Structure of PDB 8cf5 Chain Aa

Receptor sequence

>8cf5Aa (length=842) Species: 4932 (Saccharomyces cerevisiae)

MVAFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAK
AGEARFTDTRKDEQERGITIKSTAISLYSEMSDEDVKEIKQKTDGNSFLI
NLIDSPGHVDFSSEVTAALRVTDGALVVVDTIEGVCVQTETVLRQALGER
IKPVVVINKVDRALLELQVSKEDLYQTFARTVESVNVIVSTYADEVLGDV
QVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKMMDRLWGDSFF
NPKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKKDEIPVLL
EKLEIVLKGDEKDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQA
YRAEQLYEGPADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRV
FAGTVKSGQKVRIQGPNYVPGKKDDLFIKAIQRVVLMMGRFVEPIDDCPA
GNIIGLVGIDQFLLKTGTLTTSETAHNMKVMKFSVSPVVQVAVEVKNAND
LPKLVEGLKRLSKSDPCVLTYMSESGEHIVAGTGELHLEICLQDLEHDHA
GVPLKISPPVVAYRETVESESSQTALSKSPNKHNRIYLKAEPIDEEVSLA
IENGIINPRDDFKARARIMADDYGWDVTDARKIWCFGPDGNGPNLVIDQT
KAVQYLHEIKDSVVAAFQWATKEGPIFGEEMRSVRVNILDVTLHADAIHR
GGGQIIPTMRRATYAGFLLADPKIQEPVFLVEIQCPEQAVGGIYSVLNKK
RGQVVSEEQRPGTPLFTVKAYLPVNESFGFTGELRQATGGQAFPQMVFDH
WSTLGSDPLDPTSKAGEIVLAARKRHGMKEEVPGWQEYYDKL

3D structure

• PDB: 8cf5 Cryo-EM analysis of eukaryotic ribosome translocation intermediates
• Chain: Aa
• Resolution: 2.71 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	V28 R66 H108 R162 E166 Y744 N748 Q753 R785 Q786 G789	V28 R66 H108 R162 E166 Y744 N748 Q753 R785 Q786 G789
BS02	rna	Aa	P580 N581 X699	P580 N581 X699
BS03	rna	Aa	G44 I45 S47 K50 Q432 R433 Y655	G44 I45 S47 K50 Q432 R433 Y655
BS04	GTP	Aa	V28 D29 G31 K32 S33 T34 R55 I68 T69 G107 K159 D161 S213 L215	V28 D29 G31 K32 S33 T34 R55 I68 T69 G107 K159 D161 S213 L215
BS05	SO1	Aa	Y521 S523 E524 V561 A562 P727 F729 F798 W801	Y521 S523 E524 V561 A562 P727 F729 F798 W801
BS06	MG	Aa	S33 D58 T69	S33 D58 T69

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 16 07:03:13 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 = '8cf5', asym_id = 'Aa', title = 'Cryo-EM analysis of eukaryotic ribosome translocation intermediates'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='8cf5', asym_id='Aa', title='Cryo-EM analysis of eukaryotic ribosome translocation intermediates')

    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 = '8cf5', asym_id = 'Aa'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003924,0005525', uniprot='', pdbid='8cf5', 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>