Structure of PDB 4v6a Chain BH Binding Site BS01

Receptor Information
>4v6a Chain BH (length=167) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVER
PSDERRHKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALE
LTVGFSHPVVVEPPEGITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKP
SAYHEKGIYYAGEPVRL
Ligand information
>4v6a Chain BA (length=2767) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagga
gaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccag
ccuaaaccguccggcuuguccgggcggggucguggggcccucggacaccg
aauccccagccuagccgaagcuguugggaagcagcgccagagagggugaa
agccccguaggcgaaagguggggggauaggugaggguacccgaguacccc
gugguucguggagccaugggggaaucugggcggaccaccgccuaaggcua
aguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaa
agaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaag
cagucacggccccgggguuguggcgugccuauugaagcaugagccggcga
cucacggucgugggcgagcuuaagccguugaggcggaggcguagggaaac
cgaguccgaacagggcgcaguccgcggccguggacccgaaaccgggcgag
cuagcccuggccagggugaagcuggggugagacccaguggaggcccgaac
cggugggggaugcaaaccccucggaugagcuggggcuaggagugaaaagc
uaaccgagcccggagauagcugguucuccccgaaaugacuuuagggucag
ccucaggcgcugacuggggccuguagagcacugauagggcuagggggccc
accagccuaccaaacccugucaaacuccgaagggucccagguggagccug
ggagugagggcgcgagcgauaacguccgcguccgagcgcgggaacaaccg
agaccgccagcuaaggcccccaagucugggcuaagugguaaaggaugugg
cgccgcgaggucgaguggcgccgcgccgaaaaugaucggggcuuaagccc
agcgccgaagcugcgggucugggggaugaccccaggcgguaggggagcgu
ucccgaugccgaugaaggccgacccgcgagggcggcuggagguaagggaa
gugcgaaugccggcaugaguaacgauaaagagggugagaaucccucucgc
cguaagcccaaggguuccuacgcaauggucgucagcguaggguuaggcgg
gaccuaaggugaagccgaaaggcguagccgaagggcagccgguuaauauu
ccggcccuucccgcaggugcgauggggggacgcucuaggcuagggggacc
ggagccauggacgagcccggccagaagcgcagggugggagguaggcaaau
ccgccucccaacaagcucugcgugguggggaagcccaaccccccgaagcc
agggagccaagaaaagccucuaagcacaaccugcgggaacccguaccgca
aaccgacacaggugggcgggugcaagagcacucaggcgcgcgggagaacc
cucgccaaggaacucugcaaguuggccccguaacuucgggagaaggggug
cucccuggggugaugagccccggggagccgcagugaacaggcucuggcga
cuguuuaccaaaaacacagcucucugcgaacucguaagaggagguauagg
gagcgacgcuugcccggugccggaaggucaaggggaggggugcaagcccc
gaaccgaagccccggugaacggcggccguaacuauaacgguccuaaggua
gcgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacgac
cggagcgcugucucggcgagggacccggugaaauugaacuggccgugaag
augcggccuacccguggcaggacgaaaagaccccguggagcuuuacugca
gccugguguuggcucuuggucgcgccugcguaggauaggugggagcaggc
gccggugaaauaccacccuggcgcggcugggggccuaacccucggauggg
gggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaagg
uaacggaggcgcccaaagguccccucaggcgggacggaaauccgccggag
agcgcaaggguagaagggggccugacugcgaggccugcaagccgagcagg
ggcgaaagccgggccuagugaaccgguggucccguguggaagggccaucg
aucaacggauaaaaguuaccccggggauaacaggcugaucucccccgagc
guccacagcggcggggagguuuggcaccucgaugucggcucgucgcaucc
uggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcggc
acgcgagcuggguucagaacgucgugagacaguucggucucuauccgcca
cgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccggaa
gggacgcaccucugguuucccagcugucccuccaggggcauaagcugggu
agccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagcccg
ccccaagaugaggccucccacggcgucaagccgguaaggacccgggaaga
ccacccgguggaugggccggggguguaagcgccgcgaggcguugagccga
ccggucccaaucguccg
.........<<<<<<<<<<<.....<<..<<<<<<<<<<<<......<<<
<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....>>>>
>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<<
....>>>>>>.>>...<<<<<<.....<<....>>......>>>>>.>..
.......<<....>>...<<<<<.....<<.....>>....>>>>>...<
<<....<<<<<<<<.....>>>>>>>>......<<<<<<<<.......<.
..<<<<<.<<<<.<<<...<<<<<......>>>>>((......<<<....
.))>>>...>>>...>>>>..>>>>>..>...>>>>>.>>>.....<<<<
<<<<<.......>>>>>>>>>......<<<<<..((((>>>>>..>>>..
