Structure of PDB 8dgf Chain D Binding Site BS01

Receptor Information
>8dgf Chain D (length=1534) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKPNWDNFKAKFSENPQGNFEWFCYLLFCQEFKMPAGIFRYKNQSGIETN
PITKDNEIIGWQSKFYDTKLSDNKADLIEMIEKSKKAYPGLSKIIFYTNQ
EWDPKIKIEVDQKAYESGIEIVWRVASFFESPFVIVENEKIAKHFFSLNE
SIFDLLEEKRKHTENVLYEIQTNIEFKDRSIEIDRRHCIELLHENLVQKK
IVIVSGEGGVGKTAVIKKIYEAEKQYTPFYVFKASEFKKDSINELFGAHG
LDDFSNAHQDELRKVIVVDSAEKLLELTNIDPFKEFLTVLIKDKWQVVFT
TRNNYLADLNYAFIDIYKITPGNLVIKNLERGELIELSDNNGFSLPQDVR
LLELIKNPFYLSEYLRFYTGESIDYVSFKEKLWNKIIVKNKPSREQCFLA
TAFQRASEGQFFVSPACDTGILDELVKDGIVGYEAAGYFITHDIYEEWAL
EKKISVDYIRKANNNEFFEKIGESLPVRRSFRNWISERLLLDDQSIKPFI
AEIVCGEGISNFWKDELWVAVLLSDNSSIFFNYFKRYLLSSDQNLLKRLT
FLLRLACKDVDYDLLKQLGVSNSDLLSIKYVLTKPKGTGWQSVIQFIYEN
LDEIGIRNINFILPVIQEWNQRNKVGETTRLSSLIALKYYQWTIDEDVYL
SGRDNEKNILHTILHGAAMIKPEMEEVLVKVLKNRWKEHGTPYFDLMTLI
LTDLDSYPVWASLPEYVLQLADLFWYRPLDIEDEFGLFRSHHDYYPESPY
QTPIYWLLQSQFKKTIDFILDFTNKTTICFAHSHFAKNEIEEVDVFIEEG
KFIKQYICNRLWCSYRGTQVSTYLLSSIHMALEKFFLENFKNADSKVLES
WLLFLLRNTKSASISAVVTSIVLAFPEKTFNVAKVLFQTKDFFRFDMNRM
VLDRTHKSSLINSLHEEDRIKACDDVHRNTYLENLALHYQIFRSENVTEK
DAIERQQVLWDIFDKYYNQLPDEAQETEADKTWRLCLARMDRRKMKITTK
EKDEGIEISFNPEIDPKLKQYSEEAIKKNSEHMKYVTLKLWASYKREKDE
RYKNYGMYEDNPQIALQETKEIIKKLNEEGGEDFRLLNGNIPADVCSVLL
LDYFNQLNNEEREYCKDIVLAYSKLPLKEGYNYQVQDGTTSAISALPVIY
HNYPMERETIKTILLLTLFNDHSIGMAGGRYSVFPSMVIHKLWLDYFDDM
QSLLFGFLILKPKYVILSRKIIHESYRQIKKININKVFLNNYKHCISNVI
DNKISIDDLGSMDKVDLHILNTAFQLIPVDTVNIEHKKLVSLIVKRFSTS
LLSSVREDRVDYALRQSFLERFAYFTLHAPVSDIPDYIKPFLDGFNGSEP
ISELFKKFILVEDRLNTYAKFWKVWDLFFDKVVTLCKDGDRYWYVDKIIK
SYLFAESPWKENSNGWHTFKDSNSQFFCDVSRTMGHCPSTLYSLAKSLNN
IASCYLNQGITWLSEILSVNKKLWEKKLENDTVYYLECLVRRYINNERER
IRRTKQLKQEVLVILDFLVEKGSVVGYMSRENIL
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain8dgf Chain D Residue 1601 [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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PDB8dgf Prokaryotic innate immunity through pattern recognition of conserved viral proteins.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		Q198 T199 I210 G238 K239 T240 R329
Binding residue
(residue number reindexed from 1)		Q171 T172 I183 G211 K212 T213 R302
Annotation score5
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Sat Nov 30 23:59:35 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 = '8dgf', asym_id = 'D', bs = 'BS01', title = 'Prokaryotic innate immunity through pattern recognition of conserved viral proteins.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='8dgf', asym_id='D', bs='BS01', title='Prokaryotic innate immunity through pattern recognition of conserved viral proteins.')
   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 = '0016887', uniprot = '', pdbid = '8dgf', asym_id = 'D'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0016887', uniprot='', pdbid='8dgf', asym_id='D')
    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>