Structure of PDB 6blj Chain A

Receptor sequence

>6bljA (length=473) Species: 5763 (Naegleria fowleri)

HHHMLDINLFREYKGGNPEIIRESQRRRFADVTLVDKVIELDEVWRATIG
KLNHIKSFTGIISKEVGNRMKNKVPLGDDLELPKEVTDDVYALFTKEALE
QGSLAKLNTNQLKKLSTYITEVHIKNSEEEVKQKEKERDDVLLQIGNIVH
ETVVVSDNEDNNGIVRMVGNPRPKVDPETGYKCLKHIDIMRKLGGLATEE
GTQVGGGRGYFLLGDLVRMNLALQNYAIDFLAKKGYMPIYTPFFMTKEQM
KKVAQLSQFDEELYTVTGEGEDKYLIATSEQPIAAFHLEKRFDESELPIK
YCGMSTCFRKEVGAHGKDTLGIFRVHQFEKIEQFVVTSPKDNKSWEMFDE
MIGNSEAFYQSLGIPYRVVNIVSGALNNAAAKKFDLEAWFPGADEGNEYR
ELVSCSNCTDYQTRRLEVKYGEVEFCHMLNSTLTATSRTLCCIVENYQTP
EGVNVPEVLQPYMGGTKFIKFKN

3D structure

• PDB: 6blj Crystal structure of cytoplasmic Serine-tRNA ligase from Neisseria fowlerii in complex with AMP
• Chain: A
• Resolution: 2.1 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	AMP	A	R306 E308 R321 V322 F325 L399 S401 A439 R442	R309 E311 R324 V325 F328 L402 S404 A435 R438

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Wed Dec 18 19:51:39 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 = '6blj', asym_id = 'A', title = 'Crystal structure of cytoplasmic Serine-tRNA ligase from Neisseria fowlerii in complex with AMP'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='6blj', asym_id='A', title='Crystal structure of cytoplasmic Serine-tRNA ligase from Neisseria fowlerii in complex with AMP')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0000166,0004812,0004828,0005524,0006418,0006434', uniprot = '', pdbid = '6blj', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000166,0004812,0004828,0005524,0006418,0006434', uniprot='', pdbid='6blj', 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>