4YFL - Sequence, Chains, Asymmetric and Biological Units

• Title: CRYSTAL STRUCTURE OF VH1-46 GERMLINE-DERIVED CD4-BINDING SIT ANTIBODY 1B2530 IN COMPLEX WITH HIV-1 CLADE A/E 93TH057 GP1
• Keywords: HIV-1 CD4 BINDING SITE, BROADLY NEUTRALIZING ANTIBODY, IMMUN
• Experiment: X-ray diffraction
• Number of Models: 1

Database	ID code	Status	Coordinate files
			Header	Asymmetric unit	Biological unit
PDB	4YFL	released	available	available	Quaternary Structure Server

Asymmetric unit from PDB

Unit	Type	Name	Chain ID	Residues	Atoms	Hetatoms
1	Protein	ENVELOPE GLYCOPROTEIN GP160,ENVELOPE GLYCOPROTEIN ENVELOPE GLYCOPROTEIN GP160	G	347	5360	0
2	Protein	1B2530 HEAVY CHAIN	H	223	3350	0
3	Protein	1B2530 LIGHT CHAIN	L	209	3020	0
4	Protein	ENVELOPE GLYCOPROTEIN GP160,ENVELOPE GLYCOPROTEIN ENVELOPE GLYCOPROTEIN GP160	E	347	5356	0
5	Protein	1B2530 HEAVY CHAIN	F	221	3329	0
6	Protein	1B2530 LIGHT CHAIN	I	200	2914	0
7	Ligand	ENVELOPE GLYCOPROTEIN GP160,ENVELOPE GLYCOPROTEIN ENVELOPE GLYCOPROTEIN GP160	G	6	0	168
8	Ligand	ENVELOPE GLYCOPROTEIN GP160,ENVELOPE GLYCOPROTEIN ENVELOPE GLYCOPROTEIN GP160	E	10	0	280
total				1563	23329	448

