0.015015 0.000000 0.000000 0.000000 0.015015 0.000000 0.000000 0.000000 0.003746 0.00000 0.00000 0.00000 Chen, L. McLellan, J.S. Kwon, Y.D. Schmidt, S. Wu, X. Zhou, T. Yang, Y. Zhang, B. Forsman, A. Weiss, R.A. Verrips, T. Mascola, J. Kwong, P.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 66.600 66.600 266.920 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 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 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 To be Published 0353 Crystal structure of anti-HIV A12 VHH of llama antibody in complex with C1086 gp120 NAG A 734 HAS WRONG CHIRALITY AT ATOM C1 NAG A 897 HAS WRONG CHIRALITY AT ATOM C1 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 CCD 2010-04-12 MARMOSAIC 225 mm CCD SINGLE WAVELENGTH M x-ray 1 1 1.0 22-BM APS 1 SYNCHROTRON APS BEAMLINE 22-BM 42324.707 C186 gp120 1 man polymer 15888.410 Llama VHH A12 1 man polymer 221.208 2-acetamido-2-deoxy-beta-D-glucopyranose 8 man non-polymer no no DIATMYSMQLASCVTLTLVLLVNSVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKND MVEQMHEDIISLWDESLKPCVKLTGGSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIK PVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPNNGGSGSGGNIRQAHCNINESKWNNTLQKVGEE LAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGR AIYAPPIEGEITCNSNITGLLLLRDGGQSNETNDTETFRPGGGDMRDNWRSELYKYKVVEIK DIATMYSMQLASCVTLTLVLLVNSVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKND MVEQMHEDIISLWDESLKPCVKLTGGSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIK PVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPNNGGSGSGGNIRQAHCNINESKWNNTLQKVGEE LAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGR AIYAPPIEGEITCNSNITGLLLLRDGGQSNETNDTETFRPGGGDMRDNWRSELYKYKVVEIK A polypeptide(L) no no AVQLQESGGGLVQAGGSLRLSCTASGRISSSYDMGWFRQAPGKEREFVAAISWSGGTTDYADSVKGRFAISKDNAKNAVY LQMNSLKPEDTAVYYCAAKWRPLRYSDYPSNSDYYDWGQGTQVTVSSEQKLISEEDLHHHHHH AVQLQESGGGLVQAGGSLRLSCTASGRISSSYDMGWFRQAPGKEREFVAAISWSGGTTDYADSVKGRFAISKDNAKNAVY LQMNSLKPEDTAVYYCAAKWRPLRYSDYPSNSDYYDWGQGTQVTVSSEQKLISEEDLHHHHHH 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 n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n sample 11706 Human immunodeficiency virus type 1 sample 9844 Lama glama 1 2.54 51.62 VAPOR DIFFUSION, HANGING DROP 7.8 50 mM of KH2PO4, 24.2% PEG 8000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K 293 chem_comp database_PDB_caveat entity pdbx_chem_comp_identifier pdbx_entity_nonpoly pdbx_unobs_or_zero_occ_atoms struct_conn struct_site struct_site_gen repository Initial release Carbohydrate remediation repository Remediation Database references Structure summary Advisory Data collection Derived calculations Structure summary 1 0 2012-05-02 1 1 2012-06-13 1 2 2012-09-12 1 3 2020-07-29 _chem_comp.name _chem_comp.type _entity.pdbx_description _pdbx_entity_nonpoly.name _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_role _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id DGlcpNAcb N-acetyl-b-D-glucopyranosamine b-D-GlcpNAc GlcNAc RCSB Y RCSB 2011-04-15 REL REL NAG 2-acetamido-2-deoxy-beta-D-glucopyranose NAG 734 