Structure of PDB 6nak Chain D Binding Site BS02

Receptor Information
>6nak Chain D (length=165) Species: 243274 (Thermotoga maritima MSB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EEQKMRHLRFENLTEEQLKRLAKILTENLKGGEVVILSGNLGAGKTTFVK
GMIRAIGLDEKMVKSPTFTLMNVYPGLKTIYHLDLYRLQDTDFLSLDVED
ILEDEDGIMVVEWGDLFDGFWPEDSIKVKIEIADESHRNVEILIPEEVNF
LVEKIERYRKELQNT
Ligand information
Ligand IDAPC
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
InChIKeyCAWZRIXWFRFUQB-IOSLPCCCSA-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)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[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)(CP(=O)(O)OP(=O)(O)O)O)O)O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC11 H18 N5 O12 P3
NameDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL132722
DrugBankDB02596
ZINCZINC000008295117
PDB chain6nak Chain D Residue 201 [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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PDB6nak The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification.
Resolution3.14 Å
Binding residue
(original residue number in PDB)		T10 E11 L14 L37 G38 A39 G40 K41 T42 T43 E108 S132 R134
Binding residue
(residue number reindexed from 1)		T14 E15 L18 L41 G42 A43 G44 K45 T46 T47 E112 S136 R138
Annotation score1
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Wed Dec 4 20:54:09 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 = '6nak', asym_id = 'D', bs = 'BS02', title = 'The structure of the TsaB/TsaD/TsaE complex reve...echanism for the bacterial t6A tRNA-modification.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6nak', asym_id='D', bs='BS02', title='The structure of the TsaB/TsaD/TsaE complex reve...echanism for the bacterial t6A tRNA-modification.')
   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 = '0002949', uniprot = '', pdbid = '6nak', asym_id = 'D'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0002949', uniprot='', pdbid='6nak', 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>