Structure of PDB 5fdu Chain 1H

Receptor sequence

>5fdu1H (length=174) Species: 300852 (Thermus thermophilus HB8)

SRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVR
VERPSDERRHKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGR
ALELTVGFSHPVVVEPPEGITFEVPEPTRVRVSGIDKQKVGQVAANIRAI
RKPSAYHEKGIYYAGEPVRLKPGK

3D structure

• PDB: 5fdu Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome.
• Chain: 1H
• 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	1H	S2 R3 I4 R59 K62 S63 G66 L67 T70 G108 F109 S110 H111 K138 Q139 G142 Q143 R152 Y157 H158 K160 K172 K175	S1 R2 I3 R58 K61 S62 G65 L66 T69 G107 F108 S109 H110 K137 Q138 G141 Q142 R151 Y156 H157 K159 K171 K174

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 16 03:41:56 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 = '1H', 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='1H', 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 = '0003735,0005840,0006412,0019843', uniprot = '', pdbid = '5fdu', asym_id = '1H'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412,0019843', uniprot='', pdbid='5fdu', asym_id='1H')

    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>