....>>.>>>>>>.>>...............<<....>>....>>.....
....<<<<....>>>>..................>>>>>>>>>>>.....
..<<<<<<<<<<..>>>>>>>>>>...<............>.<<<<<<..
..<<<<<<<<<<<<<..<<<...<<<.....>>>...>>>...<<....>
>..<<<<.....>>>>...>>>>>>>>>>>>>..<<.<...<<<<<<...
..<<<<<<<<<..<<<....<<<<<<......>>>>>>.....>>>...<
<<..<<<<........>>>>.>>>....>>>>>>>>>...<<<.....>>
>......>>>>>>......>.>>..<<<<<<....<<<<<....>>>>><
<<<<<<<<.....<<<<<<<<<...<<<...<<<<<<<<.<.<<<<<<..
....>>>>.>>>..>>>>>>>>..>>.>...>>>>>>>>>.....>>>>>
>>.>>..<<<<<<<.<<......>>.>>>>>>>.....<<<......>>>
...<<<<.<<<...<<<(((.....<<<<<<...........<<..<<<<
<<<<<..........>>>>>>>>>.>>..........)))......>>>>
>>.>>>...>>>>>>><<<<<<<.......>>>>>>>....>>>>>>..<
<<<<...<<<......<<<<<.<<<....>>>>>>>>...>>>..>>>>>
........>>>>>><......<<.....<<<<<<.......>>>>>><<<
<....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<
<.<<...<<<...<<<....>>>...>>>...>>...<<<<<........
>>>>>))<<<<<<<<<<<<<...<<<<....<<<<<.<<<..<<<<<.<<
<<.<<..[[[[...>>>>>><<<...<<<<<<<<<<<<<<<<.<<.....
>>>>>>>>>.....>>>>>>>>>..>>><.........>>>>>>...>>>
..>>>>>.........>>>>...>>...>>>>>>>>>>>>>>>..>>...
..<<......>>>>>>>.<<<<<....>>>>>..>>>>..<<<<....<<
<<<<<<.<<.........<.....<<<<<...............>>>>><
<<<<<<<<<<<.....>>>>>>>>>>>>............<<<<<<<<<.
.<<<.........>>>..<<<<<<<.....<<<....>>>.......>>>
>>>>.<<<<<.<<<..<<<<<<<..<<<...<<...<<<<<....>>>>>
...>>...>>>>>>>>..>>>>><<<<<<.......>>>>>>........
<...........<<<<<<.....>>>>>>.....>....>>>>>..>>.>
>>>>>>..>..>>.>>>>>>>>.>>>>>>.....>.....<<<<<.....
...>>>>>..<<<<<<<<.<<<.........<<<<.<<<<<<..<<<<<.
<<<.<<<<<.<<<<<<<<<<<<<<<<...........<<<<<..<....>
............>>>>>..>>>>>>>>>>>>>>>>...<<<<<....>>>
>>....>>>>>.>>>..>>>>>..<<<<.....>>>><<<<<<.......
....>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>....
.<<...(((>>....>>>>>>>...<<<<..<<<......>>>..>>>>.
<<<....>>>.>>))).......<<<<<<<.<<..))))..>>>>>>>>>
.............>>>>..>>>>>>.......<<<<...<<<<<<...<<
.......>>...>>>>>>....>>>.>.......<<<<<.<<<<<<..<<
<<<<<<<......>>>>>>>..>>.<<<<<.....>>>>>.....>>>>>
..>...>>>.>>....<<<<<<<....>>>.>>>>........>>>>>>>
>>>>....<<<<<<<...<<<<..<<<<<<<...............>>>>
>>>.<<<<<...<<<<...<<<<<<<<<<<]]]]>>>>>>...>>>>>..
.>>>>.>>>>>...<<<....<<<<<...........>>>>>....>>>.
>>>>.......>>>>>>>...<.........>.....<<<<<<<<<....
...>>>>>....<<<<<<<<.<<<....<<<<<....>>>>>...>>>..
>>>>>.>>>...>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4v6a Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome.
Resolution3.1 Å
Binding residue
(original residue number in PDB)
R59 K62 S63 L67 F109 S110 K138 Q139 G142 Q143 K160
Binding residue
(residue number reindexed from 1)
R55 K58 S59 L63 F105 S106 K134 Q135 G138 Q139 K156
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Tue Dec 3 00:28:13 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 = '4v6a', asym_id = 'BH', bs = 'BS01', title = 'Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4v6a', asym_id='BH', bs='BS01', title='Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome.')
   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 = '0003735,0005840,0006412,0019843', uniprot = '', pdbid = '4v6a', asym_id = 'BH'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412,0019843', uniprot='', pdbid='4v6a', asym_id='BH')
    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>