Structure of PDB 7b25 Chain D

Receptor sequence

>7b25D (length=138) Species: 405948 (Saccharopolyspora erythraea NRRL 2338)

DLIDTTEMYLRTIYDLEEEGVVPLRARIAERLEQSGPTVSATVARMERDG
LLTVAEDRHLELTKAGRARAISVMRKHRLAERLLVDVIGLEWEQVHLEAC
RWEHVMSEAVERKLVKLLGNPTTSPYGNPIPGLDELGV

3D structure

• PDB: 7b25 The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout.
• Chain: D
• Resolution: 2.34 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	dna	D	T7 Q36 S37 P39 T40 R47 R50	T5 Q34 S35 P37 T38 R45 R48
BS02	dna	D	R27 A28 R29 P39 S42 R60	R25 A26 R27 P37 S40 R58
BS03	CO	D	M10 C102 E105 H106	M8 C100 E103 H104
BS04	CO	D	H79 E83 H98	H77 E81 H96

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 15 19:42:29 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 = '7b25', asym_id = 'D', title = 'The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='7b25', asym_id='D', title='The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout.')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0003677,0003700,0006355,0046914,0046983', uniprot = '', pdbid = '7b25', asym_id = 'D'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003677,0003700,0006355,0046914,0046983', uniprot='', pdbid='7b25', asym_id='D')

    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>