Structure of PDB 8vs9 Chain S19

Receptor sequence

>8vs9S19 (length=79) Species: 562 (Escherichia coli)

RSLKKGPFIDLHLLKKVEKAVESGDKKPLRTWSRRSTIFPNMIGLTIAVH
NGRQHVPVFVTDEMVGHKLGEFAPTRTYR

3D structure

• PDB: 8vs9 Endogenous trans-translation structure visualizes the decoding of the first tmRNA alanine codon.
• Chain: S19
• Resolution: 3.9 Å

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	rna	S19	R2 S3 L4 K5 F9 H13 K16 W33 R35 R36 N52 G53 R54 K69 G71 E72 T76 R77 T78 Y79	R1 S2 L3 K4 F8 H12 K15 W32 R34 R35 N51 G52 R53 K68 G70 E71 T75 R76 T77 Y78
BS02	rna	S19	Q55 F60 T62	Q54 F59 T61

Gene Ontology

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Mar 14 16:15:23 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>()

   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 = '8vs9', asym_id = 'S19', title = 'Endogenous trans-translation structure visualizes the decoding of the first tmRNA alanine codon.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='8vs9', asym_id='S19', title='Endogenous trans-translation structure visualizes the decoding of the first tmRNA alanine codon.')

    839 

    840     if go:

=>  841         display_go(go,uniprot,pdbid,asym_id)

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0003723,0003735,0005840,0006412,0015935', uniprot = '', pdbid = '8vs9', asym_id = 'S19'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003723,0003735,0005840,0006412,0015935', uniprot='', pdbid='8vs9', asym_id='S19')

    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>