3 NAG NAG 734 A NAG 741 3 NAG NAG 741 A NAG 762 3 NAG NAG 762 A NAG 776 3 NAG NAG 776 A NAG 789 3 NAG NAG 789 A NAG 886 3 NAG NAG 886 A NAG 892 3 NAG NAG 892 A NAG 897 3 NAG NAG 897 A n 1 20 A n 2 21 A n 3 22 A n 4 23 A n 5 24 A n 6 25 A n 7 26 A n 8 27 A n 9 28 A n 10 29 A n 11 30 A n 12 31 A n 13 32 A n 14 33 A n 15 34 A n 16 35 A n 17 36 A n 18 37 A n 19 38 A n 20 39 A n 21 40 A n 22 41 A n 23 42 A n 24 43 A n 25 44 A TRP 45 n 26 TRP 45 A LYS 46 n 27 LYS 46 A GLU 47 n 28 GLU 47 A ALA 48 n 29 ALA 48 A LYS 49 n 30 LYS 49 A THR 50 n 31 THR 50 A THR 51 n 32 THR 51 A LEU 52 n 33 LEU 52 A PHE 53 n 34 PHE 53 A CYS 54 n 35 CYS 54 A ALA 55 n 36 ALA 55 A SER 56 n 37 SER 56 A ASP 57 n 38 ASP 57 A ALA 58 n 39 ALA 58 A LYS 59 n 40 LYS 59 A ALA 60 n 41 ALA 60 A TYR 61 n 42 TYR 61 A GLU 62 n 43 GLU 62 A LYS 63 n 44 LYS 63 A GLU 64 n 45 GLU 64 A VAL 65 n 46 VAL 65 A HIS 66 n 47 HIS 66 A ASN 67 n 48 ASN 67 A VAL 68 n 49 VAL 68 A TRP 69 n 50 TRP 69 A ALA 70 n 51 ALA 70 A THR 71 n 52 THR 71 A HIS 72 n 53 HIS 72 A ALA 73 n 54 ALA 73 A CYS 74 n 55 CYS 74 A VAL 75 n 56 VAL 75 A PRO 76 n 57 PRO 76 A THR 77 n 58 THR 77 A ASP 78 n 59 ASP 78 A PRO 79 n 60 PRO 79 A ASN 80 n 61 ASN 80 A PRO 81 n 62 PRO 81 A GLN 82 n 63 GLN 82 A GLU 83 n 64 GLU 83 A MET 84 n 65 MET 84 A VAL 85 n 66 VAL 85 A LEU 86 n 67 LEU 86 A ALA 87 n 68 ALA 87 A ASN 88 n 69 ASN 88 A VAL 89 n 70 VAL 89 A THR 90 n 71 THR 90 A GLU 91 n 72 GLU 91 A ASN 92 n 73 ASN 92 A PHE 93 n 74 PHE 93 A ASN 94 n 75 ASN 94 A MET 95 n 76 MET 95 A TRP 96 n 77 TRP 96 A LYS 97 n 78 LYS 97 A ASN 98 n 79 ASN 98 A ASP 99 n 80 ASP 99 A MET 100 n 81 MET 100 A VAL 101 n 82 VAL 101 A GLU 102 n 83 GLU 102 A GLN 103 n 84 GLN 103 A MET 104 n 85 MET 104 A HIS 105 n 86 HIS 105 A GLU 106 n 87 GLU 106 A ASP 107 n 88 ASP 107 A ILE 108 n 89 ILE 108 A ILE 109 n 90 ILE 109 A SER 110 n 91 SER 110 A LEU 111 n 92 LEU 111 A TRP 112 n 93 TRP 112 A ASP 113 n 94 ASP 113 A GLU 114 n 95 GLU 114 A SER 115 n 96 SER 115 A LEU 116 n 97 LEU 116 A LYS 117 n 98 LYS 117 A n 99 191 A n 100 192 A n 101 193 A n 102 194 A n 103 195 A n 104 196 A n 105 197 A n 106 198 A n 107 199 A n 108 200 A n 109 201 A n 110 202 A n 111 203 A n 112 204 A n 113 205 A n 114 206 A n 115 207 A VAL 208 n 116 VAL 208 A SER 209 n 117 SER 209 A PHE 210 n 118 PHE 210 A ASP 211 n 119 ASP 211 A PRO 212 n 120 PRO 212 A ILE 213 n 121 ILE 213 A PRO 214 n 122 PRO 214 A LEU 215 n 123 LEU 215 A HIS 216 n 124 HIS 216 A TYR 217 n 125 TYR 217 A CYS 218 n 126 CYS 218 A ALA 219 n 127 ALA 219 A PRO 220 n 128 PRO 220 A ALA 221 n 129 ALA 221 A GLY 222 n 130 GLY 222 A PHE 223 n 131 PHE 223 A ALA 224 n 132 ALA 224 A ILE 225 n 133 ILE 225 A LEU 226 n 134 LEU 226 A LYS 227 n 135 LYS 227 A CYS 228 n 136 CYS 228 A ASN 229 n 137 ASN 229 A ASN 230 n 138 ASN 230 A LYS 231 n 139 LYS 231 A THR 232 n 140 THR 232 A PHE 233 n 141 PHE 233 A ASN 234 n 142 ASN 234 A GLY 235 n 143 GLY 235 A THR 236 n 144 THR 236 A GLY 237 n 145 GLY 237 A PRO 238 n 146 PRO 238 A CYS 239 n 147 CYS 239 A ARG 240 n 148 ARG 240 A ASN 241 n 149 ASN 241 A VAL 242 n 150 VAL 242 A SER 243 n 151 SER 243 A THR 244 n 152 THR 244 A VAL 245 n 153 