Structure of PDB 5vyz Chain A

Receptor sequence

>5vyzA (length=1144) Species: 1358 (Lactococcus lactis)

LVPRGSHMKKLLVANRGEIAVRVFRACNELGLSTVAVYAREDEYSVHRFK
ADESYLIGQGKKPIDAYLDIDDIIRVALESGADAIHPGYGLLSENLEFAT
KVRAAGLVFVGPELHHLDIFGDKIKAKAAADEAKVPGIPGTNGAVDIDGA
LEFAKTYGYPVMIKAALGGGGRGMRVARNDAEMHDGYARAKSEAIGAFGS
GEIYVEKYIENPKHIEVQILGDRHGNIIHLHERDCSVQRRNQKVIEIAPA
VGLSPDFRNEICEAAVKLCKNVGYVNAGTVEFLVKDDKFYFIEVNPRVQV
EHTITELITGVDIVQAQILIAQGKDLHREIGLPAQSEIPLLGSAIQCRIT
TEDPQNGFLPDTGKIDTYRSPGGFGIRLDVGNAYAGYEVTPYFDSLLVKV
CTFANEFSDSVRKMDRVLHEFRIRGVKTNIPFLINVIANENFTSGQATTT
FIDNTPSLFNFPRLRDRGTKTLHYLSMITVNGFPGIENTEKRHFEEPRQP
LLNLEKKKTAKNILDEQGADAVVDYVKNTKEVLLTDTTLRDAHQSLLATR
LRLQDMKGIAQAIDQGLPELFSAEMWGGATFDVAYRFLNESPWYRLRKLR
KLMPNTMFQMLFRGSNAVGYQNYPDNVIEEFIRVAAHEGIDVFRIFDSLN
WLPQMEKSIQAVRDNGKIAEATICYTGDILDPSRPKYNIQYYKDLAKELE
ATGAHILAVKDMAGLLKPQAAYRLISELKDTVDLPIHLHTHDTSGNGIIT
YSGATQAGVDIIDVATASLAGGTSQPSMQSIYYALEHGPRHASINVKNAE
QIDHYWEDVRKYYAPFEAGITSPQTEVYMHEMPGGQYTNLKSQAAAVGLG
HRFDEIKQMYRKVNMMFGDIIKVTPSSKVVGDMALFMIQNDLTEEDVYAR
GNELNFPESVVSFFRGDLGQPVGGFPEKLQKIIVKDKAVITDRPGLHAEK
VDFETVKADLEQKIGYEPGDHEVISYIMYPQVFLDYQKMQREFGAVTLLD
TPTFLHGMRLNEKIEVQIEKGKTLSIRLDEIGEPDLAGNRVLFFNLNGQR
REVVINDQSVQAQVVAKRKAETGNPNQIGATMPGSVLEILVKAGDKVQKG
QALMVTEAMKMETTIEAPFDGEIVDLHVVKGEAIQTQDLLIEIN

3D structure

• PDB: 5vyz Structural and functional studies of pyruvate carboxylase regulation by cyclic di-AMP in lactic acid bacteria.
• Chain: A
• 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	MN	A	D534 K703 H732 H734	D541 K710 H739 H741
BS02	ADP	A	K116 M155 K157 G161 G163 G164 M167 Y201 I202 H207 Q231 N234 L276 E286 T442	K123 M162 K164 G168 G170 G171 M174 Y208 I209 H214 Q238 N241 L283 E293 T449
BS03	MG	A	E274 E286	E281 E293
BS04	2BA	A	Q712 Y715 S745 G746 Q749	Q719 Y722 S752 G753 Q756

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sun Nov 24 09:00:39 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 = '5vyz', 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='5vyz', 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 = '5vyz', asym_id = 'A'

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