Structure of PDB 1vy7 Chain DH Binding Site BS01

Receptor Information
>1vy7 Chain DH (length=174) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVR
VERPSDERRHKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGR
ALELTVGFSHPVVVEPPEGITFEVPEPTRVRVSGIDKQKVGQVAANIRAI
RKPSAYHEKGIYYAGEPVRLKPGK
Ligand information
>1vy7 Chain DA (length=2800) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccggggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgcaagcgcgcaaaguccgcggccguggacccgaaac
cgggcgagcuagcccuggccagggugaagcuggggugagacccaguggag
gcccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggag
ugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuu
agggucagccucaggcgcugacuggggccuguagagcacugauagggcua
gggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggu
ggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggg
aacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaa
ggauguggcgccgcguggcgccgcgccgaaaaugaucggggcuuaagccc
agcgccgaagcugcgggucuggggccccaggcgguaggggagcguucccg
augccgaugaaggccgacccgcgagggcggcuggagguaagggaagugcg
aaugccggcaugaguaacgauaaagagggugagaaucccucucgccguaa
gcccaaggguuccuacgcaauggucgucagcguaggguuaggcgggaccu
aaggugaagccgaaaggcguagccgaagggcagccgguuaauauuccggc
ccuucccgcaggugcgauggggggacgcucuaggcuagggggaccggagc
cauggacgagcccggccagaagcgcagggugggagguaggcaaauccgcc
ucccaacaagcucugcgugguggggaagcccgcgggugacaaccccccga
agccagggagccaagaaaagccucuaagcacaaccugcgggaacccguac
cgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcgggag
aacccucgccaaggaacucugcaaguuggccccguaacuucgggagaagg
ggugcucccuggggugaugagccccggggagccgcagugaacaggcucug
gcgacuguuuaccaaaaacacagcucucugcgaacucguaagaggaggua
uagggagcgacgcuugcccggugccggaaggucaaggggaggggugcaag
ccccgaaccgaagccccggugaacggcggccguaacuauaacgguccuaa
gguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaa
cgaccggagcgcugucucggcgagggacccggugaaauugaacuggccgu
gaagaugcggccuacccguggcaggacgaaaagaccccguggagcuuuac
ugcagccugguguuggcucuuggucgcgccugcguaggauaggugggagc
cugugaacccccgccuccgggugggggggaggcgccggugaaauaccacc
cuggcgcggcugggggccuaacccucggauggggggacagcgcuuggcgg
gcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcccaaa
gguccccucaggcgggacggaaauccgccggagagcgcaaggguagaagg
gggccugacugcgaggccugcaagccgagcaggggcgaaagccgggccua
gugaaccgguggucccguguggaagggccaucgaucaacggauaaaaguu
accccggggauaacaggcugaucucccccgagcguccacagcggcgggga
gguuuggcaccucgaugucggcucgucgcauccuggggcugaagaagguc
ccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguucag
aacgucgugagacaguucggucucuauccgccacgggcgcaggaggcuug
aggggggcucuuccuaguacgagaggaccggaagggacgcaccucugguu
ucccagcugucccuccaggggcauaagcuggguagccaugugcggaaggg
auaaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccuc
ccggcagccgguaaggacccgggaagaccacccgguggaugggccggggg
uguaagcgccgcgaggcguugagccgaccggucccaaucguccgaggucu
<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<......<<<
<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....>>>>
>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<<
.>>>>>>.>>...<<<<<<.....<......>......>>>>>.>.....
....<<....>>...<<<<<.....<<.....>>....>>>>>...<<<.
...<<<<<<<<.....>>>>>>>>......<<<<<<<<<<....<<...<
<<<<.<<<<.<<<...<<<<<......>>>>>((......<<<.....))
>>>...>>>...>>>>..>>>>>..>>>>>>>>>.>>>.....<<<<<<<
<<.......>>>>>>>>>......<<<<<..((((>>>>>..>>>.....
.>>.>>>>>>.>>...............<<....>>....>>........
.<<<<....>>>>..................>>>>>>>>>>>.......<
<<<<<<<<<<.>>>>>>>>>>>...<............>.<<<<<<....
<<<<<<<<<<<<<..<<<...<<<.....>>>...>>>...<<....>>.
.<<<<.....>>>>....<<..>>...>>>>>>>>>>>>>..<<.<...<
<<<<<.....<<<<<<<<<..<<<....<<<<<<......>>>>>>....
