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Sequence, Chains, Asymmetric and Biological Units

Title UNCLEAVED PREFUSION OPTIMIZED GP140 TRIMER WITH AN ENGINEERE RESIDUE HR1 TURN BOUND TO BROADLY NEUTRALIZING ANTIBODIES 8 PGT128
Keywords HIV-1 TRIMER, UFO, SOSIP, VACCINE, VIRAL PROTEIN-IMMUNE SYST COMPLEX
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   5JSA     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   BROADLY NEUTRALIZING ANTIBODY PGT128 HEAVY CHAIN  A 230 1735 0
2  Protein   BROADLY NEUTRALIZING ANTIBODY PGT128 LIGHT CHAIN  B 204 1514 0
3  Protein   GP120  C 447 3519 0
4  Protein   GP41  D 132 1052 0
5  Protein    E 224 1686 0
6  Protein    F 212 1626 0
7  Ligand    G 2 0 28
8  Ligand    H 2 0 28
9  Ligand    I 2 0 28
10  Ligand    J 8 0 94
11  Ligand    K 10 0 116
12  Ligand    L 9 0 105
13  Ligand    M 7 0 83
14  Ligand    N 5 0 61
15  Ligand    O 3 0 39
16  Ligand    P 3 0 39
17  Ligand    Q 3 0 39
18  Ligand    R 3 0 39
19  Ligand    S 3 0 39
20  Ligand    T 4 0 50
21  Ligand    U 11 0 127
22  Ligand   GP120  C 1 0 14
23  Ligand   GP41  D 1 0 14
total       1526 11132 943
Proteins
Unit 1 PRO2 GLN3 LEU4 GLN5 GLU6 SER7 GLY8 PRO9 THR10 LEU11 VAL12 GLU13 ALA14 SER15 GLU16 THR17 LEU18 SER19 LEU20 THR21 CYS22 ALA23 VAL24 SER25 GLY26 ASP27 SER28 THR29 ALA30 ALA31 CYS32 ASN33 SER34 PHE35 TRP35A GLY35B TRP36 VAL37 ARG38 GLN39 PRO40 PRO41 GLY42 LYS43 GLY44 LEU45 GLU46 TRP47 VAL48 GLY49 SER50 LEU51 SER52 HIS52A CYS52B ALA52C SER52D TYR52E TRP52F ASN53 ARG54 GLY55 TRP56 THR57 TYR58 HIS59 ASN60 PRO61 SER62 LEU63 LYS64 SER65 ARG66 LEU67 THR68 LEU69 ALA70 LEU71 ASP72 THR73 PRO74 LYS75 ASN76 LEU77 VAL78 PHE79 LEU80 LYS81 LEU82 ASN82A SER82B VAL82C THR83 ALA84 ALA85 ASP86 THR87 ALA88 THR89 TYR90 TYR91 CYS92 ALA93 ARG94 PHE95 GLY96 GLY97 GLU98 VAL99 LEU100 ARG100A TYR100B THR100C ASP100D TRP100E PRO100F LYS100G PRO100H ALA100I TRP100J VAL100K ASP101 LEU102 TRP103 GLY104 ARG105 GLY106 THR107 LEU108 VAL109 THR110 VAL111 SER112 SER113 ALA114 SER115 THR116 LYS117 GLY118 PRO119 SER120 VAL121 PHE122 PRO123 LEU124 ALA125 PRO126 SER127 SER134 GLY135 GLY136 THR137 ALA138 ALA139 LEU140 GLY141 CYS142 LEU143 VAL144 LYS145 ASP146 TYR147 PHE148 PRO149 GLU150 PRO151 VAL152 THR153 VAL154 SER155 TRP157 ASN158 SER163 GLY164 ALA165 LEU166 THR167 