3SE9 - Sequence, Chains, Asymmetric and Biological Units

• Title: CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIB PG04 IN COMPLEX WITH HIV-1 GP120
• Keywords: HIV, GP120, ANTIBODY, VRC-PG04, NEUTRALIZATION, VACCINE, ENV GLYCOPROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
• Experiment: X-ray diffraction
• Number of Models: 1

Database	ID code	Status	Coordinate files
			Header	Asymmetric unit	Biological unit
PDB	3SE9	released	available	available	Quaternary Structure Server

Asymmetric unit from PDB

Unit	Type	Name	Chain ID	Residues	Atoms	Hetatoms
1	Protein	HIV-1 CLADE AE STRAIN 93TH057 GP120	G	344	5321	0
2	Protein	HEAVY CHAIN OF ANTIBODY VRC-PG04	H	225	3402	0
3	Protein	LIGHT CHAIN OF ANTIBODY VRC-PG04	L	208	3205	0
4	Ligand	HIV-1 CLADE AE STRAIN 93TH057 GP120	G	27	0	202
5	Ligand	HEAVY CHAIN OF ANTIBODY VRC-PG04	H	5	0	12
6	Ligand	LIGHT CHAIN OF ANTIBODY VRC-PG04	L	7	0	15
7	Water			555	0	555
total				1371	11928	784