VAL 245 A GLN 246 n 154 GLN 246 A CYS 247 n 155 CYS 247 A THR 248 n 156 THR 248 A HIS 249 n 157 HIS 249 A GLY 250 n 158 GLY 250 A ILE 251 n 159 ILE 251 A LYS 252 n 160 LYS 252 A PRO 253 n 161 PRO 253 A VAL 254 n 162 VAL 254 A VAL 255 n 163 VAL 255 A SER 256 n 164 SER 256 A THR 257 n 165 THR 257 A GLN 258 n 166 GLN 258 A LEU 259 n 167 LEU 259 A LEU 260 n 168 LEU 260 A LEU 261 n 169 LEU 261 A ASN 262 n 170 ASN 262 A GLY 263 n 171 GLY 263 A SER 264 n 172 SER 264 A LEU 265 n 173 LEU 265 A ALA 266 n 174 ALA 266 A GLU 267 n 175 GLU 267 A GLU 268 n 176 GLU 268 A GLU 269 n 177 GLU 269 A ILE 270 n 178 ILE 270 A ILE 271 n 179 ILE 271 A ILE 272 n 180 ILE 272 A ARG 273 n 181 ARG 273 A SER 274 n 182 SER 274 A GLU 275 n 183 GLU 275 A ASN 276 n 184 ASN 276 A LEU 277 n 185 LEU 277 A THR 278 n 186 THR 278 A ASN 279 n 187 ASN 279 A ASN 280 n 188 ASN 280 A ALA 281 n 189 ALA 281 A LYS 282 n 190 LYS 282 A THR 283 n 191 THR 283 A ILE 284 n 192 ILE 284 A ILE 285 n 193 ILE 285 A VAL 286 n 194 VAL 286 A HIS 287 n 195 HIS 287 A LEU 288 n 196 LEU 288 A ASN 289 n 197 ASN 289 A GLU 290 n 198 GLU 290 A SER 291 n 199 SER 291 A VAL 292 n 200 VAL 292 A ASN 293 n 201 ASN 293 A ILE 294 n 202 ILE 294 A VAL 295 n 203 VAL 295 A CYS 296 n 204 CYS 296 A THR 297 n 205 THR 297 A ALA 298 n 206 ARG 298 A n 207 315 A n 208 316 A n 209 317 A n 210 318 A n 211 319 A n 212 320 A n 213 321 A n 214 322 A n 215 323 A n 216 324 A n 217 325 A n 218 326 A n 219 327 A n 220 328 A ALA 329 n 221 ALA 329 A HIS 330 n 222 HIS 330 A CYS 331 n 223 CYS 331 A ASN 332 n 224 ASN 332 A ILE 333 n 225 ILE 333 A ASN 334 n 226 ASN 334 A GLU 335 n 227 GLU 335 A SER 336 n 228 SER 336 A LYS 337 n 229 LYS 337 A TRP 338 n 230 TRP 338 A ASN 339 n 231 ASN 339 A ASN 340 n 232 ASN 340 A THR 341 n 233 THR 341 A LEU 342 n 234 LEU 342 A GLN 343 n 235 GLN 343 A LYS 344 n 236 LYS 344 A VAL 345 n 237 VAL 345 A GLY 346 n 238 GLY 346 A GLU 347 n 239 GLU 347 A GLU 348 n 240 GLU 348 A LEU 349 n 241 LEU 349 A ALA 350 n 242 ALA 350 A LYS 351 n 243 LYS 351 A HIS 352 n 244 HIS 352 A PHE 353 n 245 PHE 353 A PRO 354 n 246 PRO 354 A SER 356 n 247 SER 356 A LYS 357 n 248 LYS 357 A THR 358 n 249 THR 358 A ILE 359 n 250 ILE 359 A LYS 360 n 251 LYS 360 A PHE 361 n 252 PHE 361 A GLU 362 n 253 GLU 362 A PRO 363 n 254 PRO 363 A SER 364 n 255 SER 364 A SER 365 n 256 SER 365 A GLY 366 n 257 GLY 366 A GLY 367 n 258 GLY 367 A ASP 368 n 259 ASP 368 A LEU 369 n 260 LEU 369 A GLU 370 n 261 GLU 370 A ILE 371 n 262 ILE 371 A THR 372 n 263 THR 372 A THR 373 n 264 THR 373 A HIS 374 n 265 HIS 374 A SER 375 n 266 SER 375 A PHE 376 n 267 PHE 376 A ASN 377 n 268 ASN 377 A CYS 378 n 269 CYS 378 A ARG 379 n 270 ARG 379 A GLY 380 n 271 GLY 380 A GLU 381 n 272 GLU 381 A PHE 382 n 273 PHE 382 A PHE 383 n 274 PHE 383 A TYR 384 n 275 TYR 384 A CYS 385 n 276 CYS 385 A ASN 386 n 277 ASN 386 A THR 387 n 278 THR 387 A SER 388 n 279 SER 388 A ASP 389 n 280 ASP 389 A LEU 390 n 281 LEU 390 A PHE 391 n 282 PHE 391 A ASN 392 n 283 ASN 392 A GLY 393 n 284 GLY 393 A THR 394 n 285 THR 394 A TYR 395 n 286 TYR 395 A ARG 396 n 287 ARG 396 A ASN 397 n 288 ASN 397 A GLY 398 n 289 GLY 