Structure of PDB 8apo Chain Bm

Receptor sequence

>8apoBm (length=113) Species: 353565 (Polytomella magna)

VQIQRVTLPPHQCVYMALKKVFGLGGPTSLAVVEACGISKGVRVRDLKEN
HVQQITQFIQDNFVTEDNLRRKVREDIVKLVNIKSRDGLRHDWGVSIKGH
TSCNGKTAKRLRH

3D structure

• PDB: 8apo Structure of the mitochondrial ribosome from Polytomella magna with tRNAs bound to the A and P sites
• Chain: Bm
• 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	Bm	C104 N105 K107 T108 R111	C103 N104 K106 T107 R110
BS02	rna	Bm	Q13 M17 K20 F23 G24 L25 G26 P28 T29 H92 W94 I98 K99 H101 S103 T108 K110	Q12 M16 K19 F22 G23 L24 G25 P27 T28 H91 W93 I97 K98 H100 S102 T107 K109
BS03	MG	Bm	K20 L25	K19 L24

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 16 00:53:06 2024

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 = '8apo', asym_id = 'Bm', title = 'Structure of the mitochondrial ribosome from Polytomella magna with tRNAs bound to the A and P sites'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='8apo', asym_id='Bm', title='Structure of the mitochondrial ribosome from Polytomella magna with tRNAs bound to the A and P sites')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0003676,0003723,0003735,0005840,0006412', uniprot = '', pdbid = '8apo', asym_id = 'Bm'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003676,0003723,0003735,0005840,0006412', uniprot='', pdbid='8apo', asym_id='Bm')

    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>