Proteins

Unit 1	VAL 44 TRP 45 LYS 46 ASP 47 ALA 48 ASP 49 THR 50 THR 51 LEU 52 PHE 53 CYS 54 ALA 55 SER 56 ASP 57 ALA 58 LYS 59 ALA 60 HIS 61 GLU 62 THR 63 GLU 64 VAL 65 HIS 66 ASN 67 VAL 68 TRP 69 ALA 70 THR 71 HIS 72 ALA 73 CYS 74 VAL 75 PRO 76 THR 77 ASP 78 PRO 79 ASN 80 PRO 81 GLN 82 GLU 83 ILE 84 HIS 85 LEU 86 GLU 87 ASN 88 VAL 89 THR 90 GLU 91 ASN 92 PHE 93 ASN 94 MET 95 TRP 96 LYS 97 ASN 98 ASN 99 MET 100 VAL 101 GLU 102 GLN 103 MET 104 GLN 105 GLU 106 ASP 107 VAL 108 ILE 109 SER 110 LEU 111 TRP 112 ASP 113 GLN 114 SER 115 LEU 116 GLN 117 PRO 118 CYS 119 VAL 120 LYS 121 LEU 122 THR 123 GLY 124 GLY 198 SER 199 VAL 200 ILE 201 LYS 202 GLN 203 ALA 204 CYS 205 PRO 206 LYS 207 ILE 208 SER 209 PHE 210 ASP 211 PRO 212 ILE 213 PRO 214 ILE 215 HIS 216 TYR 217 CYS 218 THR 219 PRO 220 ALA 221 GLY 222 TYR 223 VAL 224 ILE 225 LEU 226 LYS 227 CYS 228 ASN 229 ASP 230 LYS 231 ASN 232 PHE 233 ASN 234 GLY 235 THR 236 GLY 237 PRO 238 CYS 239 LYS 240 ASN 241 VAL 242 SER 243 SER 244 VAL 245 GLN 246 CYS 247 THR 248 HIS 249 GLY 250 ILE 251 LYS 252 PRO 253 VAL 254 VAL 255 SER 256 THR 257 GLN 258 LEU 259 LEU 260 LEU 261 ASN 262 GLY 263 SER 264 LEU 265 ALA 266 GLU 267 GLU 268 GLU 269 ILE 270 ILE 271 ILE 272 ARG 273 SER 274 GLU 275 ASN 276 LEU 277 THR 278 ASN 279 ASN 280 ALA 281 LYS 282 THR 283 ILE 284 ILE 285 VAL 286 HIS 287 LEU 288 ASN 289 LYS 290 SER 291 VAL 292 GLU 293 ILE 294 ASN 295 CYS 296 THR 297 ARG 298 PRO 299 SER 300 ASN 301 GLY 324 ASP 325 ILE 326 ARG 327 LYS 328 ALA 329 TYR 330 CYS 331 GLU 332 ILE 333 ASN 334 GLY 335 THR 336 LYS 337 TRP 338 ASN 339 LYS 340 VAL 341 LEU 342 LYS 343 GLN 344 VAL 345 THR 346 GLU 347 LYS 348 LEU 349 LYS 350 GLU 351 HIS 352 PHE 353 ASN 354 ASN 355 LYS 357 THR 358 ILE 359 ILE 360 PHE 361 GLN 362 PRO 363 PRO 364 SER 365 GLY 366 GLY 367 ASP 368 LEU 369 GLU 370 ILE 371 THR 372 MET 373 HIS 374 HIS 375 PHE 376 ASN 377 CYS 378 ARG 379 GLY 380 GLU 381 PHE 382 PHE 383 TYR 384 CYS 385 ASN 386 THR 387 THR 388 GLN 389 LEU 390 PHE 391 ASN 392 ASN 393 THR 394 CYS 395 ILE 396 GLY 397 MET 407 LYS 408 GLY 409 CYS 410 ASN 411 GLY 412 THR 413 ILE 414 THR 415 LEU 416 PRO 417 CYS 418 LYS 419 ILE 420 LYS 421 GLN 422 ILE 423 ILE 424 ASN 425 MET 426 TRP 427 GLN 428 GLY 429 THR 430 GLY 431 GLN 432 ALA 433 MET 434 TYR 435 ALA 436 PRO 437 PRO 438 ILE 439 ASP 440 GLY 441 LYS 442 ILE 443 ASN 444 CYS 445 VAL 446 SER 447 ASN 448 ILE 449 THR 450 GLY 451 ILE 452 LEU 453 LEU 454 THR 455 ARG 456 ASP 457 GLY 458 GLY 459 ALA 460 ASN 461 ASN 462 THR 463 SER 464 ASN 465 GLU 466 THR 467 PHE 468 ARG 469 PRO 470 GLY 471 GLY 472 GLY 473 ASN 474 ILE 475 LYS 476 ASP 477 ASN 478 TRP 479 ARG 480 SER 481 GLU 482 LEU 483 TYR 484 LYS 485 TYR 486 LYS 487 VAL 488 VAL 489 GLN 490 ILE 491 GLU 492