398 A THR 399 n 290 THR 399 A TYR 400 n 291 TYR 400 A ASN 401 n 292 ASN 401 A HIS 402 n 293 HIS 402 A THR 403 n 294 THR 403 A GLY 404 n 295 GLY 404 A n 296 408 A n 297 409 A n 298 410 A n 299 411 A n 300 412 A THR 413 n 301 THR 413 A ILE 414 n 302 ILE 414 A THR 415 n 303 THR 415 A LEU 416 n 304 LEU 416 A GLN 417 n 305 GLN 417 A CYS 418 n 306 CYS 418 A LYS 419 n 307 LYS 419 A ILE 420 n 308 ILE 420 A LYS 421 n 309 LYS 421 A GLN 422 n 310 GLN 422 A n 311 423 A n 312 424 A n 313 425 A n 314 426 A n 315 427 A n 316 428 A n 317 429 A n 318 430 A n 319 431 A n 320 432 A n 321 433 A n 322 434 A n 323 435 A n 324 436 A n 325 437 A n 326 438 A n 327 439 A n 328 440 A n 329 441 A n 330 442 A n 331 443 A THR 444 n 332 THR 444 A CYS 445 n 333 CYS 445 A ASN 446 n 334 ASN 446 A SER 447 n 335 SER 447 A ASN 448 n 336 ASN 448 A ILE 449 n 337 ILE 449 A THR 450 n 338 THR 450 A GLY 451 n 339 GLY 451 A LEU 452 n 340 LEU 452 A LEU 453 n 341 LEU 453 A LEU 454 n 342 LEU 454 A LEU 455 n 343 LEU 455 A ARG 456 n 344 ARG 456 A ASP 457 n 345 ASP 457 A GLY 458 n 346 GLY 458 A n 347 A 458 A n 348 B 458 A n 349 C 458 A n 350 D 458 A n 351 E 458 A n 352 F 458 A n 353 G 458 A ASP 464 n 354 ASP 464 A THR 465 n 355 THR 465 A GLU 466 n 356 GLU 466 A THR 467 n 357 THR 467 A PHE 468 n 358 PHE 468 A ARG 469 n 359 ARG 469 A PRO 470 n 360 PRO 470 A GLY 471 n 361 GLY 471 A GLY 472 n 362 GLY 472 A GLY 473 n 363 GLY 473 A ASP 474 n 364 ASP 474 A MET 475 n 365 MET 475 A ARG 476 n 366 ARG 476 A ASP 477 n 367 ASP 477 A ASN 478 n 368 ASN 478 A TRP 479 n 369 TRP 479 A ARG 480 n 370 ARG 480 A SER 481 n 371 SER 481 A GLU 482 n 372 GLU 482 A LEU 483 n 373 LEU 483 A TYR 484 n 374 TYR 484 A LYS 485 n 375 LYS 485 A TYR 486 n 376 TYR 486 A LYS 487 n 377 LYS 487 A VAL 488 n 378 VAL 488 A VAL 489 n 379 VAL 489 A GLU 490 n 380 GLU 490 A ILE 491 n 381 ILE 491 A n 382 492 A ALA 1 n 1 ALA 1 B VAL 2 n 2 VAL 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 GLY 9 n 9 GLY 9 B GLY 10 n 10 GLY 10 B LEU 11 n 11 LEU 11 B VAL 12 n 12 VAL 12 B GLN 13 n 13 GLN 13 B ALA 14 n 14 ALA 14 B GLY 15 n 15 GLY 15 B GLY 16 n 16 GLY 16 B SER 17 n 17 SER 17 B LEU 18 n 18 LEU 18 B ARG 19 n 19 ARG 19 B LEU 20 n 20 LEU 20 B SER 21 n 21 SER 21 B CYS 22 n 22 CYS 22 B THR 23 n 23 THR 23 B ALA 24 n 24 ALA 24 B SER 25 n 25 SER 25 B GLY 26 n 26 GLY 26 B ARG 27 n 27 ARG 27 B ILE 28 n 28 ILE 28 B SER 29 n 29 SER 29 B SER 30 n 30 SER 30 B SER 31 n 31 SER 31 B TYR 32 n 32 TYR 32 B ASP 33 n 33 ASP 33 B MET 34 n 34 MET 34 B GLY 35 n 35 GLY 35 B TRP 36 n 36 TRP 36 B PHE 37 n 37 PHE 37 B ARG 38 n 38 ARG 38 B GLN 39 n 39 GLN 39 B ALA 40 n 40 ALA 40 B PRO 41 n 41 PRO 41 B GLY 42 n 42 GLY 42 B LYS 43 n 43 LYS 43 B GLU 44 n 44 GLU 44 B ARG 45 n 45 ARG 45 B GLU 46 n 46 GLU 46 B PHE 47 n 47 PHE 47 B VAL 48 n 48 VAL 48 B ALA 49 n 49 ALA 49 B ALA 50 n 50 ALA 50 B ILE 51 n 51 ILE 51 B SER 52 n 52 SER 52 B TRP 52 n 53 A TRP 52 B SER 53 n 54 SER 53 B GLY 54 n 55 GLY 54 B GLY 55 n 56 GLY 55 B THR 56 n 57 THR 56 B THR 57 n 58 THR 57 B ASP 58 n 59 ASP 58 B TYR 59 n 60 TYR 59 B ALA 60 n 61 ALA 60 B ASP 61 n 62 ASP 61 B SER 62 n 63 SER 62 B VAL 63 n 64 