Structure of PDB 4v8i Chain AQ Binding Site BS01

Receptor Information
>4v8i Chain AQ (length=99) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKY
KLGDVVEIIESRPISKRKRFRVLRLVESGRMDLVEKYLIRRQNYESLSK
Ligand information
>4v8i Chain AA (length=1493) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
guuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaag
acaugcaagucgugcgggccgcggguccguggucagcggcggacggguga
guaacgcgugggugaccuacccggaagagggggacaacccggggaaacuc
gggcuaaucccccauguggacccgccccuugggguguguccaaagggcuu
ugcccgcuuccggaugggcccgcgucccaucagcuaguuggugggguaau
ggcccaccaaggcgacgacggguagccggucugagaggauggccggccac
aggggcacugagacacgggccccacucgaggcagcaguuaggaaucuucc
gcaaugggcgcaagccugacggagcgacgccgcuuggaggaagaagcccu
ucgggguguaaacuccugaacccgggacgaaacccccgacgaggggacug
acgguaccgggguaauagcgccggccaacuccgugccagcagccgcggua
auacggagggcgcgagcguuacccggauucacugggcguaaagggcgugu
aggcggccuggggcgucccaugugaaagaccacggcucaaccguggggga
gcgugggauacgcucaggcuagacggugggagagggugguggaauucccg
gaguagcggugaaaugcgcagauaccgggaggaacgccgauggcgaaggc
agccaccugguccacccgugacgcugaggcgcgaaagcguggggagcaaa
ccggauuagauacccggguaguccacgcccuaaacgaugcgcgcuagguc
ucugggucuccugggggccgaagcuaacgcguuaagcgcgccgccugggg
aguacggccgcaaggcugaaacucaaaggaauugacgggggcccgcacaa
gcgguggagcaugugguuuaauucgaagcaacgcgaagaaccuuaccagg
ccuugacaugcuagggaacccgggugaaagccuggggugccccgcgaggg
gagcccuagcacaggugcugcauggccgucgucagcucgugccgugaggu
guuggguuaagucccgcaacgagcgcaacccccgccguuaguugccagcg
guucggccgggcacucuaacgggacugcccgcgaaagcgggaggaaggag
gggacgacgucuggucagcauggcccuuacggccugggcgacacacgugc
uacaaugcccacuacaaagcgaugccacccggcaacggggagcuaaucgc
aaaaaggugggcccaguucggauuggggucugcaacccgaccccaugaag
ccggaaucgcuaguaaucgcggaucagccaugccgcggugaauacguucc
cgggccuuguacacaccgcccgucacgccaugggagcgggcucuacccga
agucgccgggagccuacgggcaggcgccgaggguagggcccgugacuggg
gcgaagucguaacaagguagcuguaccggaaggugcggcugga
......<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<..<..<
<<.<<<..<<<..<<.<<<<<<<<..>>>>>>>>.>>>>>......<<..
.....<<<<<<<<..<<...<<<<<<<.<<<<<....<<<<<......>>
>>>.....>>>>>...<<<<<.<<<<<....>>>>>.>>>>>..<<<<..
.>>>>.>>>>>>>..>>>>>>>>>><<<....<<<..<<<<<<<<.....
..>>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>>>.>>
.<<<<<.<.........>>>>>>.<<..>>...>>>>>>>........<<
<....<<<<....>>>>..>>>..>>.>>>>>>..<<<<......<<<<.
...>>>>.....>>>>....<<<<<......<.<<<<.....>>>>..>.
......>>>>>......<<<<<(((...<<<<<.....<<.)))>>....
...>>>>>>>>>>..>>>>>>>>>..........<<<((.....<<<<..
.<<<.<<<<<<<.<<<<<<<<<<......<<<<<<.....>>>>>>....
>>>>>>>>..>>>>>>>>>...<<<<<<<<...<<<<<<<....<<<<<<
<.<..<<<......>>>.....>.>>>>>>>...........<<....>>
.>>>>>>>..>>>>>.>>>...>>>...>>>>....<<<<<<...<<...
<<<<.........>>>>...>>>>>>>>..........<<<<<<..<<<<
<<<<<<...>>>>>>>>>>...<<..))>>.....>>>>>>.>>>.<<<.
.....<<<<....>>>>....>>>..)))).]<<<<<.<<<<<<<.<<.<
<<<<<..<<<<<<<<<<......<<........>>..........<<<<<
<<......<<<<<<<<..<<<<<<<....>>>>>>>.....<......>.
...>>>>>>>>.<<<.<<<..<<<<<<.......<<<<<<<<<....>>>
..<<<<......>>>>..>>>>>>.....<<<<.<<<<<<<...<...<<
<.....>>>>.....>>>>>>>.....<<<<<....>>>>>........>
>>>.........>>>...>>>>>>>>>...>>>>>>>...>>.>>>>>>>
>.....<<<<<<<.....<<<..<<..<<<<....>>>>..>>....>>>
.....>>>>>>>......<....<<<<<<<........>>>>>>>....>
.....>>>>>>....<<<<<<<..........>>>>>>>......>>...
>>>>>>>>>>.>>....<..<<.<.<<<<.<<<..<<<<<<<<<<<<<..
.<.<<<<.....<<....>>..>>>>.>..>>>>>>>>>>>>>..>>>.>
>>>..>.>>...>.....<<<<<<<<<....>>>>>>>>>...
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4v8i How hibernation factors RMF, HPF, and YfiA turn off protein synthesis.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		P2 K3 S12 K14 M15 Q16 K17 T18 R25 L31 Y32 K34 R38 S39 K40 K41 Y42 E61 S62 R63 P64 I65 S66 K67 R68 K69 R70 R72 K87 R91 R92 N94 Y95 L98 S99 K100
Binding residue
(residue number reindexed from 1)		P1 K2 S11 K13 M14 Q15 K16 T17 R24 L30 Y31 K33 R37 S38 K39 K40 Y41 E60 S61 R62 P63 I64 S65 K66 R67 K68 R69 R71 K86 R90 R91 N93 Y94 L97 S98 K99
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Nov 29 06:44:50 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 = '4v8i', asym_id = 'AQ', bs = 'BS01', title = 'How hibernation factors RMF, HPF, and YfiA turn off protein synthesis.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4v8i', asym_id='AQ', bs='BS01', title='How hibernation factors RMF, HPF, and YfiA turn off protein synthesis.')
   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 = '0003735,0005840,0006412', uniprot = '', pdbid = '4v8i', asym_id = 'AQ'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='4v8i', asym_id='AQ')
    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>