Structure of PDB 5vyz Chain C Binding Site BS01

Receptor Information

>5vyz Chain C (length=1083) Species: 1358 (Lactococcus lactis)

GLVPRGSHMKKLLVANRGEIAVRVFRACNELGLSTVAVYAREDEYSVHRF
KADESYLIGQGKKPIDAYLDIDDIIRVALESGADAIHPGYGLLSENLEFA
TKVRAAGLVFVGPELHHLDIFGDKIKAKAAADEAKVPGIPGTYVEKYIEN
PKHIEVQILGDRHGNIIHLHERDCSVQRRNQKVIEIAPAVGLSPDFRNEI
CEAAVKLCKNVGYVNAGTVEFLVKDDKFYFIEVNPRVQVEHTITELITGV
DIVQAQILIAQGKDLHREIGLPAQSEIPLLGSAIQCRITTEDPQNGFLPD
TGKIDTYRSPGGFGIRLDVGNAYAGYEVTPYFDSLLVKVCTFANEFSDSV
RKMDRVLHEFRIRGVKTNIPFLINVIANENFTSGQATTTFIDNTPSLFNF
PRLRDRGTKTLHYLSMITVNGFPGIENTEKRHFEEPRQPLLNLEKKKTAK
NILDEQGADAVVDYVKNTKEVLLTDTTLRDAHQSLLATRLRLQDMKGIAQ
AIDQGLPELFSAEMWGGATFDVAYRFLNESPWYRLRKLRKLMPNTMFQML
FRGSNAVGYQNYPDNVIEEFIRVAAHEGIDVFRIFDSLNWLPQMEKSIQA
VRDNGKIAEATICYTGDILDPSRPKYNIQYYKDLAKELEATGAHILAVKD
MAGLLKPQAAYRLISELKDTVDLPIHLHTHDTSGNGIITYSGATQAGVDI
IDVATASLAGGTSQPSMQSIYYALEHGPRHASINVKNAEQIDHYWEDVRK
YYAPFEAGITSPQTEVYMHEMPGGQYTNLKSQAAAVGLGHRFDEIKQMYR
KVNMMFGDIIKVTPSSKVVGDMALFMIQNDLTEEDVYARGNELNFPESVV
SFFRGDLGQPVGGFPEKLQKIIVKDKAVITDRPGLHAEKVDFETVKADLE
QKIGYEPGDHEVISYIMYPQVFLDYQKMQREFGAVTLLDTPTFLHGMRLN
EKIEVQIEKGKTLSIRLDEIGEPDLAGNRVLFFNLNGQRREVVINDQSVQ
AQVVAKRKAETGNPNQIGATMPGSVLEILVKAGDKVQKGQALMVTEAMKM
ETTIEAPFDGEIVDLHVVKGEAIQTQDLLIEIN

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 5vyz Chain C Residue 1201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5vyz Structural and functional studies of pyruvate carboxylase regulation by cyclic di-AMP in lactic acid bacteria.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): D534 K703 H732 H734
• Binding residue (residue number reindexed from 1): D480 K649 H678 H680
• Annotation score: 1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sun Nov 24 10:31:36 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>()

   1435     title=pdb2title(pdbid)

   1436     if bs.startswith("BS"):

=> 1437         pubmed,uniprot=display_interaction(pdbid,asym_id,bs,title)

   1438     else:

   1439         if lig3:

pubmed = '', uniprot = '', display_interaction = <function display_interaction>, pdbid = '5vyz', asym_id = 'C', bs = 'BS01', 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_interaction(pdbid='5vyz', asym_id='C', bs='BS01', title='Structural and functional studies of pyruvate ca...ulation by cyclic di-AMP in lactic acid bacteria.')

   1295         display_ec(ec,csaOrig,csaRenu)

   1296     if go:

=> 1297         display_go(go,uniprot,pdbid,asym_id)

   1298     return pubmed,uniprot

   1299 

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

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

    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>