SER168 GLY169 VAL170 HIS172 THR173 PHE174 PRO175 ALA176 VAL177 LEU178 GLN179 SER180 SER181 GLY183 LEU184 TYR185 SER186 LEU187 SER188 SER189 VAL190 VAL191 THR192 VAL193 PRO194 SER195 SER196 SER197 LEU198 GLY199 THR200 GLN201 THR205 TYR206 ILE207 CYS208 ASN209 VAL210 ASN211 HIS212 LYS213 PRO214 SER215 ASN216 THR217 LYS218 VAL219 ASP220 LYS221 ARG222 VAL225 GLU226 PRO227
Unit 2 LEU4 THR5 GLN6 PRO7 PRO8 SER9 ALA11 SER12 GLY13 SER14 PRO15 GLY16 GLN17 SER18 ILE19 THR20 ILE21 SER22 CYS23 THR24 GLY25 THR26 SER27 ASN30 ASN31 PHE32 VAL33 SER34 TRP35 TYR36 GLN37 GLN38 HIS39 ALA40 GLY41 LYS42 ALA43 PRO44 LYS45 LEU46 VAL47 ILE48 TYR49 ASP50 VAL51 ASN52 LYS53 ARG54 PRO55 SER56 GLY57 VAL58 PRO59 ASP60 ARG61 PHE62 SER63 GLY64 SER65 LYS66 SER67 GLY68 ASN69 THR70 ALA71 SER72 LEU73 THR74 VAL75 SER76 GLY77 LEU78 GLN79 THR80 ASP81 ASP82 GLU83 ALA84 VAL85 TYR86 TYR87 CYS88 GLY89 SER90 LEU91 VAL92 GLY93 ASN94 TRP95 ASP95A VAL96 ILE97 PHE98 GLY99 GLY100 GLY101 THR102 LYS103 LEU104 THR105 VAL106 LEU106A GLY107 GLN108 PRO109 LYS110 ALA111 ALA112 PRO113 SER114 VAL115 THR116 LEU117 PHE118 PRO119 PRO120 SER121 SER122 GLU123 GLU124 LEU125 GLN126 ALA127 ASN128 LYS129 ALA130 THR131 LEU132 VAL133 CYS134 LEU135 ILE136 SER137 ASP138 PHE139 TYR140 PRO141 GLY142 ALA143 VAL144 THR145 VAL146 ALA147 TRP148 LYS149 ALA150 ASP151 SER152 SER153 PRO154 VAL155 LYS156 ALA157 GLY158 VAL159 GLU160 THR161 THR162 THR163 PRO164 SER165 LYS166 GLN167 SER168 ASN170 ASN171 LYS172 TYR173 ALA174 ALA175 SER176 SER177 TYR178 LEU179 SER180 LEU181 THR182 PRO183 GLU184 GLN185 TRP186 LYS187 SER188 HIS189 ARG190 SER191 TYR192 SER193 CYS194 GLN195 VAL196 THR197 HIS198 GLU199 GLY200 SER203 THR204 VAL205 GLU206 LYS207 THR208 VAL209 ALA210 PRO211
Unit 3 ASN33 LEU34 TRP35 VAL36 THR37 VAL38 TYR39 TYR40 GLY41 VAL42 PRO43 VAL44 TRP45 LYS46 ASP47 ALA48 GLU49 THR50 THR51 LEU52 PHE53 CYS54 ALA55 SER56 ASP57 ALA58 LYS59 ALA60 TYR61 GLU62 THR63 GLU64 LYS65 HIS66 ASN67 VAL68 TRP69 ALA70 THR71 HIS72 ALA73 CYS74 VAL75 PRO76 THR77 ASP78 PRO79 ASN80 PRO81 GLN82 GLU83 ILE84 HIS85 LEU86 GLU87 ASN88 VAL89 THR90 GLU91 GLU92 PHE93 ASN94 MET95 TRP96 LYS97 ASN98 ASN99 MET100 VAL101 GLU102 GLN103 MET104 HIS105 THR106 ASP107 ILE108 ILE109 SER110 LEU111 TRP112 ASP113 GLN114 SER115 LEU116 LYS117 PRO118 CYS119 VAL120 LYS121 LEU122 THR123 