Structure of PDB 3vqy Chain A

Receptor sequence

>3vqyA (length=257) Species: 2209 (Methanosarcina mazei)

PALTKSQTDRLEVLLNPKDESGKPFRELESELLSRRKKDLQQIYAEEREN
YLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRV
DKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEE
FTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGGDTLDVMHGDLEL
SSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYY
NGISTNL

3D structure

• PDB: 3vqy A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site
• Chain: A
• Resolution: 2.4 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	ANP	A	R330 E332 H338 L339 F342 M344 E396 L397 S399 G423 R426	R139 E141 H147 L148 F151 M153 E199 L200 S202 G226 R229
BS02	LBY	A	Y306 N346 S399 W417 A420 G421	Y115 N155 S202 W220 A223 G224
BS03	MG	A	E396 S399	E199 S202

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 16 14:22:30 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 = '3vqy', asym_id = 'A', title = 'A novel crystal form of pyrrolysyl-tRNA syntheta... and an asparagine residue in the catalytic site '

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='3vqy', asym_id='A', title='A novel crystal form of pyrrolysyl-tRNA syntheta... and an asparagine residue in the catalytic site ')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0000049,0004812,0005524,0043039', uniprot = '', pdbid = '3vqy', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000049,0004812,0005524,0043039', uniprot='', pdbid='3vqy', 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>