Structure of PDB 5vyz Chain B Binding Site BS01

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 ID2BA
InChIInChI=1S/C20H24N10O12P2/c21-15-9-17(25-3-23-15)29(5-27-9)19-11(31)13-7(39-19)1-37-43(33,34)42-14-8(2-38-44(35,36)41-13)40-20(12(14)32)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-32H,1-2H2,(H,33,34)(H,35,36)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKeyPDXMFTWFFKBFIN-XPWFQUROSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6ncnc7N)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO[P](O)(=O)O[CH]4[CH]3O)n6cnc7c(N)ncnc67
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@](=O)(O[C@@H]5[C@@H](CO[P@](=O)(O4)O)O[C@H]([C@@H]5O)n6cnc7c6ncnc7N)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P@](O)(=O)O[C@H]5[C@@H](O)[C@@H](O[C@@H]5CO[P@](O)(=O)O[C@H]4[C@H]3O)n6cnc7c(N)ncnc67
ACDLabs 10.04O=P5(OCC7OC(n1c2ncnc(N)c2nc1)C(O)C7OP(=O)(O)OCC6OC(n3c4ncnc(N)c4nc3)C(O)C6O5)O
FormulaC20 H24 N10 O12 P2
Name(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide;
bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate
ChEMBLCHEMBL1229884
DrugBank
ZINCZINC000058661162
PDB chain5vyz Chain A Residue 1204 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		P711 Q712 Y715 S745 G746 Q749
Binding residue
(residue number reindexed from 1)		P716 Q717 Y720 S750 G751 Q754
Annotation score2
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Mon Nov 25 11:08:27 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 = 'B', 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='B', 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 = '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>