VAL 63 B LYS 64 n 65 LYS 64 B GLY 65 n 66 GLY 65 B ARG 66 n 67 ARG 66 B PHE 67 n 68 PHE 67 B ALA 68 n 69 ALA 68 B ILE 69 n 70 ILE 69 B SER 70 n 71 SER 70 B LYS 71 n 72 LYS 71 B ASP 72 n 73 ASP 72 B ASN 73 n 74 ASN 73 B ALA 74 n 75 ALA 74 B LYS 75 n 76 LYS 75 B ASN 76 n 77 ASN 76 B ALA 77 n 78 ALA 77 B VAL 78 n 79 VAL 78 B TYR 79 n 80 TYR 79 B LEU 80 n 81 LEU 80 B GLN 81 n 82 GLN 81 B MET 82 n 83 MET 82 B ASN 82 n 84 A ASN 82 B SER 82 n 85 B SER 82 B LEU 82 n 86 C LEU 82 B LYS 83 n 87 LYS 83 B PRO 84 n 88 PRO 84 B GLU 85 n 89 GLU 85 B ASP 86 n 90 ASP 86 B THR 87 n 91 THR 87 B ALA 88 n 92 ALA 88 B VAL 89 n 93 VAL 89 B TYR 90 n 94 TYR 90 B TYR 91 n 95 TYR 91 B CYS 92 n 96 CYS 92 B ALA 93 n 97 ALA 93 B ALA 94 n 98 ALA 94 B LYS 95 n 99 LYS 95 B TRP 96 n 100 TRP 96 B ARG 97 n 101 ARG 97 B PRO 98 n 102 PRO 98 B LEU 99 n 103 LEU 99 B ARG 100 n 104 ARG 100 B TYR 100 n 105 A TYR 100 B SER 100 n 106 B SER 100 B ASP 100 n 107 C ASP 100 B TYR 100 n 108 D TYR 100 B PRO 100 n 109 E PRO 100 B SER 100 n 110 F SER 100 B ASN 100 n 111 G ASN 100 B SER 100 n 112 H SER 100 B ASP 100 n 113 I ASP 100 B TYR 100 n 114 J TYR 100 B TYR 101 n 115 TYR 101 B ASP 102 n 116 ASP 102 B TRP 103 n 117 TRP 103 B GLY 104 n 118 GLY 104 B GLN 105 n 119 GLN 105 B GLY 106 n 120 GLY 106 B THR 107 n 121 THR 107 B GLN 108 n 122 GLN 108 B VAL 109 n 123 VAL 109 B THR 110 n 124 THR 110 B VAL 111 n 125 VAL 111 B SER 112 n 126 SER 112 B SER 113 n 127 SER 113 B n 128 114 B n 129 115 B n 130 116 B n 131 117 B n 132 118 B n 133 119 B n 134 120 B n 135 121 B n 136 122 B n 137 123 B n 138 124 B n 139 125 B n 140 126 B n 141 127 B n 142 128 B n 143 129 B 0.8374 -0.6084 -1.0408 0.5895 0.6533 4.0228 0.5977 0.6023 -0.0512 -0.4281 -0.0659 0.1225 -0.5574 -2.2135 -0.1954 0.4195 0.4383 0.1650 1.4789 0.3519 0.2315 refined 3.0248 23.5660 -36.4179 X-RAY DIFFRACTION 0.5265 0.0462 -0.7987 0.1602 -0.3620 2.1062 0.3256 0.6774 -0.0794 0.0265 -0.1858 0.4323 -0.1330 -2.6376 -0.0324 0.1861 0.0876 0.1697 2.3419 0.0571 0.4104 refined -13.3920 16.1432 -20.0504 X-RAY DIFFRACTION 0.2489 0.0316 -0.0961 0.2396 -0.0059 0.2989 0.2684 0.1807 0.2235 0.2101 0.2506 0.0259 0.4038 -0.4011 0.7572 0.0912 -0.7114 -0.0553 0.5295 -0.1010 -0.0686 refined 16.1712 7.2438 -12.1085 X-RAY DIFFRACTION A 45 A 256 X-RAY DIFFRACTION 1 ( CHAIN A AND RESID 45:256 ) A 257 A 472 X-RAY DIFFRACTION 2 ( CHAIN A AND RESID 257:472 ) B 1 B 113 X-RAY DIFFRACTION 3 ( CHAIN B AND RESID 1:113 ) author_and_software_defined_assembly PISA 2 dimeric 4110 23 20000 A ASN 386 GLYCOSYLATION SITE A ASN 277 ASN A ASN 289 GLYCOSYLATION SITE A ASN 197 ASN A ASN 276 GLYCOSYLATION SITE A ASN 184 ASN A ASN 262 GLYCOSYLATION SITE A ASN 170 ASN A ASN 234 GLYCOSYLATION SITE A ASN 142 ASN A ASN 397 GLYCOSYLATION SITE A ASN 288 ASN A ASN 241 GLYCOSYLATION SITE A ASN 149 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 LYS 46 A N LYS 27 A O GLU 490 A O GLU 380 A O VAL 489 A O VAL 379 A N ALA 224 A N ALA 132 A N ILE 225 A N ILE 133 A O VAL 245 A O VAL 153 A O THR 244 A O THR 152 A N MET 84 A N MET 65 A O VAL 75 A O VAL 56 A N CYS 54 A N CYS 35 A N PHE 53 A N PHE 34 A O CYS 218 