Structure of PDB 4v6m Chain BA

Receptor sequence

>4v6mBA (length=435) Species: 362663 (Escherichia coli 536)

DFQSAKGGLGELKRRLLFVIGALIVFRIGSFIPIPGIDAAVLAKLLEQQR
GTIIEMFNMFSGGALSRASIFALGIMPYISASIIIQLLTVVHPTLAEIKK
EGESGRRKISQYTRYGTLVLAIFQSIGIATGLPNMPGMQGLVINPGFAFY
FTAVVSLVTGTMFLMWLGEQITERGIGNGISIIIFAGIVAGLPPAIAHTI
EQARQGDLHFLVLLLVAVLVFAVTFFVVFVERGQRRIVVNYAKRQQGRRV
YAAQSTHLPLKVNMAGVIPAIFASSIILFPATIASWFGGGTGWNWLTTIS
LYLQPGQPLYVLLYASAIIFFCFFYTALVFNPRETADNLKKSGAFVPGIR
PGEQTAKYIDKVMTRLTLVGALYITFICLIPEFMRDAMKVPFYFGGTSLL
IVVVVIMDFMAQVQTLMMSSQYESALKKANLKGYG

3D structure

• PDB: 4v6m Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.
• Chain: BA
• Resolution: 7.1 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	BA	R243 I244 V245 V246 N247 K250 R251 R255 R256 V257 K348 F352 V353 I356 R357 L433 K434 A436 N437 K439 G440 Y441 G442	R236 I237 V238 V239 N240 K243 R244 R248 R249 V250 K341 F345 V346 I349 R350 L426 K427 A429 N430 K432 G433 Y434 G435

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Mon Mar 10 11:05:38 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 = '4v6m', asym_id = 'BA', title = 'Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='4v6m', asym_id='BA', title='Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0015031,0016020', uniprot = '', pdbid = '4v6m', asym_id = 'BA'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0015031,0016020', uniprot='', pdbid='4v6m', asym_id='BA')

    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>