Structure of PDB 8jjr Chain a Binding Site BS34

Receptor Information

>8jjr Chain a (length=665) Species: 2950 (Symbiodinium sp.)

AIFRYVNATLWSKAGHFNKALSKGAKTTTWIWNLHASAHDFDIQQGSAGL
IARKVFSSGLAHLSLVFFWLGGMHFHGAYLSNYSAWLKDPKSVAPSSHIA
YSLVGQDILNSYTSQYFSGITITSGFFQLYRSEGIVTQSQLKYACAASLI
ATLICLSGSYLHMQLMSKFTSFYKKFQSLSQSHLIIMFGFGSVSFSAHQI
HEALPINSLLDSGIWDPQLFSAILLGTPSAITGKLLNPSTGSIFLSQVAA
HHLAVGIVFITLGLIKWCNLFFSRNAILSLRLAYMDYHAQLSINLAVWAS
LSMVAAHHLTEIPVYPYESTDYPTVLCLFVHHACLSGFFTVASGAHASIF
VIRQLPTSEIRHRDPIIGHLIWVCIALGLHSFGLYCHNDTLEALGRPEDT
FCDNSIQLKPIFAKQFLGLQPGIEVLDGKIVRMTQELGTADFMVHHIHAF
TIHVTLLILLKGVLYARNSRLVSDKLELGFAYPCDGPGRGGTCQISPWDH
LFLAVFWMYNCLSVVIFHYFWKMQSDVWGSYVHHSSLTCSHYSQGDFSVN
SITINGWLRNLLWSEASQVIQSYALPSICSYGFIFLAAHFVWAFSLMFLF
SGRAYWQELIESILWSHHKLKIVPHIQPRALSISQGRAVGLTHYVLGGIG
CTWAFIISRMLVLTT

Ligand information

• Ligand ID: PQN
• InChI: InChI=1S/C31H46O2/c1-22(2)12-9-13-23(3)14-10-15-24(4)16-11-17-25(5)20-21-27-26(6)30(32)28-18-7-8-19-29(28)31(27)33/h7-8,18-20,22-24H,9-17,21H2,1-6H3/b25-20+/t23-,24-/m1/s1
• InChIKey: MBWXNTAXLNYFJB-NKFFZRIASA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1=C(C(=O)c2ccccc2C1=O)CC=C(C)CCCC(C)CCCC(C)CCCC(C)C
  ACDLabs 10.04: O=C2c1c(cccc1)C(=O)C(=C2C)C\C=C(/C)CCCC(C)CCCC(C)CCCC(C)C
  OpenEye OEToolkits 1.5.0: CC1=C(C(=O)c2ccccc2C1=O)C\C=C(/C)\CCC[C@H](C)CCC[C@H](C)CCCC(C)C
  CACTVS 3.341: CC(C)CCC[CH](C)CCC[CH](C)CCCC(C)=CCC1=C(C)C(=O)c2ccccc2C1=O
  CACTVS 3.341: CC(C)CCC[C@@H](C)CCC[C@@H](C)CCCC(/C)=C/CC1=C(C)C(=O)c2ccccc2C1=O
• Formula: C31 H46 O2
• Name: PHYLLOQUINONE;
  VITAMIN K1;
  2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE
• ChEMBL: CHEMBL1550
• DrugBank: DB01022
• ZINC: ZINC000003831332
• PDB chain: 8jjr Chain a Residue 832

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8jjr Architecture of symbiotic dinoflagellate photosystem I-light-harvesting supercomplex in Symbiodinium.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): M619 F620 W628 A652 L653
• Binding residue (residue number reindexed from 1): M597 F598 W606 A630 L631
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Thu Apr 17 06:01:25 2025

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>()

   1435     title=pdb2title(pdbid)

   1436     if bs.startswith("BS"):

=> 1437         pubmed,uniprot=display_interaction(pdbid,asym_id,bs,title)

   1438     else:

   1439         if lig3:

pubmed = '', uniprot = '', display_interaction = <function display_interaction>, pdbid = '8jjr', asym_id = 'a', bs = 'BS34', title = 'Architecture of symbiotic dinoflagellate photosy... I-light-harvesting supercomplex in Symbiodinium.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='8jjr', asym_id='a', bs='BS34', title='Architecture of symbiotic dinoflagellate photosy... I-light-harvesting supercomplex in Symbiodinium.')

   1295         display_ec(ec,csaOrig,csaRenu)

   1296     if go:

=> 1297         display_go(go,uniprot,pdbid,asym_id)

   1298     return pubmed,uniprot

   1299 

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>