PRO124 LEU125 CYS126 VAL127 THR128 LEU129 GLN130 CYS131 THR132 ASN133 VAL134 THR135 ASP140 MET141 ARG142 GLY143 GLU144 LEU145 LYS146 ASN147 CYS148 SER149 PHE150 ASN151 MET152 THR153 THR154 GLU155 LEU156 ARG157 ASP158 LYS159 LYS160 GLN161 LYS162 VAL163 TYR164 SER165 LEU166 PHE167 TYR168 ARG169 LEU170 ASP171 VAL172 VAL173 GLN174 ILE175 ASN176 ASN187 LYS188 GLU189 TYR190 ARG191 LEU192 ILE193 ASN194 CYS195 ASN196 THR197 SER198 ALA199 ILE200 THR201 GLN202 ALA203 CYS204 PRO205 LYS206 VAL207 SER208 PHE209 GLU210 PRO211 ILE212 PRO213 ILE214 HIS215 TYR216 CYS217 ALA218 PRO219 ALA220 GLY221 PHE222 ALA223 ILE224 LEU225 LYS226 CYS227 LYS228 ASP229 LYS230 LYS231 PHE232 ASN233 GLY234 THR235 GLY236 PRO237 CYS238 PRO239 SER240 VAL241 SER242 THR243 VAL244 GLN245 CYS246 THR247 HIS248 GLY249 ILE250 LYS251 PRO252 VAL253 VAL254 SER255 THR256 GLN257 LEU258 LEU259 LEU260 ASN261 GLY262 SER263 LEU264 ALA265 GLU266 GLU267 GLU268 VAL269 MET270 ILE271 ARG272 SER273 GLU274 ASN275 ILE276 THR277 ASN278 ASN279 ALA280 LYS281 ASN282 ILE283 LEU284 VAL285 GLN286 PHE287 ASN288 THR289 PRO290 VAL291 GLN292 ILE293 ASN294 CYS295 THR296 ARG297 PRO298 ASN299 ASN300 ASN301 THR302 ARG303 LYS304 SER305 ILE306 ARG307 ILE308 GLY309 PRO310 GLY311 GLN312 ALA313 PHE314 TYR315 ALA316 THR317 GLY318 ASP319 ILE320 ILE321 GLY322 ASP323 ILE324 ARG325 GLN326 ALA327 HIS328 CYS329 ASN330 VAL331 SER332 LYS333 ALA334 THR335 TRP336 ASN337 GLU338 THR339 LEU340 GLY341 LYS342 VAL343 VAL344 LYS345 GLN346 LEU347 ARG348 LYS349 HIS350 PHE351 GLY352 ASN353 ASN354 THR355 ILE356 ILE357 ARG358 PHE359 ALA360 ASN361 SER362 SER363 GLY364 GLY365 ASP366 LEU367 GLU368 VAL369 THR370 THR371 HIS372 SER373 PHE374 ASN375 CYS376 GLY377 GLY378 GLU379 PHE380 PHE381 TYR382 CYS383 ASN384 THR385 SER386 GLY387 LEU388 PHE389 ASN390 SER391 THR392 TRP393 ILE394 SER395 ASN396 THR397 SER398 VAL399 ASN408 ASP409 SER410 ILE411 THR412 LEU413 PRO414 CYS415 ARG416 ILE417 LYS418 GLN419 ILE420 ILE421 ASN422 MET423 TRP424 GLN425 ARG426 ILE427 GLY428 GLN429 ALA430 MET431 TYR432 ALA433 PRO434 PRO435 ILE436 GLN437 GLY438 VAL439 ILE440 ARG441 CYS442 VAL443 SER444 ASN445 ILE446 THR447 GLY448 LEU449 ILE450 LEU451 THR452 ARG453 ASP454 GLY455 GLY456 SER457 THR458 ASN459 SER460 THR461 THR462 GLU463 THR464 PHE465 ARG466 PRO467 GLY468 GLY469 GLY470 ASP471 MET472 ARG473 ASP474 ASN475 TRP476 ARG477 SER478 GLU479 LEU480 TYR481 LYS482 TYR483 LYS484 VAL485 VAL486 LYS487 ILE488 GLU489 PRO490 LEU491 GLY492 VAL493 ALA494 PRO495 THR496 ARG497 CYS498 LYS499 ARG500 ARG501
