Structure of PDB 5vyz Chain B Binding Site BS03

Receptor Information
>5vyz Chain B (length=1142) Species: 1358 (Lactococcus lactis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLVPRGSHMKKLLVANRGEIAVRVFRACNELGLSTVAVYAREDEYSVHRF
KADESYLIGQGKKPIDAYLDIDDIIRVALESGADAIHPGYGLLSENLEFA
TKVRAAGLVFVGPELHHLDIFGDKIKAKAAADEAKVPGIPGTNGAVDIDG
ALEFAKTYGYPVMIKAALGGGMRVARNDAEMHDGYARAKSEAIGAFGSGE
IYVEKYIENPKHIEVQILGDRHGNIIHLHERDCSVQRRNQKVIEIAPAVG
LSPDFRNEICEAAVKLCKNVGYVNAGTVEFLVKDDKFYFIEVNPRVQVEH
TITELITGVDIVQAQILIAQGKDLHREIGLPAQSEIPLLGSAIQCRITTE
DPQNGFLPDTGKIDTYRSPGGFGIRLDVGNAYAGYEVTPYFDSLLVKVCT
FANEFSDSVRKMDRVLHEFRIRGVKTNIPFLINVIANENFTSGQATTTFI
DNTPSLFNFPRLRDRGTKTLHYLSMITVNGFPGIENTEKRHFEEPRQPLL
NLEKKKTAKNILDEQGADAVVDYVKNTKEVLLTDTTLRDAHQSLLATRLR
LQDMKGIAQAIDQGLPELFSAEMWGGATFDVAYRFLNESPWYRLRKLRKL
MPNTMFQMLFRGSNAVGYQNYPDNVIEEFIRVAAHEGIDVFRIFDSLNWL
PQMEKSIQAVRDNGKIAEATICYTGDILDPSRPKYNIQYYKDLAKELEAT
GAHILAVKDMAGLLKPQAAYRLISELKDTVDLPIHLHTHDTSGNGIITYS
GATQAGVDIIDVATASLAGGTSQPSMQSIYYALEHGPRHASINVKNAEQI
DHYWEDVRKYYAPFEAGITSPQTEVYMHEMPGGQYTNLKSQAAAVGLGHR
FDEIKQMYRKVNMMFGDIIKVTPSSKVVGDMALFMIQNDLTEEDVYARGN
ELNFPESVVSFFRGDLGQPVGGFPEKLQKIIVKDKAVITDRPGLHAEKVD
FETVKADLEQKIGYEPGDHEVISYIMYPQVFLDYQKMQREFGAVTLLDTP
TFLHGMRLNEKIEVQIEKGKTLSIRLDEIGEPDLAGNRVLFFNLNGQRRE
VVINDQSVQAQVVAKRKAETGNPNQIGATMPGSVLEILVKAGDKVQKGQA
LMVTEAMKMETTIEAPFDGEIVDLHVVKGEAIQTQDLLIEIN
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain5vyz Chain B Residue 1202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5vyz Structural and functional studies of pyruvate carboxylase regulation by cyclic di-AMP in lactic acid bacteria.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		K116 M155 K157 G162 M167 Y201 I202 H207 Q231 N234 L276 E286 T442
Binding residue
(residue number reindexed from 1)		K124 M163 K165 G170 M172 Y206 I207 H212 Q236 N239 L281 E291 T447
Annotation score5
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Mon Feb 17 21:01:53 2025

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 = 'B', bs = 'BS03', 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='B', bs='BS03', 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 = '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>