Structure of PDB 5vyz Chain B

Receptor sequence

>5vyzB (length=1142) Species: 1358 (Lactococcus lactis)

GLVPRGSHMKKLLVANRGEIAVRVFRACNELGLSTVAVYAREDEYSVHRF
KADESYLIGQGKKPIDAYLDIDDIIRVALESGADAIHPGYGLLSENLEFA
TKVRAAGLVFVGPELHHLDIFGDKIKAKAAADEAKVPGIPGTNGAVDIDG
ALEFAKTYGYPVMIKAALGGGMRVARNDAEMHDGYARAKSEAIGAFGSGE
IYVEKYIENPKHIEVQILGDRHGNIIHLHERDCSVQRRNQKVIEIAPAVG
LSPDFRNEICEAAVKLCKNVGYVNAGTVEFLVKDDKFYFIEVNPRVQVEH
TITELITGVDIVQAQILIAQGKDLHREIGLPAQSEIPLLGSAIQCRITTE
DPQNGFLPDTGKIDTYRSPGGFGIRLDVGNAYAGYEVTPYFDSLLVKVCT
FANEFSDSVRKMDRVLHEFRIRGVKTNIPFLINVIANENFTSGQATTTFI
DNTPSLFNFPRLRDRGTKTLHYLSMITVNGFPGIENTEKRHFEEPRQPLL
NLEKKKTAKNILDEQGADAVVDYVKNTKEVLLTDTTLRDAHQSLLATRLR
LQDMKGIAQAIDQGLPELFSAEMWGGATFDVAYRFLNESPWYRLRKLRKL
MPNTMFQMLFRGSNAVGYQNYPDNVIEEFIRVAAHEGIDVFRIFDSLNWL
PQMEKSIQAVRDNGKIAEATICYTGDILDPSRPKYNIQYYKDLAKELEAT
GAHILAVKDMAGLLKPQAAYRLISELKDTVDLPIHLHTHDTSGNGIITYS
GATQAGVDIIDVATASLAGGTSQPSMQSIYYALEHGPRHASINVKNAEQI
DHYWEDVRKYYAPFEAGITSPQTEVYMHEMPGGQYTNLKSQAAAVGLGHR
FDEIKQMYRKVNMMFGDIIKVTPSSKVVGDMALFMIQNDLTEEDVYARGN
ELNFPESVVSFFRGDLGQPVGGFPEKLQKIIVKDKAVITDRPGLHAEKVD
FETVKADLEQKIGYEPGDHEVISYIMYPQVFLDYQKMQREFGAVTLLDTP
TFLHGMRLNEKIEVQIEKGKTLSIRLDEIGEPDLAGNRVLFFNLNGQRRE
VVINDQSVQAQVVAKRKAETGNPNQIGATMPGSVLEILVKAGDKVQKGQA
LMVTEAMKMETTIEAPFDGEIVDLHVVKGEAIQTQDLLIEIN

3D structure

• PDB: 5vyz Structural and functional studies of pyruvate carboxylase regulation by cyclic di-AMP in lactic acid bacteria.
• Chain: B
• Resolution: 2.3 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	2BA	B	P711 Q712 Y715 S745 G746 Q749	P716 Q717 Y720 S750 G751 Q754
BS02	MN	B	D534 K703 H732 H734	D539 K708 H737 H739
BS03	ADP	B	K116 M155 K157 G162 M167 Y201 I202 H207 Q231 N234 L276 E286 T442	K124 M163 K165 G170 M172 Y206 I207 H212 Q236 N239 L281 E291 T447
BS04	MG	B	E274 E286	E279 E291

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Thu Nov 28 06:09:52 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 = '5vyz', asym_id = 'B', 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='5vyz', asym_id='B', 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 = '5vyz', asym_id = 'B'

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

    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>