Unit 4 PHE522 LEU523 GLY524 ALA525 ALA526 GLY527 SER528 THR529 MET530 GLY531 ALA532 ALA533 SER534 MET535 THR536 LEU537 THR538 VAL539 GLN540 ALA541 ARG542 ASN543 LEU544 LEU545 SER546 GLY547 GLU548 ASP549 PHE550 THR551 ILE552 ASP553 ILE554 PRO555 ASP556 VAL557 THR558 VAL559 TRP560 GLY561 ILE562 LYS563 GLN564 LEU565 GLN566 ALA567 ARG568 VAL569 LEU570 ALA571 VAL572 GLU573 ARG574 TYR575 LEU576 ARG577 ASP578 GLN579 GLN580 LEU581 LEU582 GLY583 ILE584 TRP585 GLY586 CYS587 SER588 GLY589 LYS590 LEU591 ILE592 CYS593 CYS594 THR595 ASN596 VAL597 PRO598 TRP599 ASN600 SER601 SER602 TRP603 SER604 ASN605 ARG606 ASN607 LEU608 SER609 GLU610 ILE611 TRP612 ASP613 ASN614 MET615 THR616 TRP617 LEU618 GLN619 TRP620 ASP621 LYS622 GLU623 ILE624 SER625 ASN626 TYR627 THR628 GLN629 ILE630 ILE631 TYR632 GLY633 LEU634 LEU635 GLU636 GLU637 SER638 GLN639 ASN640 GLN641 GLN642 GLU643 LYS644 ASN645 GLU646 GLN647 ASP648 LEU649 LEU650 ALA651 LEU652 ASP653
Unit 5 GLN1 ILE2 HIS3 LEU4 VAL5 GLN6 SER7 GLY8 THR9 GLU10 VAL11 LYS12 LYS13 PRO14 GLY15 SER16 SER17 VAL18 THR19 VAL20 SER21 CYS22 LYS23 ALA24 TYR25 GLY26 VAL27 ASN28 THR29 PHE30 GLY31 LEU32 TYR33 ALA34 VAL35 ASN36 TRP37 VAL38 ARG39 GLN40 ALA41 PRO42 GLY43 GLN44 SER45 LEU46 GLU47 TYR48 ILE49 GLY50 GLN51 ILE52 TRP53 ARG54 TRP55 LYS56 SER57 SER58 ALA59 SER60 HIS61 HIS62 PHE63 ARG64 GLY65 ARG66 VAL67 LEU68 ILE69 SER70 ALA71 VAL72 ASP73 LEU74 THR75 GLY76 SER77 SER78 PRO79 PRO80 ILE81 SER82 SER83 LEU84 GLU85 ILE86 LYS87 ASN88 LEU89 THR90 SER91 ASP92 ASP93 THR94 ALA95 VAL96 TYR97 PHE98 CYS99 THR100 THR101 THR102 SER103 THR104 TYR105 ASP106 LYS107 TRP108 SER109 GLY110 LEU111 HIS112 HIS113 ASP114 GLY115 VAL116 MET117 ALA118 PHE119 SER120 SER121 TRP122 GLY123 GLN124 GLY125 THR126 LEU127 ILE128 SER129 VAL130 SER131 ALA132 ALA133 SER134 THR135 LYS136 GLY137 PRO138 SER139 VAL140 PHE141 PRO142 LEU143 ALA144 PRO145 SER146 SER147 GLY153 THR154 ALA155 ALA156 LEU157 GLY158 CYS159 LEU160 VAL161 LYS162 ASP163 TYR164 PHE165 PRO166 GLU167 PRO168 VAL169 THR170 VAL171 SER172 TRP173 ASN174 SER175 GLY176 ALA177 LEU178 THR179 SER180 GLY181 VAL182 HIS183 THR184 PHE185 PRO186 ALA187 VAL188 LEU189 GLN190 SER191 SER192 GLY193 LEU194 TYR195 SER196 LEU197 SER198 SER199 VAL200 VAL201 THR202 VAL203 PRO204 SER205 THR210 GLN211 THR212 TYR213 ILE214 CYS215 ASN216 VAL217 ASN218 HIS219 LYS220 PRO221 SER222 ASN223 THR224 LYS225 VAL226 ASP227 LYS228 LYS229 VAL230 GLU231 PRO232 LYS233