A O CYS 126 A N PHE 93 A N PHE 74 A O GLY 237 A O GLY 145 A N LEU 260 A N LEU 168 A O THR 450 A O THR 338 A O ILE 449 A O ILE 337 A N VAL 292 A N VAL 200 A O HIS 287 A O HIS 195 A N ILE 271 A N ILE 179 A N LEU 260 A N LEU 168 A O THR 450 A O THR 338 A N LEU 455 A N LEU 343 A O ARG 469 A O ARG 359 A N ILE 333 A N ILE 225 A O ILE 414 A O ILE 302 A O LYS 419 A O LYS 307 A N TYR 384 A N TYR 275 A O CYS 385 A O CYS 276 A N HIS 374 A N HIS 265 A N ILE 359 A N ILE 250 A O TYR 395 A O TYR 286 A N THR 394 A N THR 285 A O TYR 400 A O TYR 291 B N SER 7 B N SER 7 B O SER 21 B O SER 21 B N LEU 18 B N LEU 18 B O MET 82 B O MET 83 B O TYR 79 B O TYR 80 B N SER 70 B N SER 71 B N GLY 10 B N GLY 10 B O THR 110 B O THR 124 B O THR 107 B O THR 121 B N TYR 90 B N TYR 94 B O TYR 91 B O TYR 95 B N PHE 37 B N PHE 37 B N TRP 36 B N TRP 36 B O ALA 49 B O ALA 49 B N ALA 50 B N ALA 50 B O ASP 58 B O ASP 59 B N GLY 10 B N GLY 10 B O THR 110 B O THR 124 B O THR 107 B O THR 121 B N TYR 90 B N TYR 94 B N ALA 94 B N ALA 98 B O ASP 102 B O ASP 116 1 A CG ARG 298 A CG ARG 206 1 Y 1 A CD ARG 298 A CD ARG 206 1 Y 1 A NE ARG 298 A NE ARG 206 1 Y 1 A CZ ARG 298 A CZ ARG 206 1 Y 1 A NH1 ARG 298 A NH1 ARG 206 1 Y 1 A NH2 ARG 298 A NH2 ARG 206 1 Y 1 A O1 NAG 892 I O1 NAG 1 1 N 1 A ASP 20 A ASP 1 1 Y 1 A ILE 21 A ILE 2 1 Y 1 A ALA 22 A ALA 3 1 Y 1 A THR 23 A THR 4 1 Y 1 A MET 24 A MET 5 1 Y 1 A TYR 25 A TYR 6 1 Y 1 A SER 26 A SER 7 1 Y 1 A MET 27 A MET 8 1 Y 1 A GLN 28 A GLN 9 1 Y 1 A LEU 29 A LEU 10 1 Y 1 A ALA 30 A ALA 11 1 Y 1 A SER 31 A SER 12 1 Y 1 A CYS 32 A CYS 13 1 Y 1 A VAL 33 A VAL 14 1 Y 1 A THR 34 A THR 15 1 Y 1 A LEU 35 A LEU 16 1 Y 1 A THR 36 A THR 17 1 Y 1 A LEU 37 A LEU 18 1 Y 1 A VAL 38 A VAL 19 1 Y 1 A LEU 39 A LEU 20 1 Y 1 A LEU 40 A LEU 21 1 Y 1 A VAL 41 A VAL 22 1 Y 1 A ASN 42 A ASN 23 1 Y 1 A SER 43 A SER 24 1 Y 1 A VAL 44 A VAL 25 1 Y 1 A PRO 191 A PRO 99 1 Y 1 A CYS 192 A CYS 100 1 Y 1 A VAL 193 A VAL 101 1 Y 1 A LYS 194 A LYS 102 1 Y 1 A LEU 195 A LEU 103 1 Y 1 A THR 196 A THR 104 1 Y 1 A GLY 197 A GLY 105 1 Y 1 A GLY 198 A GLY 106 1 Y 1 A SER 199 A SER 107 1 Y 1 A ALA 200 A ALA 108 1 Y 1 A ILE 201 A ILE 109 1 Y 1 A THR 202 A THR 110 1 Y 1 A GLN 203 A GLN 111 1 Y 1 A ALA 204 A ALA 112 1 Y 1 A CYS 205 A CYS 113 1 Y 1 A PRO 206 A PRO 114 1 Y 1 A LYS 207 A LYS 115 1 Y 1 A PRO 315 A PRO 207 1 Y 1 A ASN 316 A ASN 208 1 Y 1 A ASN 317 A ASN 209 1 Y 1 A GLY 318 A GLY 210 1 Y 1 A GLY 319 A GLY 211 1 Y 1 A SER 320 A SER 212 1 Y 1 A GLY 321 A GLY 213 1 Y 1 A SER 322 A SER 214 1 Y 1 A GLY 323 A GLY 215 1 Y 1 A GLY 324 A GLY 216 1 Y 1 A ASN 325 A ASN 217 1 Y 1 A ILE 326 A ILE 218 1 Y 1 A ARG 327 A ARG 219 1 Y 1 A GLN 328 A GLN 220 1 Y 1 A ARG 408 A ARG 296 1 Y 1 A SER 409 A SER 297 1 Y 1 A SER 410 A SER 298 1 Y 1 A ASN 411 A ASN 299 1 Y 1 A GLY 412 A GLY 300 1 Y 1 A ILE 423 A ILE 311 1 Y 1 A ILE 424 A ILE 312 1 Y 1 A ASN 425 A ASN 313 1 Y 1 A MET 426 A MET 314 1 Y 1 A TRP 427 A TRP 315 1 Y 1 A GLN 428 A GLN 316 1 Y 1 A GLU 429 A GLU 317 1 Y 1 A VAL 430 A VAL 318 1 Y 1 A GLY 431 A GLY 319 1 Y 1 A ARG 432 A ARG 320 1 Y 1 A ALA 433 A ALA 321 1 Y 1 A ILE 434 A ILE 322 1 Y 1 A