Structure of PDB 5fdu Chain 2n

Receptor sequence

>5fdu2n (length=60) Species: 300852 (Thermus thermophilus HB8)

ARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKG
QLPGVRKASW

3D structure

• PDB: 5fdu Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome.
• Chain: 2n
• Resolution: 2.9 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	2n	A2 R3 K4 A5 L6 E8 K9 K15 F16 K17 V18 R19 Y21 T22 R29 R31 S32 V33 Y34 R35 R41 I42 R45 E46 K58 S60 W61	A1 R2 K3 A4 L5 E7 K8 K14 F15 K16 V17 R18 Y20 T21 R28 R30 S31 V32 Y33 R34 R40 I41 R44 E45 K57 S59 W60
BS02	ZN	2n	C24 C27 C40 C43	C23 C26 C39 C42
BS03	MG	2n	T22 V33	T21 V32

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Thu Dec 5 11:13:08 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 = '5fdu', asym_id = '2n', title = 'Structure of the mammalian antimicrobial peptide...d within the exit tunnel of a bacterial ribosome.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='5fdu', asym_id='2n', title='Structure of the mammalian antimicrobial peptide...d within the exit tunnel of a bacterial 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 = '5fdu', asym_id = '2n'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='5fdu', asym_id='2n')

    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>