Unit 6 ASP1 ILE2 GLN3 MET4 THR5 GLN6 SER7 PRO8 SER9 THR10 LEU11 SER12 ALA13 SER14 ILE15 GLY16 ASP17 THR18 VAL19 ARG20 ILE21 SER22 CYS23 ARG24 ALA25 SER26 GLN27 SER28 ILE29 THR30 GLY30A ASN31 TRP32 VAL33 ALA34 TRP35 TYR36 GLN37 GLN38 ARG39 PRO40 GLY41 LYS42 ALA43 PRO44 ARG45 LEU46 LEU47 ILE48 TYR49 ARG50 GLY51 ALA52 ALA53 LEU54 LEU55 GLY56 GLY57 VAL58 PRO59 SER60 ARG61 PHE62 SER63 GLY64 SER65 ALA66 ALA67 GLY68 THR69 ASP70 PHE71 THR72 LEU73 THR74 ILE75 GLY76 ASN77 LEU78 GLN79 ALA80 GLU81 ASP82 PHE83 GLY84 THR85 PHE86 TYR87 CYS88 GLN89 GLN90 TYR91 ASP92 THR93 TYR94 PRO95 GLY96 THR97 PHE98 GLY99 GLN100 GLY101 THR102 LYS103 VAL104 GLU105 VAL106 LYS107 ARG108 THR109 VAL110 ALA111 ALA112 PRO113 SER114 VAL115 PHE116 ILE117 PHE118 PRO119 PRO120 SER121 ASP122 GLU123 GLN124 LEU125 LYS126 SER127 GLY128 THR129 ALA130 SER131 VAL132 VAL133 CYS134 LEU135 LEU136 ASN137 ASN138 PHE139 TYR140 PRO141 ARG142 GLU143 ALA144 LYS145 VAL146 GLN147 TRP148 LYS149 VAL150 ASP151 ASN152 ALA153 LEU154 GLN155 SER156 GLY157 ASN158 SER159 GLN160 GLU161 SER162 VAL163 THR164 GLU165 GLN166 ASP167 SER168 LYS169 ASP170 SER171 THR172 TYR173 SER174 LEU175 SER176 SER177 THR178 LEU179 THR180 LEU181 SER182 LYS183 ALA184 ASP185 TYR186 GLU187 LYS188 HIS189 LYS190 VAL191 TYR192 ALA193 CYS194 GLU195 VAL196 THR197 HIS198 GLN199 GLY200 LEU201 SER202 SER203 PRO204 VAL205 THR206 LYS207 SER208 PHE209 ASN210 ARG211
Ligands
Unit 7 NAG1 NAG2
Unit 8 NAG1 NAG2
Unit 9 NAG1 NAG2
Unit 10 NAG1 NAG2 BMA3 MAN4 MAN5 MAN6 MAN7 MAN8
Unit 11 NAG1 NAG2 BMA3 MAN4 MAN5 MAN6 MAN7 MAN8 MAN9 MAN10
Unit 12 NAG1 NAG2 BMA3 MAN4 MAN5 MAN6 MAN7 MAN8 MAN9
Unit 13 NAG1 NAG2 BMA3 MAN4 MAN5 MAN6 MAN7
Unit 14 NAG1 NAG2 BMA3 MAN4 MAN5
Unit 15 NAG1 NAG2 BMA3
Unit 16 NAG1 NAG2 BMA3
Unit 17 NAG1 NAG2 BMA3
Unit 18 NAG1 NAG2 BMA3
Unit 19 NAG1 NAG2 BMA3
Unit 20 NAG1 NAG2 BMA3 MAN4
Unit 21 NAG1 NAG2 BMA3 MAN4 MAN5 MAN6 MAN7 MAN8 MAN9 MAN10 MAN11
Unit 22 NAG615
Unit 23 NAG705
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany