Structure of PDB 6gz4 Chain AD Binding Site BS01

Receptor Information
>6gz4 Chain AD (length=294) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIV
RVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGL
LLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLART
TTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQN
VADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENPVY
EKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
Ligand information
>6gz4 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
.........................<<<<<<.....<<....>>......
>>>>>.>.........<<....>>..<<<<<<.....<<.....>>....
>>>>>>..[[[..<...<.....<<<<.<.........>>>>>.......
>..>...<.<<..<<.<....<<<<<...<<...<<.<<.......<.<.
.......>..>.................................>>>>.>
>>>>.>>...>>>..>>.>.......<<<<<<<........>>>>>>>..
...(((((..<<<<<<)))))..]]]........................
..........<<....>>...............<<<......>>>.....
.............................<<<<<<<<..<<<.<.....<
..<<.<.<<<<....<<.<..<.<<<....<...<<.<<<<......<<<
<<.<<<..<<<<<<<<<.>>>..>>>>>>>>>>>>>>.>>.>>>>.....
.>...>>>>..>.>>....>>>>.>.>>..>..<<<<<<<<.<<<<<<<<
<<.<<<........<<.<<<.<<.<......<<<<<<<<.>>>>>>>>..
......>>>.>>>>>...........>>>...>>>>>>>>>>........
............<<<....<<<<<<..>>>>>>..<.<<<..<<<.<<..
..<<<<<.<<<<<...<<...>>.<<<<<<<.<<<<....>>>>.>>>>>
>>>>>>>.>.>>>>....>>....>>>.>>>..>.....<<<<<..>>>>
>..........>>>......>>>.>>>>>...>>>>...>>>>>>>>..<
<<<........>>>><<<<<<....<<<<<<<<<<<<<..<<<...<<<<
........>>>>.....>>>...<<....>>...<<<<<<<......>>>
>>>>..<<<<<..<<<...<..............>...>>>...>>>>>.
<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>>>>>>>>>>>>
>..<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....
>>>>>>>.....>>>...<<<..<<.<<........>>>>.>>>....>>
>>>>>>>...<<.......>>......>>>>>>...>..>.>>..<<<<<
<....<.<<<....>>>.><<<<<<<<<<........<<<.<<<<<<<<<
...<<<....<<<..<.<<<...<<<<<.........>>>>>.>>>.>..
>>>..>.>>...>>>>>>>....<<<<<<<<.<......>>>>>>>>>..
..>>>>>>>>>>>>.>>>..<<<<.<<<<<.....>>>>>.>>>>....<
<<......>>>...<<<<<<<...<<<(((.......<<<<<.....<<.
.........<<<.<<<<<<<<<<.......<<<<<.<<<...<<......
...>>...>>>.........<<......>>...>>>>>...>>>>>>>>>
>>>>..........))).>>...>>>>>..>>>...>>>>>>><<<<<<.
<.......>.>>>>>>....>>>>>>...<<<<<<<<.<<......<<<<
.<<<<....>>>>>>>>...>>>>>>>>>>........>>>>>><<....
.<<.....<<<<<<.......>>>>>>.<<<.....<<<<<.<<...<<<
<<<...<<.....>>.>>>>>>....((<<<<<<...<<....<<<....
>>>..........<<.<<<<<<<<<...>>>>>>>>>>>......>>...
.>>>..<<<<<........>>>>>))<<<<....<<<<<...<<<<<<<.
...>>>>>>>...<<<....>>>...<..<<<<<<<...<<<<<<<<<<<
<<<<<<<<<<<<..{{{..>>>>>>....<<<<<.<<<<.<<<<.....<
<<.....>>>.....>>>>>>>>..>>>>>.....<<<<<<<.......>
>>>>>>>>>>.>.>>>>>>>>>>>>.........>>>>>>>..>......
....>>.>>>.>>>>.>>>..>>.....<<......>>>>>>>.<<<<..
...>>>>..>>>....<<<<.....<<<<<<<.<<.........<.....
<<<<<....<<..>>.....>>>>><<.<<<<<<<<<<<.>>>>>..>>>
>>>.>>............<<<<<<<<<..<<<.........>>>..<<<<
<<<....<<<<.....>>>>......>>>>>>>...<<..<<<..<<<<<
<....<<<....<<<<<....>>>>.>...>>>.>>>>..>>>>>.<<<<
<.......>>>>>.........<...........<<<<<.......>>>>
>.....>.....>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>
>....>>....<<<<<........>>>>>....[[[[[..{{{.{{....
..[[[[.{{[[[[..<<<<<.<<<<<<<<<.<<<<<<<<<<<<.<<<<..
........<<<<<..<<<<..>>>>............>>>>>.>>>>.>>
.>>>>>>>>>>...<<<<<.....<<<<....<...<<<...>>>.....
>.............<<<<<<<......>>>>>>>..>>>>..>>>>>...
.>>>>>>>>>..>>>>>...<<<.....>>>..<<<<<<...........
>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.
..(((>>....>>>>>>>...<<<..<<<<.......>>>>..>>>.<<<
....>>>.>>))).......((((((..(((..>>>>>>.))))))))).
.........]]]]..}}]]]].......<<.<.<.<<<<<<...<<....
...>>...>>>>>>...>>.>.>.......<<<<<.<<<<<<..<.<.<<
<<<......>>>>>...>.>.<<<.<.....>.>>>.....>>>>>..>.
..>>>.>>....<<<<<<<....>>>.>>>>....}}..}}}.]]]]]..
...<<<<<<.<..<<<..<.<<<<<.................>>>>>.><
<<<....<<<<....<<.<<<<<<<}}}.>>>>>..>>.>>...>>>>..
.>>>><<<<....<<<<<...........>>>>>....>>>>.>>>...>
.>>>>>>.....<<<<<<<..<..<<<...................<.<<
<>>>.>..................<<<..<<<<.......<.<<<<<<<.
.....>>>>>>>.>.....>>>>..>>>..............>.>>..>.
>>>>>>><<<<<.<.............>.....<.<<<<<<<.<<.....
<<<<....<<<<<......>>>>>...>>>>....>>....>>>>.>>>.
>...>>>>>...
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6gz4 tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.
Resolution3.6 Å
Binding residue
(original residue number in PDB)
V4 K5 V6 V7 K10 Y12 K14 R15 Y16 Q17 K19 R23 G26 T28 D29 Y31 R35 L36 K43 Y44 N45 K48 F113 G140 A141 Y145 L146 A148 T153 F160 P174 S176 K178 R179 S272 Q275 R279 K283 S286 R289 A290
Binding residue
(residue number reindexed from 1)
V1 K2 V3 V4 K7 Y9 K11 R12 Y13 Q14 K16 R20 G23 T25 D26 Y28 R32 L33 K40 Y41 N42 K45 F110 G137 A138 Y142 L143 A145 T150 F157 P171 S173 K175 R176 S269 Q272 R276 K280 S283 R286 A287
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Tue Dec 3 01:43:10 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 = '6gz4', asym_id = 'AD', 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='6gz4', asym_id='AD', 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 = '0003735,0005840,0006412,0008097', uniprot = '', pdbid = '6gz4', asym_id = 'AD'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412,0008097', uniprot='', pdbid='6gz4', asym_id='AD')
    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>