Structure of PDB 5vz0 Chain A Binding Site BS02

Receptor Information
>5vz0 Chain A (length=1139) Species: 1358 (Lactococcus lactis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPRGSHMKKLLVANRGEIAVRVFRACNELGLSTVAVYAREDEYSVHRFKA
DESYLIGQGKKPIDAYLDIDDIIRVALESGADAIHPGYGLLSENLEFATK
VRAAGLVFVGPELHHLDIFGDKIKAKAAADEAKVPGIPGTNGAVDIDGAL
EFAKTYGYPVMIKAALGGMRVARNDAEMHDGYARAKSEAIGAFGSGEIYV
EKYIENPKHIEVQILGDRHGNIIHLHERDCSVQRRNQKVIEIAPAVGLSP
DFRNEICEAAVKLCKNVGYVNAGTVEFLVKDDKFYFIEVNPRVQVEHTIT
ELITGVDIVQAQILIAQGKDLHREIGLPAQSEIPLLGSAIQCRITTEDPQ
NGFLPDTGKIDTYRSPGGFGIRLDVGNAYAGYEVTPYFDSLLVKVCTFAN
EFSDSVRKMDRVLHEFRIRGVKTNIPFLINVIANENFTSGQATTTFIDNT
PSLFNFPRLRDRGTKTLHYLSMITVNGFPGIENTEKRHFEEPRQPLLNLE
KKKTAKNILDEQGADAVVDYVKNTKEVLLTDTTLRDAHQSLLATRLRLQD
MKGIAQAIDQGLPELFSAEMWGGATFDVAYRFLNESPWYRLRKLRKLMPN
TMFQMLFRGSNAVGYQNYPDNVIEEFIRVAAHEGIDVFRIFDSLNWLPQM
EKSIQAVRDNGKIAEATICYTGDILDPSRPKYNIQYYKDLAKELEATGAH
ILAVKDMAGLLKPQAAYRLISELKDTVDLPIHLHTHDTSGNGIITYSAAT
QAGVDIIDVATASLAGGTSQPSMQSIYYALEHGPRHASINVKNAEQIDHY
WEDVRKYYAPFEAGITSPQTEVYMHEMPGGQYTNLKSQAAAVGLGHRFDE
IKQMYRKVNMMFGDIIKVTPSSKVVGDMALFMIQNDLTEEDVYARGNELN
FPESVVSFFRGDLGQPVGGFPEKLQKIIVKDKAVITDRPGLHAEKVDFET
VKADLEQKIGYEPGDHEVISYIMYPQVFLDYQKMQREFGAVTLLDTPTFL
HGMRLNEKIEVQIEKGKTLSIRLDEIGEPDLAGNRVLFFNLNGQRREVVI
NDQSVQAQVVAKRKAETGNPNQIGATMPGSVLEILVKAGDKVQKGQALMV
TEAMKMETTIEAPFDGEIVDLHVVKGEAIQTQDLLIEIN
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 chain5vz0 Chain A 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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PDB5vz0 Structural and functional studies of pyruvate carboxylase regulation by cyclic di-AMP in lactic acid bacteria.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		K116 M155 K157 G161 M167 Y201 I202 H207 Q231 N234 L276 E286 T442
Binding residue
(residue number reindexed from 1)		K122 M161 K163 G167 M169 Y203 I204 H209 Q233 N236 L278 E288 T444
Annotation score5
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Sun Nov 24 05:46:53 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 = '5vz0', asym_id = 'A', bs = 'BS02', 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='5vz0', asym_id='A', bs='BS02', 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 = '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>