Structure of PDB 6gz3 Chain Ai Binding Site BS01

Receptor Information
>6gz3 Chain Ai (length=97) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YPMAVGLNKGHKVTKNVSKPRHSRRRGRLTKHTKFVRDMIREVCGFAPYE
RRAMELLKVSKDKRALKFIKKRVGTHIRAKRKREELSNVLAAMRKAA
Ligand information
>6gz3 Chain A2 (length=3612) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggggcgcgggacaugug
gcguacggaagacccgcuccccggcgccgcucguggggggcccaaguccu
ucugaucgaggcccagcccguggacggugugaggccgguagcggcccccg
gcgcgcgcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcggguccggccgugucggcggcccggc
ggaucuuucccgcccccggggucggcgggggaccgucccccggaccggcg
accggccgccgccgggcgcauuuccaggcggugcgccgcgaccggcuccg
ggacggcugggaaggcccggcggggaagguggcucggggcccccgagugu
uacagcccccccggcagcagcacucgccgaaucccggggccgagggagcg
agacccgucgccgcgcucuccccccugggggggccgggccaccccuccca
cggcgcgaccgcucucccagggggcggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccggggggccacgcgcgcgucccgggac
ggcggagcgagcgcacggggucggcggcgacgucggcuacccacccgacc
cgucuugaaacacggaccaaggagucuaacacgugcgcgagucgggggcu
cgcacgaaagccgccguggcgcaaugaaggugaaggccggcgcgcucgcc
ggccgaggugggaucccgaggccucuccaguccgccgaggggcaccaccg
gcccgucucgcccgccgcgccggggagguggagcacgagcgcacguguua
ggacccgaaagauggugaacuaugccugggcagggcgaagccagaggaaa
cucugguggagguccguagcgguccugacgugcaaaucggucguccgacc
uggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucccuc
cgaaguuucccucaggauagcuggcgcucucgcccacgcaguuuuauccg
guaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccuauuc
ucaaacuuuaaauggguaagaagcccggcucgcuggcguggagccggggu
ggaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcugc
gggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucaga
ccccagaaaagguguugguugauauagacagcaggacgguggccauggaa
gucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacuag
cccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgcc
ggccuacgccgcgacgaguaggagggccgcugcggugagccuugaagccu
agggcgcgggcccggguggagccgccgcaggugcagaucuuggugguagu
agcaaauauucaaacgagaacuuugaaggccgaaguggagaaggguucca
ugugaacagcaguugaacaugggucagucgguccugagagaugggcgagc
gccguuccgaagggacgggcgauggccuccguugcccucggccgaucgaa
agggagucggguucagauccccgaauccggaguggcggagaugggcgccg
cgaggcguccagugcgguaacgcgaccgaucccggagaagccggcgggag
ccccggggagaguucucuuuucuuugugaagggcagggcgcccuggaaug
gguucgccccgagagaggggcccgugccuuggaaagcgucgcgguuccgg
cggcguccggugagcucucgcuggcccuugaaaauccgggggagagggug
uaaaucucgcgccgggccguacccauauccgcagcaggucuccaagguga
acagccucuggcauguuggaacaauguagguaagggaagucggcaagccg
gauccguaacuucgggauaaggauuggcucuaagggcuggcagccgacuu
agaacuggugcggaccaggggaauccgacuguuuaauuaaaacaaagcau
cgcgaaggcccgcggcggguguugacgcgaugugauuucugcccagugcu
cugaaugucaaagugaagaaauucaaugaagcgcggguaaacggcgggag
uaacuaugacucucuuaagguagccaaaugccucgucaucuaauuaguga
cgcgcaugaauggaugaacgagauucccacugucccuaccuacuauccag
