Structure of PDB 5vz0 Chain A

Receptor sequence

>5vz0A (length=1139) Species: 1358 (Lactococcus lactis)

VPRGSHMKKLLVANRGEIAVRVFRACNELGLSTVAVYAREDEYSVHRFKA
DESYLIGQGKKPIDAYLDIDDIIRVALESGADAIHPGYGLLSENLEFATK
VRAAGLVFVGPELHHLDIFGDKIKAKAAADEAKVPGIPGTNGAVDIDGAL
EFAKTYGYPVMIKAALGGMRVARNDAEMHDGYARAKSEAIGAFGSGEIYV
EKYIENPKHIEVQILGDRHGNIIHLHERDCSVQRRNQKVIEIAPAVGLSP
DFRNEICEAAVKLCKNVGYVNAGTVEFLVKDDKFYFIEVNPRVQVEHTIT
ELITGVDIVQAQILIAQGKDLHREIGLPAQSEIPLLGSAIQCRITTEDPQ
NGFLPDTGKIDTYRSPGGFGIRLDVGNAYAGYEVTPYFDSLLVKVCTFAN
EFSDSVRKMDRVLHEFRIRGVKTNIPFLINVIANENFTSGQATTTFIDNT
PSLFNFPRLRDRGTKTLHYLSMITVNGFPGIENTEKRHFEEPRQPLLNLE
KKKTAKNILDEQGADAVVDYVKNTKEVLLTDTTLRDAHQSLLATRLRLQD
MKGIAQAIDQGLPELFSAEMWGGATFDVAYRFLNESPWYRLRKLRKLMPN
TMFQMLFRGSNAVGYQNYPDNVIEEFIRVAAHEGIDVFRIFDSLNWLPQM
EKSIQAVRDNGKIAEATICYTGDILDPSRPKYNIQYYKDLAKELEATGAH
ILAVKDMAGLLKPQAAYRLISELKDTVDLPIHLHTHDTSGNGIITYSAAT
QAGVDIIDVATASLAGGTSQPSMQSIYYALEHGPRHASINVKNAEQIDHY
WEDVRKYYAPFEAGITSPQTEVYMHEMPGGQYTNLKSQAAAVGLGHRFDE
IKQMYRKVNMMFGDIIKVTPSSKVVGDMALFMIQNDLTEEDVYARGNELN
FPESVVSFFRGDLGQPVGGFPEKLQKIIVKDKAVITDRPGLHAEKVDFET
VKADLEQKIGYEPGDHEVISYIMYPQVFLDYQKMQREFGAVTLLDTPTFL
HGMRLNEKIEVQIEKGKTLSIRLDEIGEPDLAGNRVLFFNLNGQRREVVI
NDQSVQAQVVAKRKAETGNPNQIGATMPGSVLEILVKAGDKVQKGQALMV
TEAMKMETTIEAPFDGEIVDLHVVKGEAIQTQDLLIEIN

3D structure

• PDB: 5vz0 Structural and functional studies of pyruvate carboxylase regulation by cyclic di-AMP in lactic acid bacteria.
• 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	MN	A	D534 H732 H734	D536 H734 H736
BS02	ADP	A	K116 M155 K157 G161 M167 Y201 I202 H207 Q231 N234 L276 E286 T442	K122 M161 K163 G167 M169 Y203 I204 H209 Q233 N236 L278 E288 T444
BS03	MG	A	E274 E286	E276 E288
BS04	2BA	A	Y715 S745 A746 Q749	Y717 S747 A748 Q751

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Thu Nov 28 01:04:21 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 = '5vz0', asym_id = 'A', title = 'Structural and functional studies of pyruvate ca...ulation by cyclic di-AMP in lactic acid bacteria.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='5vz0', asym_id='A', title='Structural and functional studies of pyruvate ca...ulation by cyclic di-AMP in lactic acid bacteria.')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0003824,0004736,0005524,0006090,0006094,0046872', uniprot = '', pdbid = '5vz0', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003824,0004736,0005524,0006090,0006094,0046872', uniprot='', pdbid='5vz0', 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>