Structure of PDB 8jjr Chain a

Receptor sequence
>8jjra (length=665) Species: 2950 (Symbiodinium sp.) [Search protein sequence]
AIFRYVNATLWSKAGHFNKALSKGAKTTTWIWNLHASAHDFDIQQGSAGL
IARKVFSSGLAHLSLVFFWLGGMHFHGAYLSNYSAWLKDPKSVAPSSHIA
YSLVGQDILNSYTSQYFSGITITSGFFQLYRSEGIVTQSQLKYACAASLI
ATLICLSGSYLHMQLMSKFTSFYKKFQSLSQSHLIIMFGFGSVSFSAHQI
HEALPINSLLDSGIWDPQLFSAILLGTPSAITGKLLNPSTGSIFLSQVAA
HHLAVGIVFITLGLIKWCNLFFSRNAILSLRLAYMDYHAQLSINLAVWAS
LSMVAAHHLTEIPVYPYESTDYPTVLCLFVHHACLSGFFTVASGAHASIF
VIRQLPTSEIRHRDPIIGHLIWVCIALGLHSFGLYCHNDTLEALGRPEDT
FCDNSIQLKPIFAKQFLGLQPGIEVLDGKIVRMTQELGTADFMVHHIHAF
TIHVTLLILLKGVLYARNSRLVSDKLELGFAYPCDGPGRGGTCQISPWDH
LFLAVFWMYNCLSVVIFHYFWKMQSDVWGSYVHHSSLTCSHYSQGDFSVN
SITINGWLRNLLWSEASQVIQSYALPSICSYGFIFLAAHFVWAFSLMFLF
SGRAYWQELIESILWSHHKLKIVPHIQPRALSISQGRAVGLTHYVLGGIG
CTWAFIISRMLVLTT
3D structure
PDB8jjr Architecture of symbiotic dinoflagellate photosystem I-light-harvesting supercomplex in Symbiodinium.
Chaina
Resolution2.8 Å
3D
structure
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Interaction with ligand
Site
#
Ligand Ligand
chain
Binding residues on receptor
(original residue number in PDB)
Binding residues on receptor
(residue number reindexed from 1)
Binding affinity
BS01 CLA a F420 K422 F412 K414
BS02 CLA a L232 I239 T240 Q255 A258 L224 I231 T232 Q247 A250
BS03 CLA a F458 Y517 N518 S521 I576 W579 F607 H611 W614 Y666 G670 C673 T674 F677 F450 Y509 N510 S513 I554 W557 F585 H589 W592 Y644 G648 C651 T652 F655
BS04 CLA a F612 A615 F616 L618 M619 Y627 W628 F590 A593 F594 L596 M597 Y605 W606
BS05 CLA a H16 F17 A38 H39 H16 F17 A38 H39
BS06 CLA a H39 F41 V55 S58 H62 L63 F67 Y295 H296 L299 N302 H39 F41 V55 S58 H62 L63 F67 Y287 H288 L291 N294
BS07 CLA a H62 L65 V66 W69 F347 H62 L65 V66 W69 F339
BS08 CLA a F68 W69 G72 F75 H76 Y101 F68 W69 G72 F75 H76 Y101
BS09 CLA a M73 H98 I122 T123 S602 Y603 A609 M73 H98 I122 T123 S580 Y581 A587
BS10 CLA a I99 Y101 L103 Q106 L109 S602 F605 I99 Y101 L103 Q106 L109 S580 F583
BS11 CLA a F56 I154 G158 H162 L165 F172 F56 I154 G158 H162 L165 F172
BS12 CLA a F56 L60 F172 Y173 L179 S182 H183 M187 W306 F56 L60 F172 Y173 L179 S182 H183 M187 W298
BS13 CLA a E133 G134 Q140 Y143 A147 S194 F195 H198 E202 E133 G134 Q140 Y143 A147 S194 F195 H198 E202
BS14 CLA a A197 H201 L261 A197 H201 L253
BS15 CLA a S139 Y143 S139 Y143
BS16 CLA a I239 T240 A258 H259 A262 H316 I231 T232 A250 H251 A254 H308
BS17 CLA a S192 F195 V256 H259 H260 V263 F267 L309 A313 Y323 S192 F195 V248 H251 H252 V255 F259 L301 A305 Y315
BS18 CLA a M311 H315 T348 I460 M303 H307 T340 I452
BS19 CLA a V305 V312 H316 E319 I320 F424 V297 V304 H308 E311 I312 F416
BS20 CLA a W69 S124 F126 V338 H339 C342 W675 W69 S124 F126 V330 H331 C334 W653
BS21 CLA a L129 F188 L309 S310 L317 Y323 L336 H339 H340 L343 L129 F188 L301 S302 L309 Y315 L328 H331 H332 L335
BS22 CLA a A36 H39 D40 H296 L299 A350 H354 I357 F488 W506 L509 T664 A36 H39 D40 H288 L291 A342 H346 I349 F480 W498 L501 T642
BS23 CLA a W380 A384 L387 H388 W372 A376 L379 H380
BS24 CLA a H315 F420 A421 F424 Q443 H453 H456 V523 H526 H307 F412 A413 F416 Q435 H445 H448 V515 H518
BS25 CLA a L385 P418 I419 F420 F450 H453 H454 A457 L377 P410 I411 F412 F442 H445 H446 A449
BS26 CLA a L378 V381 H461 L464 L370 V373 H453 L456
BS27 CLA a F616 V661 T664 H665 F594 V639 T642 H643
BS28 CLA a F605 L608 H611 F612 A615 F583 L586 H589 F590 A593
BS29 CLA a Y173 F176 L179 H183 R289 M293 D294 Y295 Q298 I301 N302 W306 Y173 F176 L179 H183 R281 M285 D286 Y287 Q290 I293 N294 W298
BS30 CLA a F279 F280 S281 F271 F272 S273
BS31 CLA a N7 W11 H16 K54 L65 L156 S159 Y160 M163 N7 W11 H16 K54 L65 L156 S159 Y160 M163
BS32 CLA a I635 H639 I644 I613 H617 I622
BS33 CLA a I31 L34 H35 I31 L34 H35
BS34 PQN a M619 F620 W628 A652 L653 M597 F598 W606 A630 L631
BS35 CLA a F390 D397 F458 W515 N518 I576 Y666 F382 D389 F450 W507 N510 I554 Y644
BS36 SF4 a C492 G494 C501 I655 C484 G486 C493 I633
BS37 CLA a T28 W32 L636 P646 P650 T28 W32 L614 P624 P628
BS38 CLA a L580 L584 L558 L562
BS39 CLA a I383 G386 F390 F514 W515 I375 G378 F382 F506 W507
BS40 CLA a A401 L402 A393 L394
BS41 CLA a P373 H377 W380 P365 H369 W372
BS42 CLA a L387 G391 H395 L399 R404 D407 F409 L379 G383 H387 L391 R396 D399 F401
BS43 CLA a H370 H377 H362 H369
BS44 CLA a L288 Y292 L280 Y284
BS45 CLA a Y292 A297 E367 L468 Y284 A289 E359 L460
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Fri Nov 15 20:54:09 2024