TYR 435 A TYR 323 1 Y 1 A ALA 436 A ALA 324 1 Y 1 A PRO 437 A PRO 325 1 Y 1 A PRO 438 A PRO 326 1 Y 1 A ILE 439 A ILE 327 1 Y 1 A GLU 440 A GLU 328 1 Y 1 A GLY 441 A GLY 329 1 Y 1 A GLU 442 A GLU 330 1 Y 1 A ILE 443 A ILE 331 1 Y A 1 A GLY 458 A GLY 347 1 Y B 1 A GLN 458 A GLN 348 1 Y C 1 A SER 458 A SER 349 1 Y D 1 A ASN 458 A ASN 350 1 Y E 1 A GLU 458 A GLU 351 1 Y F 1 A THR 458 A THR 352 1 Y G 1 A ASN 458 A ASN 353 1 Y 1 A LYS 492 A LYS 382 1 Y 1 B GLU 114 B GLU 128 1 Y 1 B GLN 115 B GLN 129 1 Y 1 B LYS 116 B LYS 130 1 Y 1 B LEU 117 B LEU 131 1 Y 1 B ILE 118 B ILE 132 1 Y 1 B SER 119 B SER 133 1 Y 1 B GLU 120 B GLU 134 1 Y 1 B GLU 121 B GLU 135 1 Y 1 B ASP 122 B ASP 136 1 Y 1 B LEU 123 B LEU 137 1 Y 1 B HIS 124 B HIS 138 1 Y 1 B HIS 125 B HIS 139 1 Y 1 B HIS 126 B HIS 140 1 Y 1 B HIS 127 B HIS 141 1 Y 1 B HIS 128 B HIS 142 1 Y 1 B HIS 129 B HIS 143 1 Y 1 A C1 NAG 734 WRONG HAND 1 A C1 NAG 897 PLANAR 1 A A ND2 C1 ASN NAG 392 892 1.17 1 A A CG C1 ASN NAG 241 741 1.93 1 A A ND2 C2 ASN NAG 289 789 1.94 1 A A OD1 C1 ASN NAG 241 741 1.97 1 A A OD1 CG2 ASP THR 389 403 2.06 1 A A OD1 C2 ASN NAG 241 741 2.07 1 A A ND2 C2 ASN NAG 234 734 2.17 1 A A OD1 OG ASN SER 386 388 2.18 1 A GLN 82 139.96 61.77 1 A ASN 88 65.51 -4.31 1 A ASN 94 -164.03 94.16 1 A PHE 210 -164.60 110.54 1 A ASP 211 -164.45 115.80 1 A PRO 212 -46.94 156.40 1 A ASN 230 -58.04 103.02 1 A GLN 258 80.02 -46.45 1 A GLU 268 72.17 -118.02 1 A SER 274 -170.68 146.85 1 A PRO 354 -74.90 -117.45 1 A PHE 376 177.67 167.96 1 A ARG 379 53.95 15.07 1 A PHE 391 -93.85 59.98 1 A ARG 396 -74.39 -131.07 1 B SER 31 -86.72 38.96 1 B VAL 48 -132.44 -54.30 I 1 B ASP 100 47.65 85.11 -33.1835 -0.0000 -0.0000 -33.1835 -0.0000 -15.7071 0.2988 0.2551 0.26 0.2572 2.601 23.473 659 13402 4.92 68.98 0.37 1 1.33 MOLECULAR REPLACEMENT 0.95 1.20 ML FLAT BULK SOLVENT MODEL 68.266 0.263 2.601 23.473 0 3390 112 0 3278 0.004 3470 0.883 4698 15.461 1264 0.055 529 0.003 593 0.5101 0.3566 2.8014 22 380 11.00 0.3464 0.3476 3.0827 87 1490 42.00 0.3605 0.3115 3.5275 180 3335 91.00 0.2788 0.2504 4.4394 179 3675 99.00 0.2735 0.2203 23.4735 191 3863 98.00 2.601 50 3RJQ 13406 1 1 1 68.2 data collection SERGUI phasing PHASER refinement PHENIX (phenix.refine: 1.6.4_486) data reduction HKL-2000 data scaling HKL-2000 C186 gp120, Llama VHH A12 Crystal structure of anti-HIV llama VHH antibody A12 in complex with C186 gp120 1 N N 2 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N A GLU 64 A GLU 45 HELX_P A CYS 74 A CYS 55 1 1 11 A ASN 98 A ASN 79 HELX_P A LEU 116 A LEU 97 1 2 19 A ASN 334 A ASN 226 HELX_P A PHE 353 A PHE 245 1 3 20 A ASP 368 A ASP 259 HELX_P A THR 373 A THR 264 1 4 6 A MET 475 A MET 365 HELX_P A SER 481 A SER 371 1 5 7 B LYS 83 B LYS 87 HELX_P B THR 87 B THR 91 5 6 5 disulf 2.024 A CYS 54 A SG CYS 35 1_555 A CYS 74 A SG CYS 55 1_555 disulf 2.034 A CYS 218 A SG CYS 126 1_555 A CYS 247 A SG CYS 155 1_555 disulf 2.032 A CYS 228 A SG CYS 136 1_555 A CYS 239 A SG CYS 147 1_555 disulf 2.021 A CYS 296 A SG CYS 204 1_555 A CYS 331 A SG CYS 223 1_555 disulf 2.032 A CYS 378 A SG CYS 269 1_555 A CYS 445 A SG CYS 333 1_555 