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 ASN 404 GLU 405 THR 406 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 3 LEU 4 GLU 5 GLN 6 SER 7 GLY 8 THR 9 ALA 10 VAL 11 ARG 12 LYS 13 PRO 14 GLY 15 ALA 16 SER 17 VAL 18 THR 19 LEU 20 SER 21 CYS 22 GLN 23 ALA 24 SER 25 GLY 26 TYR 27 ASN 28 PHE 29 VAL 30 LYS 31 TYR 32 ILE 33 ILE 34 HIS 35 TRP 36 VAL 37 ARG 38 GLN 39 LYS 40 PRO 41 GLY 42 LEU 43 GLY 44 PHE 45 GLU 46 TRP 47 VAL 48 GLY 49 MET 50 ILE 51 ASP 52 PRO 53 TYR 54 ARG 55 GLY 56 ARG 57 PRO 58 TRP 59 SER 60 ALA 61 HIS 62 LYS 63 PHE 64 GLN 65 GLY 66 ARG 67 LEU 68 SER 69 LEU 70 SER 71 ARG 72 ASP 73 THR 74 SER 75 MET 76 GLU 77 ILE 78 LEU 79 TYR 80 MET 81 THR 82 LEU 83 THR 84 SER 85 LEU 86 LYS 87 SER 88 ASP 89 ASP 90 THR 91 ALA 92 THR 93 TYR 94 PHE 95 CYS 96 ALA 97 ARG 98 ALA 99 GLU 100 ALA 101 ALA 102 SER 103 ASP 104 SER 105 HIS 106 SER 107 ARG 108 PRO 109 ILE 110 MET 111 PHE 112 ASP 113 HIS 114 TRP 115 GLY 116 GLN 117 GLY 118 SER 119 LEU 120 VAL 121 THR 122 VAL 123 SER 124 SER 125 ALA 126 SER 127 THR 128 LYS 129 GLY 130 PRO 131 SER 132 VAL 133 PHE 134 PRO 135 LEU 136 ALA 137 PRO 138 SER 139 SER 140 LYS 141 SER 144 GLY 145 GLY 146 THR 147 ALA 148 ALA 149 LEU 150 GLY 151 CYS 152 LEU 153 VAL 154 LYS 155 ASP 156 TYR 157 PHE 158 PRO 159 GLU 160 PRO 161 VAL 162 THR 163 VAL 164 SER 165 TRP 166 ASN 167 SER 168 GLY 169 ALA 170 LEU 171 THR 172 SER 173 GLY 174 VAL 175 HIS 176 THR 177 PHE 178 PRO 179 ALA 180 VAL 181 LEU 182 GLN 183 SER 184 SER 185 GLY 186 LEU 187 TYR 188 SER 189 LEU 190 SER 191 SER 192 VAL 193 VAL 194 THR 195 VAL 196 PRO 197 SER 198 SER 199 SER 200 LEU 201 GLY 202 THR 203 GLN 204 THR 205 TYR 206 ILE 207 CYS 208 ASN 209 VAL 210 ASN 211 HIS 212 LYS 213 PRO 214 SER 215 ASN 216 THR 217 LYS 218 VAL 219 ASP 220 LYS 221 LYS 222 VAL 223 GLU 224 PRO 225 LYS 226 SER 227
Unit 3	GLN 1 SER 2 ALA 3 LEU 4 THR 5 GLN 6 PRO 7 PRO 8 SER 9 ALA 11 SER 12 GLY 13 ALA 14 PRO 15 GLY 16 GLN 17 ARG 18 VAL 19 THR 20 ILE 21 SER 22 CYS 23 SER 24 GLY 25 GLY 26 PRO 27 SER 27A ASN 27B VAL 28 GLY 29 GLY 30 ASN 31 TYR 32 VAL 33 TYR 34 TRP 35 TYR 36 ARG 37 GLN 38 PHE 39 PRO 40 GLY 41 THR 42 ALA 43 PRO 44 THR 45 LEU 46 LEU 47 ILE 48 LEU 49 ARG 50 ASP 51 ASP 52 GLN 53 ARG 54 PRO 55 SER 56 GLY 57 VAL 58 PRO 59 ASP 60 ARG 61 PHE 62 SER 63 ALA 64 SER 65 LYS 66 SER 67 GLY 68 ASN 69 SER 70 ALA 71 SER 72 LEU 73 ALA 74 ILE 75 SER 76 GLY 77 LEU 78 ARG 79 PRO 80 ASP 81 ASP 82 GLU 83 GLY 84 PHE 85 TYR 86 PHE 87 CYS 88 ALA 89 THR 90 TYR 91 ASP 92 SER 93 ASP 94 GLY 95 SER 95A ILE 95B ARG 96 LEU 97 PHE 98 GLY 99 GLY 100 GLY 101 THR 102 ALA 103 LEU 104 THR 105 VAL 106 PRO 109 LYS 110 ALA 111 ALA 112 PRO 113 SER 114 VAL 115 THR 116 LEU 117 PHE 118 PRO 119 PRO 120 SER 121 SER 122 GLU 123 GLU 124 LEU 125 GLN 126 ALA 127 ASN 128 LYS 129 ALA 130 THR 131 LEU 132 VAL 133 CYS 134 LEU 135 ILE 136 SER 137 ASP 138 PHE 139 TYR 140 PRO 141 GLY 142 ALA 143 VAL 144 THR 145 VAL 146 ALA 147 TRP 148 LYS 149 ALA 150 ASP 151 SER 152 SER 153 PRO 154 VAL 155 LYS 156 ALA 157 GLY 158 VAL 159 GLU 160 THR 161 THR 162 THR 163 PRO 164 SER 165 LYS 166 GLN 167 SER 168 ASN 169 ASN 170 LYS 171 TYR 172 ALA 173 ALA 174 SER 175 SER 176 TYR 177 LEU 178 SER 179 LEU 180 THR 181 PRO 182 GLU 183 GLN 184 TRP 185 LYS 186 SER 187 HIS 188 LYS 189 SER 190 TYR 191 SER 192 CYS 193 GLN 194 VAL 195 THR 196 HIS 197 GLU 198 GLY 199 SER 200 THR 201 VAL 202 GLU 203 LYS 204 THR 205 VAL 206 ALA 207 PRO 208
