Structure of PDB 6gz5 Chain AQ Binding Site BS01

Receptor Information
>6gz5 Chain AQ (length=187) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GVDIRHNKDRKVRRKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRL
FMSRTNRPPLSLSRMIRKMKLPGRENKTAVVVGTITDDVRVQEVPKLKVC
ALRVTSRARSRILRAGGKILTFDQLALDSPKGCGTVLLSGPRKGREVYRH
FGKAPGTPHSHTKPYVRSKGRKFERARGRRASRGYKN
Ligand information
>6gz5 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6gz5 tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.
Resolution3.5 Å
Binding residue
(original residue number in PDB)
G2 V3 N8 D10 R11 V13 R14 R15 E17 K19 S20 R26 K30 F34 R37 R38 T42 F43 M53 S54 R55 T56 P60 S62 S64 R65 R68 K69 K71 L72 P73 R75 K78 T85 T87 D88 D89 V90 R91 R104 T106 S107 R108 R115 C134 G135 T136 L138 S140 G141 P142 R143 K144 G145 R146 E147 V148 R150 F152 T158 H160 H162 K164 Y166 V167 R168 K170 R172 K173 F174 R176 R178 R180 R181 S183 R184 G185 Y186 K187 N188
Binding residue
(residue number reindexed from 1)
G1 V2 N7 D9 R10 V12 R13 R14 E16 K18 S19 R25 K29 F33 R36 R37 T41 F42 M52 S53 R54 T55 P59 S61 S63 R64 R67 K68 K70 L71 P72 R74 K77 T84 T86 D87 D88 V89 R90 R103 T105 S106 R107 R114 C133 G134 T135 L137 S139 G140 P141 R142 K143 G144 R145 E146 V147 R149 F151 T157 H159 H161 K163 Y165 V166 R167 K169 R171 K172 F173 R175 R177 R179 R180 S182 R183 G184 Y185 K186 N187
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Sat Nov 16 00:55:12 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 = '6gz5', asym_id = 'AQ', 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='6gz5', asym_id='AQ', 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 = '6gz5', asym_id = 'AQ'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='6gz5', 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>