disulf 2.033 A CYS 385 A SG CYS 276 1_555 A CYS 418 A SG CYS 306 1_555 disulf 2.033 B CYS 22 B SG CYS 22 1_555 B CYS 92 B SG CYS 96 1_555 covale 1.441 one N-Glycosylation A ASN 234 A ND2 ASN 142 1_555 A NAG 734 C C1 NAG 1_555 covale 1.483 one N-Glycosylation A ASN 241 A ND2 ASN 149 1_555 A NAG 741 D C1 NAG 1_555 covale 1.440 one N-Glycosylation A ASN 262 A ND2 ASN 170 1_555 A NAG 762 E C1 NAG 1_555 covale 1.440 one N-Glycosylation A ASN 276 A ND2 ASN 184 1_555 A NAG 776 F C1 NAG 1_555 covale 1.439 one N-Glycosylation A ASN 289 A ND2 ASN 197 1_555 A NAG 789 G C1 NAG 1_555 covale 1.438 one N-Glycosylation A ASN 386 A ND2 ASN 277 1_555 A NAG 886 H C1 NAG 1_555 covale 1.442 one N-Glycosylation A ASN 397 A ND2 ASN 288 1_555 A NAG 897 J C1 NAG 1_555 Viral Protein/Immune system Ig VH domain, anti-HIV, Viral Protein-Immune system complex A PRO 81 A PRO 62 1 A GLN 82 A GLN 63 -16.45 3RJQ PDB 1 3RJQ DIATMYSMQLASCVTLTLVLLVNSVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKND MVEQMHEDIISLWDESLKPCVKLTGGSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIK PVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPNNGGSGSGGNIRQAHCNINESKWNNTLQKVGEE LAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGR AIYAPPIEGEITCNSNITGLLLLRDGGQSNETNDTETFRPGGGDMRDNWRSELYKYKVVEIK 3RJQ PDB 2 3RJQ AVQLQESGGGLVQAGGSLRLSCTASGRISSSYDMGWFRQAPGKEREFVAAISWSGGTTDYADSVKGRFAISKDNAKNAVY LQMNSLKPEDTAVYYCAAKWRPLRYSDYPSNSDYYDWGQGTQVTVSSEQKLISEEDLHHHHHH 20 492 3RJQ 20 492 3RJQ A 1 1 382 1 129 3RJQ 1 129 3RJQ B 2 1 143 5 3 2 4 3 4 3 4 6 4 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 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel A LYS 46 A LYS 27 A GLU 47 A GLU 28 A TYR 486 A TYR 376 A GLU 490 A GLU 380 A PHE 223 A PHE 131 A CYS 228 A CYS 136 A VAL 242 A VAL 150 A VAL 245 A VAL 153 A MET 84 A MET 65 A VAL 85 A VAL 66 A VAL 75 A VAL 56 A PRO 76 A PRO 57 A PHE 53 A PHE 34 A SER 56 A SER 37 A HIS 216 A HIS 124 A CYS 218 A CYS 126 A GLU 91 A GLU 72 A ASN 94 A ASN 75 A THR 236 A THR 144 A CYS 239 A CYS 147 A LEU 259 A LEU 167 A LEU 261 A LEU 169 A CYS 445 A CYS 333 A ARG 456 A ARG 344 A ILE 284 A ILE 192 A CYS 296 A CYS 204 A ILE 271 A ILE 179 A ARG 273 A ARG 181 A LEU 259 A LEU 167 A LEU 261 A LEU 169 A CYS 445 A CYS 333 A ARG 456 A ARG 344 A PHE 468 A PHE 358 A PRO 470 A PRO 360 A HIS 330 A HIS 222 A ILE 333 A ILE 225 A ILE 414 A ILE 302 A LYS 419 A LYS 307 A GLU 381 A GLU 272 A CYS 385 A CYS 276 A HIS 374 A HIS 265 A CYS 378 A CYS 269 A ILE 359 A ILE 250 A LYS 360 A LYS 251 A GLY 393 A GLY 284 A TYR 395 A TYR 286 A TYR 400 A TYR 291 A ASN 401 A ASN 292 B LEU 4 B LEU 4 B SER 7 B SER 7 B LEU 18 B LEU 18 B ALA 24 B ALA 24 B ALA 77 B ALA 78 B MET 82 B MET 83 B PHE 67 B PHE 68 B ASP 72 B ASP 73 B GLY 10 B GLY 10 B GLN 13 B GLN 13 B THR 107 B THR 121 B SER 112 B SER 126 B ALA 88 B ALA 92 B TRP 96 B TRP 100 B TYR 32 B TYR 32 B GLN 39 B GLN 39 B ARG 45 B ARG 45 B SER 52 B SER 52 B THR 57 B THR 58 B TYR 59 B TYR 60 B GLY 10 B GLY 10 B GLN 13 B GLN 13 B THR 107 B THR 121 B SER 112 B SER 126 B ALA 88 B ALA 92 B TRP 96 B TRP 100 B ASP 102 B ASP 116 B TRP 103 B TRP 117 96 P 43 21 2