Unit 4	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 ASN 404 GLU 405 THR 406 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 5	GLN 3 LEU 4 GLU 5 GLN 6 SER 7 GLY 8 THR 9 ALA 10 VAL 11 ARG 12 LYS 13 PRO 14 GLY 15 ALA 16 SER 17 VAL 18 THR 19 LEU 20 SER 21 CYS 22 GLN 23 ALA 24 SER 25 GLY 26 TYR 27 ASN 28 PHE 29 VAL 30 LYS 31 TYR 32 ILE 33 ILE 34 HIS 35 TRP 36 VAL 37 ARG 38 GLN 39 LYS 40 PRO 41 GLY 42 LEU 43 GLY 44 PHE 45 GLU 46 TRP 47 VAL 48 GLY 49 MET 50 ILE 51 ASP 52 PRO 52A TYR 53 ARG 54 GLY 55 ARG 56 PRO 57 TRP 58 SER 59 ALA 60 HIS 61 LYS 62 PHE 63 GLN 64 GLY 65 ARG 66 LEU 67 SER 68 LEU 69 SER 70 ARG 71 ASP 72 THR 73 SER 74 MET 75 GLU 76 ILE 77 LEU 78 TYR 79 MET 80 THR 81 LEU 82 THR 82A SER 82B LEU 82C LYS 83 SER 84 ASP 85 ASP 86 THR 87 ALA 88 THR 89 TYR 90 PHE 91 CYS 92 ALA 93 ARG 94 ALA 95 GLU 96 ALA 97 ALA 98 SER 99 ASP 100 SER 100A HIS 100B SER 100C ARG 100D PRO 100E ILE 100F MET 100G PHE 100H ASP 101 HIS 102 TRP 103 GLY 104 GLN 105 GLY 106 SER 107 LEU 108 VAL 109 THR 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 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
Unit 6	THR 5 GLN 6 PRO 7 PRO 8 SER 9 ALA 11 SER 12 GLY 13 ALA 14 PRO 15 GLY 16 GLN 17 ARG 18 VAL 19 THR 20 ILE 21 SER 22 CYS 23 SER 24 GLY 25 GLY 26 PRO 27 SER 27A ASN 27B VAL 28 GLY 29 GLY 30 ASN 31 TYR 32 VAL 33 TYR 34 TRP 35 TYR 36 ARG 37 GLN 38 PHE 39 PRO 40 GLY 41 THR 42 ALA 43 PRO 44 THR 45 LEU 46 LEU 47 ILE 48 LEU 49 ARG 50 ASP 51 ASP 52 GLN 53 ARG 54 PRO 55 SER 56 GLY 57 VAL 58 PRO 59 ASP 60 ARG 61 PHE 62 SER 63 ALA 64 SER 65 LYS 66 SER 67 GLY 68 ASN 69 SER 70 ALA 71 SER 72 LEU 73 ALA 74 ILE 75 SER 76 GLY 77 LEU 78 ARG 79 PRO 80 ASP 81 ASP 82 GLU 83 GLY 84 PHE 85 TYR 86 PHE 87 CYS 88 ALA 89 THR 90 TYR 91 ASP 92 SER 93 ASP 94 GLY 95 SER 95A ILE 95B ARG 96 LEU 97 PHE 98 GLY 99 GLY 100 GLY 101 THR 102 ALA 103 LEU 104 THR 105 PRO 113 SER 114 VAL 115 THR 116 LEU 117 PHE 118 PRO 119 PRO 120 SER 121 SER 122 GLU 123 GLU 124 LEU 125 GLN 126 ALA 127 ASN 128 LYS 129 ALA 130 THR 131 LEU 132 VAL 133 CYS 134 LEU 135 ILE 136 SER 137 ASP 138 PHE 139 TYR 140 PRO 141 GLY 142 ALA 143 VAL 144 THR 145 VAL 146 ALA 147 TRP 148 LYS 149 ALA 150 ASP 151 SER 152 SER 153 PRO 154 VAL 155 LYS 156 ALA 157 GLY 158 VAL 159 GLU 160 THR 161 THR 162 THR 163 PRO 164 SER 165 LYS 166 GLN 167 SER 168 ASN 169 ASN 170 LYS 171 TYR 172 ALA 173 ALA 174 SER 175 SER 176 TYR 177 LEU 178 SER 179 LEU 180 THR 181 PRO 182 GLU 183 GLN 184 TRP 185 LYS 186 SER 187 HIS 188 LYS 189 SER 190 TYR 191 SER 192 CYS 193 GLN 194 VAL 195 THR 196 HIS 197 GLU 198 GLY 199 SER 200 THR 201 VAL 202 GLU 203 LYS 204 THR 205 VAL 206 ALA 207 PRO 208

Ligands

Unit 7	NAG 501 NAG 502 NAG 503 NAG 504 NAG 505 NAG 506
Unit 8	NAG 501 NAG 502 NAG 503 NAG 504 NAG 505 NAG 506 NAG 507 NAG 508 NAG 509 NAG 510