Structure of PDB 4d5y Chain p

Receptor sequence

>4d5yp (length=91) Species: 9986 (Oryctolagus cuniculus)

AKRTKKVGIVGKYGTRYGASLRKMVKKIEISQHAKYTCSFCGKTKMKRRA
VGIWHCGSCMKTVAGGAWTYNTTSAVTVKSAIRRLKELKDQ

3D structure

• PDB: 4d5y Cryo-Em Structures of Ribosomal 80S Complexes with Termination Factors and Cricket Paralysis Virus Ires Reveal the Ires in the Translocated State
• Chain: p
• Resolution: 9.0 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	p	A2 K3 R4 T5 K6 V8 G9 I10 G12 K13 G15 T16 R17 Y18 G19 S21 R23 H34 K44 K46 R49 R50 V52	A1 K2 R3 T4 K5 V7 G8 I9 G11 K12 G14 T15 R16 Y17 G18 S20 R22 H33 K43 K45 R48 R49 V51

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Mon Mar 3 04:51:27 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 = '4d5y', asym_id = 'p', title = 'Cryo-Em Structures of Ribosomal 80S Complexes wi...s Ires Reveal the Ires in the Translocated State '

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='4d5y', asym_id='p', title='Cryo-Em Structures of Ribosomal 80S Complexes wi...s Ires Reveal the Ires in the Translocated State ')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0003735,0005840,0006412', uniprot = '', pdbid = '4d5y', asym_id = 'p'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='4d5y', asym_id='p')

    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>