Structure of PDB 8civ Chain Aa

Receptor sequence

>8civAa (length=816) Species: 4932 (Saccharomyces cerevisiae)

MVAFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGKSTAIS
LYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALRVTDGAL
VVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVSKEDLYQ
TFARTVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFA
TRYAKKFGVDKAKMMDRLWGDSFFNPKTKKWTNKDTDAEGKPLERAFNMF
ILDPIFRLFTAIMNFKKDEIPVLLEKLEIVLKGDEKDLEGKALLKVVMRK
FLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIAIKNCDPKA
DLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVPGKKDDL
FIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLTTSETAH
NMKVMKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMSESG
EHIVAGTGELHLEICLQDLEHDHAGVPLKISPPVVAYRETVESESSQTAL
SKSPNKHNRIYLKAEPIDEEVSLAIENGIINPRDDFKARARIMADDYGWD
VTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIKDSVVAAFQWATKEGPI
FGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFLLADPKIQE
PVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTVKAYLPVNE
SFGFTGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVLAARKRH
GMKEEVPGWQEYYDKL

3D structure

• PDB: 8civ mRNA reading frame maintenance during eukaryotic ribosome translocation
• Chain: Aa
• Resolution: 2.47 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	Aa	H27 V28 H108 G703 I706 V740 Y744 K749 V754 V755 E757 F766 R785 Q786 G789 G790	H27 V28 H82 G677 I680 V714 Y718 K723 V728 V729 E731 F740 R759 Q760 G763 G764
BS02	rna	Aa	H583 R585 H694 D696 X699	H557 R559 H668 D670 X673
BS03	rna	Aa	K613 R617 H657 I698	K587 R591 H631 I672
BS04	SO1	Aa	L519 Y521 S523 E524 A562 F729 V774 V797 F798 W801	L493 Y495 S497 E498 A536 F703 V748 V771 F772 W775
BS05	GDP	Aa	V28 G31 K32 S33 T34 N158 K159 D161 S213 L215	V28 G31 K32 S33 T34 N132 K133 D135 S187 L189

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Mon Nov 25 04:25:41 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 = '8civ', asym_id = 'Aa', title = 'mRNA reading frame maintenance during eukaryotic ribosome translocation'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='8civ', asym_id='Aa', title='mRNA reading frame maintenance during eukaryotic ribosome translocation')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0003924,0005525', uniprot = '', pdbid = '8civ', asym_id = 'Aa'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003924,0005525', uniprot='', pdbid='8civ', asym_id='Aa')

    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>