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Structure of PDB 4v87 Chain DH

Receptor sequence

>4v87DH (length=170) Species: 300852 (Thermus thermophilus HB8)

SRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVR
VERPSDERRHKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGR
ALELTVGFSHPVVVEPPEGITFEVPEPTRVRVSGIDKQKVGQVAANIRAI
RKPSAYHEKGIYYAGEPVRL

3D structure

• PDB: 4v87 A new understanding of the decoding principle on the ribosome.
• Chain: DH
• Resolution: 3.1 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	DH	S2 R3 G5 R6 E58 R59 K62 S63 G66 L67 T70 F109 S110 K138 Q139 G142 Q143 A146 Y157 H158 K160 R170	S1 R2 G4 R5 E57 R58 K61 S62 G65 L66 T69 F108 S109 K137 Q138 G141 Q142 A145 Y156 H157 K159 R169

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat May 17 10:36:48 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>()

   1709                 pubmed=display_regular_ligand(pdbid,asym_id,lig3,ligIdx,title)

   1710         else:

=> 1711             pubmed,uniprot=display_protein_receptor(pdbid,asym_id,title)

   1712     

   1713     uniprot_line=''

pubmed = '', uniprot = '', display_protein_receptor = <function display_protein_receptor>, pdbid = '4v87', asym_id = 'DH', title = 'A new understanding of the decoding principle on the ribosome.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='4v87', asym_id='DH', title='A new understanding of the decoding principle on the ribosome.')

    843 

    844     if go:

=>  845         display_go(go,uniprot,pdbid,asym_id)

    846     return pubmed,uniprot

    847 

global display_go = <function display_go>, go = '0003735,0005840,0006412,0019843', uniprot = '', pdbid = '4v87', asym_id = 'DH'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412,0019843', uniprot='', pdbid='4v87', asym_id='DH')

    484         '''.replace("$namespace_link",namespace_link

    485           ).replace("$namespace",namespace

=>  486           ).replace("$uniprot",u

    487         ))

    488         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>