Structure of PDB 6s84 Chain B Binding Site BS03

Receptor Information
>6s84 Chain B (length=159) Species: 243274 (Thermotoga maritima MSB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QKMRHLRFENLTEEQLKRLAKILTENLKGGEVVILSGNLGAGKTTFVKGM
IRAIGLDEKMVKSPTFTLMNVYPGLKTIYHLDLYRLQDTDFLSLDVEDIL
EDEDGIMVVEWGDLFDGFWPEDSIKVKIEIADESHRNVEILIPEEVNFLV
EKIERYRKE
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 chain6s84 Chain B Residue 203 [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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PDB6s84 The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification.
Resolution2.89 Å
Binding residue
(original residue number in PDB)		E11 L37 A39 K41 T42 T43 E108 R134
Binding residue
(residue number reindexed from 1)		E13 L39 A41 K43 T44 T45 E110 R136
Annotation score1
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Mon Dec 2 04:50:14 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 = '6s84', asym_id = 'B', bs = 'BS03', 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='6s84', asym_id='B', bs='BS03', 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 = '6s84', asym_id = 'B'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0002949', uniprot='', pdbid='6s84', 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>