Structure of PDB 6xir Chain r Binding Site BS01

Receptor Information

>6xir Chain r (length=214) Species: 4932 (Saccharomyces cerevisiae)

VVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDALKGRVVEVC
LADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQT
LIEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVIS
EILTKEVQGSTLAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLK
QPKFDVGALMALHG

Ligand information

>6xir Chain 2 (length=1708)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuuuacuacaugguauaacu
gugguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaaga
gauguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauuc
auaauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaa
auuucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuu
caacggguaacggggaauaaggguucgauuccggagagggagccugagaa
acggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccu
aauucagggagguagugacaauaaauaacgauacagggcccauucggguc
uuguaauuggaaugaguacaauguaaauaccuuaacgaggaacaauugga
gggcaagucuggugccagcagccgcgguaauuccagcuccaauagcguau
auuaaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguu
ggaacggggccuuuccuucuggcuaagcgaaccaggacuuuuacuuugaa
aaaauuagaguguucaaagcaggcguauugcucgaauauauuagcaugga
auaauagaauaggacguuugguucuauuuuguugguuucuaggaccaucg
uaaugauuaauagggacggucgggggcaucaguauucaauugucagaggu
gaaauucuuggauuuauugaagacuaacuacugcgaaagcauuugccaag
gacguuuucauuaaucaagaacgaaaguuaggggaucgaagaugaucaga
uaccgucguagucuuaaccauaaacuaugccgacuagggaucggguggug
uuuaugacccacucggcaccuuacgagaaaucaaagucuuuggguucugg
ggggaguauggucgcaaggcugaaacuuaaaggaauugacggaagggcac
caccaggaguggagccugcggcuuaauuugacucaacacggggaaacuca
ccagguccagacacaauuuugugggugguggugcauggccguucuuaguu
gguggagugauuugucugcuuaauugcgauaacgaacgagaccuuaaccu
acuaaauaguggugcuagcauuugcugguuauccacuucuuagagggacu
aucgguuucaagccgauggaaguuugaggcaauaacaggucugugaugcc
cuuagacguucugggccgcacgcgcgcuacacugacggagccagcgaguc
uaaccuuggccgagaggucuugguaaucuugugaaacuccgucgugcugg
ggauagagcauuguaauuauugcucuucaacgaggaauuccuaguaagcg
caagucaucagcuugcguugauuacgucccugcccuuuguacacaccgcc
cgucgcuaguaccgauugaauggcuuagugaggccucaggaucugcuuag
agaagggggcaacuccaucucagagcggagaauuuggacaaacuugguca
uuuagaggaacuaaaagucguaacaagguuuccguaggugaaccugcgga
aggaucau

...<<<<<...((((>>>>><<<..<<<<<<................<<<
.<<<...<....<<.....................>>.>.......<<..
......<<<..<<..<<......<..................<.....<.
..............>......>...........<.<...<....>...>.
>..........<<......[.[.[.................<........
>>>.............<<<<..<<<.....>>>.>>>>....>.....>>
>>..>>>.<<<....<<<....<<<<<<<<.......>>>>>>>>>>>..
....>>>...<<<.<<<<....>>>>....>>>.>>.<<.<<<.......
...>>>.>>....<....>......>>>>>>.........<<<....<<<
.....>>>..>>>...............<<......<<.<<....>>..>
>......>>......<<<..............>.>>.........<<<<<
((......<<<<.....<<..))>>.......>>>>.>>>>>..>>>>>>
.>>>.........<<<((.....<.<<...<<<.<<.....<<<......
........>>>.......<<.<.........>.>>.....<<.....<..
.......................<.....>..............>.....
..>>..............<<..<<.........].].]...>>..>>...
......>>....<<<<<<.<<...<<<<..<<..<<<<<<.<...<<<..
....>>>......>.>>>>>>..>>......<<<....>>>..>>>>..>
>.>>>.>>>...>>>...>>.>....<<<<<<<...<...<<<<......
...>>>>...>>>>>>>>..........<<<.<<.<<<..<<<<<<<<.<
<.....>>>>>>>>>>..>>>...<<..))>>...>>.....>>>.>>>.
<<<......<<<<....>>>>....>>>..))))..<<<<<.<<<<<<<.
.<<..<<<<<..<<<..<<.<<......<<........>>..........
<<.........<.<......>.>......<<......<<<<<<....<<<
.<<.<<....>>....<<<......>>>...>>.>>>....<<<...<<.
....<..<<<........................>>>..>....>>....
.<<<<.......>>>>..........>>>....>>>.>>>........>>
............>>...>>..>>..>>>.....<<<<<........<<..
.......<<<<....>>>>........>>........>.>>>>.......
....<<<<<<..........>>>>>>..........>>>>>......<<<
<<<<.......>>>>>>>.......>>...>>>>>>>>>>.>>....<..
<<.<..............<........<<..<.<<...............
...................................>>.>..>>.......
.>..............>.>>...>.....<<.<<.<<<....>>>.>>.>
>.......

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xir Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): R111 K116 Q118 L120 R136 Q146 Q149 K151 H153 Y155 Q157 S158 R165 D203 I204
• Binding residue (residue number reindexed from 1): R92 K97 Q99 L101 R117 Q127 Q130 K132 H134 Y136 Q138 S139 R146 D184 I185

Gene Ontology

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 15 23:32:38 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 = '6xir', asym_id = 'r', bs = 'BS01', title = 'Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6xir', asym_id='r', bs='BS01', title='Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.')

   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 = '6xir', asym_id = 'r'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='6xir', asym_id='r')

    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>