cgaaaccacagccaagggaacgggcuuggcggaaucagcggggaaagaag
acccuguugagcuugacucuagucuggcacggugaagagacaugagaggu
guagaauaagugggaggcccgggccgccggugaaauaccacuacucugau
cguuuuuucacugacccggugaggcgggggggcgagcccgaggggcucuc
gcuucuggcgccaagcgcccgcccggccgggcgcgacccgcuccggggac
agugccagguggggaguuugacuggggcgguacaccugucaaacgguaac
gcagguguccuaaggcgagcucagggaggacagaaaccucccguggagca
gaagggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccgu
gaaagcggggccucacgauccuucugaccuuuuggguuuuaagcaggagg
ugucagaaaaguuaccacagggauaacuggcuuguggcggccaagcguuc
auagcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauugu
gaagcagaauucgccaagcguuggauuguucacccacuaauagggaacgu
gagcuggguuuagaccgucgugagacagguuaguuuuacccuacugauga
uguguuguugccaugguaauccugcucaguacgagaggaaccgcagguuc
agacauuugguguaugugcuuggcugaggagccaauggggcgaagcuacc
aucugugggauuaugacugaacgccucuaagucagaaucccgcccaggcg
gaacgauacggcagcgccgcggagccucgguuggccucggauagccgguc
cgggguccggugcggagugcccuucguccugggaaacggggcgcggccgg
aaaggcggccgcccccucgcccgucacgcaccgcacguucguggggaacc
uggcgcuaaaccauucguagacgaccugcuucugggucgggguuucguac
guagcagagcagcucccucgcugcgaucuauugaaagucagcccucgaca
caaggguuuguc
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.......>..>.................................>>>>.>
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...(((((..<<<<<<)))))..]]]........................
..........<<....>>...............<<<<....>>>>.....
.............................<<<<<<<<..<<<.<.....<
..<<.<..<<<.....<<<..<..<.....<...<<.<<<<.<....<<<
<<.<<<..<<<<<<<<<.>>>..>>>>>>>>>>>>>>>>>.>>>>.....
.>...>..>..>.>>....>>>..>.>>..>..<<<<<<<<.<<<<<<<<
<<.<<<........<<.<<<.<.<<...<..<<<<<<<<.>>>>>>>>..
>.....>>>.>>>>>...........>>>...>>>>>>>>>>........
............<<<.....<<<<<..>>>>.>..<.<<<..<<<.<<..
.<.<<<<<<<<<<...<<...>>.<<<<<<<.<<<<....>>>>.>>>>>
>>>>>>>.>>>>>>....>>....>>>.>>>..>.....<<<<<..>>>>
>..........>>>......>>>.>>>>>...>>>>...>>>>>>>>..<
<<<........>>>><<<<<<....<<<<<<<<<<<<<..<<<...<<<<
........>>>>.....>>>...<<....>>...<<<<<<<......>>>
>>>>..<<<<<..<<<...<..............>...>>>...>>>>>.
<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>>>>>>>>>>>>
>..<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....
>>>>>>>.....>>>...<<<..<<.<<........>>>>.>>>....>>
>>>>>>>...<<.......>>......>>>>>>......>.>>..<<<<<
<....<.<<<....>>>.><<<<<<<<<<........<<<.<<<<<<<<<
...<<<....<<<..<.<<<...<<<<<.........>>>>>.>>>.>..
>>>..>.>>...>>>>>>>...<<<<<<<<<.<......>>>>>>>>>.>
..>>>>>>>>>>>>.>>>..<<<<.<<<<<.....>>>>>.>>>>....<
<<......>>>...<<<<<<<...<<<(((.......<<<<<.....<<.
.........<<<.<<<<<<<<<<.....<.<<<<<.<<<...<<......
...>>...>>>.........<<......>>...>>>>>.>.>>>>>>>>>
>>>>..........))).>>...>>>>>..>>>...>>>>>>><<<<<<.
<.......>.>>>>>>....>>>>>>.<.<<<<<<<<.<<......<<<<
.<<<<....>>>>>>>>...>>>>>>>>>>..>.....>>>>>><<....
