGYVHKSGDTNYSPSLKSRVNLSLDTSKNQVSL SLVAATAADSGKYYCARTLHGRRIYGIVAFNEWFTYFYMDVWGNGTQVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCL VKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC 8 213 4JY4 8 213 4JY4 A 1 1 211 1 214 4JY4 1 214 4JY4 B 2 1 235 5 3 4 4 4 4 6 4 4 4 3 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 parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A ILE 11 B ILE 3 A VAL 13 B VAL 5 A GLY 99 B GLY 97 A VAL 106 B VAL 104 A ALA 84 B ALA 79 A ASP 92 B ASP 87 A ARG 31 B ARG 23 A HIS 38 B HIS 30 A SER 45 B SER 37 A ILE 48 B ILE 40 A ALA 19 B ALA 11 A LYS 26 B LYS 18 A THR 70 B THR 65 A ILE 75 B ILE 70 A PHE 62 B PHE 54 A SER 63 B SER 55 A SER 115 B SER 113 A PHE 119 B PHE 117 A ALA 131 B ALA 129 A PHE 140 B PHE 138 A TYR 173 B TYR 171 A LEU 181 B LEU 179 A VAL 160 B VAL 158 A THR 162 B THR 160 A SER 115 B SER 113 A PHE 119 B PHE 117 A ALA 131 B ALA 129 A PHE 140 B PHE 138 A TYR 173 B TYR 171 A LEU 181 B LEU 179 A SER 166 B SER 164 A LYS 167 B LYS 165 A SER 154 B SER 152 A PRO 155 B PRO 153 A THR 146 B THR 144 A ALA 151 B ALA 149 A TYR 192 B TYR 190 A HIS 198 B HIS 196 A SER 201 B SER 199 A VAL 207 B VAL 205 B GLN 3 A GLN 3 B SER 7 A SER 7 B LEU 18 A LEU 18 B SER 25 A SER 25 B GLN 77 A GLN 77 B LEU 82 A LEU 82 B VAL 67 A VAL 67 B ASP 72 A ASP 72 B LEU 11 A LEU 11 B VAL 12 A VAL 12 B THR 105 A THR 126 B VAL 109 A VAL 130 B GLY 88 A GLY 91 B ILE 100 A ILE 104 A B TYR 33 A TYR 33 B ARG 39 A ARG 39 B LEU 45 A LEU 45 B VAL 51 A VAL 51 B ASN 58 A ASN 58 B TYR 59 A TYR 59 B LEU 11 A LEU 11 B VAL 12 A VAL 12 B THR 105 A THR 126 B VAL 109 A VAL 130 B GLY 88 A GLY 91 B ILE 100 A ILE 104 A B TRP 100 A TRP 113 B TRP 101 A TRP 122 J B SER 118 A SER 139 B SER 125 A SER 146 B THR 133 A THR 154 B TYR 143 A TYR 164 B TYR 174 A TYR 195 B PRO 183 A PRO 204 B VAL 161 A VAL 182 B THR 163 A THR 184 B SER 118 A SER 139 B SER 125 A SER 146 B THR 133 A THR 154 B TYR 143 A TYR 164 B TYR 174 A TYR 195 B PRO 183 A PRO 204 B VAL 167 A VAL 188 B LEU 168 A LEU 189 B THR 149 A THR 170 B TRP 152 A TRP 173 B ILE 193 A ILE 214 B HIS 198 A HIS 219 B THR 203 A THR 224 B ARG 208 A ARG 229 19 P 21 21 21