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

 /var/www/html/BioLiP/pdb.cgi in <module>()
   1443                 pubmed=display_regular_ligand(pdbid,asym_id,lig3,ligIdx,title)
   1444         else:
=> 1445             pubmed,uniprot=display_protein_receptor(pdbid,asym_id,title)
   1446     
   1447     uniprot_line=''
pubmed = '', uniprot = '', display_protein_receptor = <function display_protein_receptor>, pdbid = '8jjr', asym_id = 'a', title = 'Architecture of symbiotic dinoflagellate photosy... I-light-harvesting supercomplex in Symbiodinium.'
 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='8jjr', asym_id='a', title='Architecture of symbiotic dinoflagellate photosy... I-light-harvesting supercomplex in Symbiodinium.')
    839 
    840     if go:
=>  841         display_go(go,uniprot,pdbid,asym_id)
    842     return pubmed,uniprot
    843 
global display_go = <function display_go>, go = '0009579,0015979,0016020', uniprot = '', pdbid = '8jjr', asym_id = 'a'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0009579,0015979,0016020', uniprot='', pdbid='8jjr', asym_id='a')
    480         '''.replace("$namespace_link",namespace_link
    481           ).replace("$namespace",namespace
=>  482           ).replace("$uniprot",u
    483         ))
    484         for l,(term,name) in enumerate(go2aspect[Aspect]):
u undefined

UnboundLocalError: local variable 'u' referenced before assignment
      args = ("local variable 'u' referenced before assignment",)
      with_traceback = <built-in method with_traceback of UnboundLocalError object>