Unit 2	GLN 1 VAL 2 GLN 3 LEU 4 VAL 5 GLN 6 SER 7 GLY 8 SER 9 GLY 10 VAL 11 LYS 12 LYS 13 PRO 14 GLY 15 ALA 16 SER 17 VAL 18 ARG 19 VAL 20 SER 21 CYS 22 TRP 23 THR 24 SER 25 GLU 26 ASP 27 ILE 28 PHE 29 GLU 30 ARG 31 THR 32 GLU 33 LEU 34 ILE 35 HIS 35A TRP 36 VAL 37 ARG 38 GLN 39 ALA 40 PRO 41 GLY 42 GLN 43 GLY 44 LEU 45 GLU 46 TRP 47 ILE 48 GLY 49 TRP 50 VAL 51 LYS 52 THR 52A VAL 52B THR 53 GLY 54 ALA 55 VAL 56 ASN 57 PHE 58 GLY 59 SER 60 PRO 61 ASP 62 PHE 63 ARG 64 GLN 65 ARG 66 VAL 67 SER 68 LEU 69 THR 70 ARG 71 ASP 72 ARG 73 ASP 74 LEU 75 PHE 76 THR 77 ALA 78 HIS 79 MET 80 ASP 81 ILE 82 ARG 82A GLY 82B LEU 82C THR 83 GLN 84 GLY 85 ASP 86 THR 87 ALA 88 THR 89 TYR 90 PHE 91 CYS 92 ALA 93 ARG 94 GLN 95 LYS 96 PHE 97 TYR 98 THR 99 GLY 100 GLY 100A GLN 100B GLY 100C TRP 100D TYR 100E PHE 100F ASP 101 LEU 102 TRP 103 GLY 104 ARG 105 GLY 106 THR 107 LEU 108 ILE 109 VAL 110 VAL 111 SER 112 SER 113 ALA 114 SER 115 THR 116 LYS 117 GLY 118 PRO 119 SER 120 VAL 121 PHE 122 PRO 123 LEU 124 ALA 125 PRO 126 SER 127 SER 128 LYS 129 SER 132 GLY 133 GLY 134 THR 135 ALA 136 ALA 137 LEU 138 GLY 139 CYS 140 LEU 141 VAL 142 LYS 143 ASP 144 TYR 145 PHE 146 PRO 147 GLU 148 PRO 149 VAL 150 THR 151 VAL 152 SER 153 TRP 154 ASN 155 SER 156 GLY 157 ALA 158 LEU 159 THR 160 SER 161 GLY 162 VAL 163 HIS 164 THR 165 PHE 166 PRO 167 ALA 168 VAL 169 LEU 170 GLN 171 SER 172 SER 173 GLY 174 LEU 175 TYR 176 SER 177 LEU 178 SER 179 SER 180 VAL 181 VAL 182 THR 183 VAL 184 PRO 185 SER 186 SER 187 SER 188 LEU 189 GLY 190 THR 191 GLN 192 THR 193 TYR 194 ILE 195 CYS 196 ASN 197 VAL 198 ASN 199 HIS 200 LYS 201 PRO 202 SER 203 ASN 204 THR 205 LYS 206 VAL 207 ASP 208 LYS 209 LYS 210 VAL 211 GLU 212 PRO 213 LYS 214 SER 215
Unit 3	GLU 1 ILE 2 VAL 3 LEU 4 THR 5 GLN 6 SER 7 PRO 8 GLY 9 THR 10 LEU 11 SER 12 LEU 13 SER 14 PRO 15 GLY 16 GLU 17 THR 18 ALA 19 SER 20 LEU 21 SER 22 CYS 23 THR 24 ALA 25 ALA 26 SER 27 TYR 30 GLY 31 HIS 32 MET 33 THR 34 TRP 35 TYR 36 GLN 37 LYS 38 LYS 39 PRO 40 GLY 41 GLN 42 PRO 43 PRO 44 LYS 45 LEU 46 LEU 47 ILE 48 PHE 49 ALA 50 THR 51 SER 52 LYS 53 ARG 54 ALA 55 SER 56 GLY 57 ILE 58 PRO 59 ASP 60 ARG 61 PHE 62 SER 63 GLY 64 SER 65 GLN 66 PHE 67 GLY 68 LYS 69 GLN 70 TYR 71 THR 72 LEU 73 THR 74 ILE 75 THR 76 ARG 77 MET 78 GLU 79 PRO 80 GLU 81 ASP 82 PHE 83 ALA 84 ARG 85 TYR 86 TYR 87 CYS 88 GLN 89 GLN 90 LEU 91 GLU 96 PHE 97 PHE 98 GLY 99 GLN 100 GLY 101 THR 102 ARG 103 LEU 104 GLU 105 ILE 106 ARG 107 ARG 108 THR 109 VAL 110 ALA 111 ALA 112 PRO 113 SER 114 VAL 115 PHE 116 ILE 117 PHE 118 PRO 119 PRO 120 SER 121 ASP 122 GLU 123 GLN 124 LEU 125 LYS 126 SER 127 GLY 128 THR 129 ALA 130 SER 131 VAL 132 VAL 133 CYS 134 LEU 135 LEU 136 ASN 137 ASN 138 PHE 139 TYR 140 PRO 141 ARG 142 GLU 143 ALA 144 LYS 145 VAL 146 GLN 147 TRP 148 LYS 149 VAL 150 ASP 151 ASN 152 ALA 153 LEU 154 GLN 155 SER 156 GLY 157 ASN 158 SER 159 GLN 160 GLU 161 SER 162 VAL 163 THR 164 GLU 165 GLN 166 ASP 167 SER 168 LYS 169 ASP 170 SER 171 THR 172 TYR 173 SER 174 LEU 175 SER 176 SER 177 THR 178 LEU 179 THR 180 LEU 181 SER 182 LYS 183 ALA 184 ASP 185 TYR 186 GLU 187 LYS 188 HIS 189 LYS 190 VAL 191 TYR 192 ALA 193 CYS 194 GLU 195 VAL 196 THR 197 HIS 198 GLN 199 GLY 200 LEU 201 SER 202 SER 203 PRO 204 VAL 205 THR 206 LYS 207 SER 208 PHE 209 ASN 210 ARG 211 GLY 212 GLU 213 CYS 214

Ligands

Unit 4	NAG 734 NAG 741 NAG 762 NAG 776 NAG 789 NAG 795 NAG 834 NAG 886 NAG 892 NAG 948 SO4 1000 SO4 1001 SO4 1002 GOL 1005 GOL 1006 GOL 1007 GOL 1008 CL 1013 CL 1014 CL 1015 CL 1016 CL 1017 CL 1019 CL 1022 CL 1027 CL 1028 BU3 1030
Unit 5	CL 1010 CL 1021 CL 1023 CL 1026 TRS 1040
Unit 6	SO4 1003 SO4 1004 CL 1011 CL 1012 CL 1018 CL 1020 CL 1024