.<<.....<<<<<<.......>>>>>>.<<<.....<<<<<.<<...<<<
<<<...<<.....>>.>>>>>>....((<<<<<<...<<....<<<....
>>>..........<<.<<<<<<<<<...>>>>>>>>>>>......>>...
.>>>..<<<<<........>>>>>))<<<<....<<<<<...<<<<<<<.
...>>>>>>>...<<<....>>>...<..<<<<<<<...<<<<<<<<<<<
<<<<<<<<<<<<..{{{..>>>>>>....<<<<<.<<<<.<<<<.....<
<<.....>>>.....>>>>>>>>..>>>>>.....<<<<<<<.......>
>>>>>>>>>>.>.>>>>>>>>>>>>.........>>>>>>>..>......
....>>.>>>.>>>>.>>>..>>.....<<......>>>>>>>.<<<<..
...>>>>..>>>....<<<<.....<<<<<<<.<<.........<.....
<<<<<....<<..>>.....>>>>><<.<<<<<<<<<<<.>>>>>..>>>
>>>.>>............<<<<<<<<<..<<<.........>>>..<<<<
<<<....<<<<.....>>>>......>>>>>>>...<<..<<<..<<<<<
<....<<<.....<<<<....>>>>.....>>>.>>>>..>>>>>..<<<
.........>>>..........<...........<<<<<.......>>>>
>.....>.....>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>
>....>>....<<<<<........>>>>>....[[[[[..{{{.{{....
..[[[[.{{[[[[..<<<<<.<<<<<<<<<.<<<<<<<<<<<<.<<<<..
........<<<<<..<<<<..>>>>............>>>>>.>>>>.>>
.>>>>>>>>>>...<<<<<.....<<<<....<..<<<<...>>>.>...
>.............<<<<<<<......>>>>>>>..>>>>..>>>>>...
.>>>>>>>>>..>>>>>...<<<.....>>>..<<<<<<...........
>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.
..(((>>....>>>>>>>...<<<..<<<<.......>>>>..>>>.<<<
....>>>.>>))).......((((((..(((..>>>>>>.))))))))).
.........]]]]..}}]]]].......<<.<.<.<<<<<<...<<....
...>>...>>>>>>...>>.>.>.......<<<<<.<<<<<<..<.<.<<
<<<......>>>>>...>.>.<<<.........>>>.....>>>>>..>.
..>>>.>>....<<<<<<<....>>>.>>>>....}}..}}}.]]]]]..
...<<<<<<.<..<<<..<.<<<<<.................>>>>>.><
<<<....<<<<....<<.<<<<<<<}}}.>>>>>..>>.>>...>>>>..
.>>>><<<<<...<<<<<...........>>>>>...>>>>>.>>>...>
.>>>>>>.....<<<<<<..<<..<<<...................<.<<
<>>>.>..................<<<..<<<<.......<.<<<<<<<.
.....>>>>>>>.>.....>>>>..>>>..............>>>...>>
.>>>>>><<<<<.<.............>.....<.<<<<<<<.<<.....
<<<<....<<<<<......>>>>>...>>>>....>>....>>>>.>>>.
>...>>>>>...
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6gz3 tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.
Resolution3.6 Å
Binding residue
(original residue number in PDB)
Y5 K13 G14 H15 V17 H26 S27 R28 R29 R30 G31 R32 L33 T34 H36 R41 Y53 R68 K74 R76 G78 H80 R82 R85 E89
Binding residue
(residue number reindexed from 1)
Y1 K9 G10 H11 V13 H22 S23 R24 R25 R26 G27 R28 L29 T30 H32 R37 Y49 R64 K70 R72 G74 H76 R78 R81 E85
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Wed Dec 4 07:07:58 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 = '6gz3', asym_id = 'Ai', bs = 'BS01', title = 'tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6gz3', asym_id='Ai', bs='BS01', title='tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.')
   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 = '6gz3', asym_id = 'Ai'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='6gz3', asym_id='Ai')
    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>