Structure of PDB 4v8a Chain DH

Receptor sequence

>4v8aDH (length=138) Species: 300852 (Thermus thermophilus HB8)

MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYER
VDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEI
PRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW

3D structure

• PDB: 4v8a The antibiotic thermorubin inhibits protein synthesis by binding to inter-subunit bridge b2a of the ribosome.
• Chain: DH
• Resolution: 3.2 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	DH	M1 L2 T3 P5 A7 D8 T11 R12 R14 N15 K21 S29 R30 F31 R75 K88 P89 G90 R91 R92 Y94 G96 V97 R105 S113 T114 S115 V129 G130 E132	M1 L2 T3 P5 A7 D8 T11 R12 R14 N15 K21 S29 R30 F31 R75 K88 P89 G90 R91 R92 Y94 G96 V97 R105 S113 T114 S115 V129 G130 E132

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Mon Mar 10 22:34:59 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 = '4v8a', asym_id = 'DH', title = 'The antibiotic thermorubin inhibits protein synt...ding to inter-subunit bridge b2a of the ribosome.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='4v8a', asym_id='DH', title='The antibiotic thermorubin inhibits protein synt...ding to inter-subunit bridge b2a of the ribosome.')

    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 = '4v8a', asym_id = 'DH'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='4v8a', asym_id='DH')

    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>