Structure of PDB 4jml Chain A

Receptor sequence

>4jmlA (length=394) Species: 536056 (Escherichia coli DH1)

SGRPIGVVPFQWAAPEDIGGIVAADLRNSGKFNPLDRARLPQQPGSAQEV
QPAAWSALGIDAVVVGQVTPNPDGSYNVAYQLVDTGGAPGTVLAQNSYKV
NKQWLRYAGHTASDEVFEKLTGIKGAFRTRIAYVVQTNGGQFPYELRVSD
YDGYNQFVVHRSPQCLMSPAWSPDGSKLAYVTFESGRSALVIQTLANGAV
RQVASFPRHNGAPAFSPDGSKLAFALSKTGSLNLYVMDLASGQIRQVTDG
RSNNTEPTWFPDSQNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQD
ADVSSDGKFMVMVSSNGGQQHIAKQDLATGGVQVLSSTFLDETPSLAPNG
TMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAWSPYL

3D structure

• PDB: 4jml Intrinsically disordered protein threads through the bacterial outer-membrane porin OmpF.
• Chain: A
• Resolution: 2.0 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	peptide	A	Q172 Y180 C201 L202 M203 S204 F219 H245 A248 L268 N289 T291 E292 T305 D307 P312 K422 F423	Q136 Y144 C165 L166 M167 S168 F183 H209 A212 L232 N253 T255 E256 T269 D271 P276 K386 F387

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 29 05:27:14 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 = '4jml', asym_id = 'A', title = 'Intrinsically disordered protein threads through the bacterial outer-membrane porin OmpF.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='4jml', asym_id='A', title='Intrinsically disordered protein threads through the bacterial outer-membrane porin OmpF.')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0015031,0017038,0042597', uniprot = '', pdbid = '4jml', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0015031,0017038,0042597', uniprot='', pdbid='4jml', asym_id='A')

    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>