.>>>...<<<..<<<<........>>>>.>>>....>>>>>>>>>...<<
<.....>>>......>>>>>>......>.>>..<<<<<<....<<<<<..
..>>>>><<<<<<<<<.....<<<<<<<<<....<<...<<<<<<<<...
<<<<<<......>>>>.>>...>>>>>>>>..>>.....>>>>>>>>>..
...>>>>>>>.>>..<<<<<<<.<<......>>.>>>>>>>.....<<<.
.....>>>...<<<<.<<<...<<<(((.....<<<<<<...........
<<..<<<<<<<<<..>>>>>>>>>.>>..........)))......>>>>
>>.>>>...>>>>>>><<<<<<<..>>>>>>>....>>>>>>..<<<<<.
..<<<......<<<<<.<<<....>>>>>>>>...>>>..>>>>>.....
...>>>>>>.......<<.....<<<<<<.......>>>>>><<<<....
<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<.<<.
..<<<...<<<....>>>...>>>...>>...<<<<<........>>>>>
))<<<<<<<<<<<<<...<<<<....<<<<<.<<<..<<<<<.<<<<.<<
..[[[[...>>>>>><<<...<<<<<<<<<<<<<<<<.<<.....>>>>>
>>>>.....>>>>>>>>>..>>><...<<<<..>>>>.....>>>>>>..
.>>>..>>>>>.........>>>>...>>...>>>>>>>>>>>>>>>..>
>.....<<......>>>>>>>.<<<<<....>>>>>..>>>>..<<<<..
..<<<<<<<<.<<.........<.....<<<<<...............>>
>>><<<<<<<<<<<<.....>>>>>>>>>>>>............<<<<<<
<<<..<<<.........>>>..<<<<<<<.....<<<....>>>......
.>>>>>>>.<<<<<.<<<..<<<<<<<..<<<...<<...<<<<<....>
>>>>...>>...>>>>>>>>..>>>>><<<<<<.......>>>>>>....
....<...........<<<<<<.....>>>>>>.....>....>>>>>..
>>.>>>>>>>..>..>>.>>>>>>>>.>>>>>>...........<<<<<.
.......>>>>>..<<<<<<<<.<<<.........<<<<.<<<<<<..<<
<<<.<<<.<<<<<.<<<<<<<<<<<<<<<<...........<<<<<..<<
<......<<<<<<<<....>>>>>>>>...>>>............>>>>>
..>>>>>>>>>>>>>>>>...<<<<<....>>>>>....>>>>>.>>>..
>>>>>..<<<<.....>>>><<<<<<...........>>>>>>..<<...
<<<<<<<...<<<<<<.......>>>>>>.....<<...(((>>....>>
>>>>>...<<<<..<<<......>>>..>>>>.<<<....>>>.>>))).
......<<<<<<<.<<..))))..>>>>>>>>>.............>>>>
..>>>>>>.......<<<<...<<<<<<...<<.......>>...>>>>>
>....>>>.>.......<<<<<.<<<<<<..<<<<<<<<<......>>>>
>>..>>>.<<<<<.....>>>>>.....>>>>>..>...>>>.>>....<
<<<<<<....>>>.>>>>........>>>>>>>>>>>....<<<<<<<..
.<<<<..<<<<<<<...............>>>>>>>.<<<<<...<<<<.
..<<<<<<<<<<<]]]]>>>>>>...>>>>>...>>>>.>>>>>...<<<
....<<<<<...........>>>>>....>>>.>>>>.......>>>>>>
>.<<<.>>>.....<<<<<<<<<.......>>>>>....<<<<<<<<.<<
<....<<<<<....>>>>>...>>>..>>>>>.>>>...>>>>....>>>
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1vy7 A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.
Resolution2.8 Å
Binding residue
(original residue number in PDB)
S2 R3 I4 K62 S63 G66 L67 T70 K85 F109 S110 H111 K138 Q139 G142 Q143 R152 Y157 H158 K160 K172 K175
Binding residue
(residue number reindexed from 1)
S1 R2 I3 K61 S62 G65 L66 T69 K84 F108 S109 H110 K137 Q138 G141 Q142 R151 Y156 H157 K159 K171 K174
Gene Ontology
--> -->
 
 
UnboundLocalError
Python 3.6.8: /usr/bin/python3
Fri Nov 22 11:24:24 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 = '1vy7', asym_id = 'DH', bs = 'BS01', title = 'A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='1vy7', asym_id='DH', bs='BS01', title='A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the 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 = '1vy7', asym_id = 'DH'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412,0019843', uniprot='', pdbid='1vy7', asym_id='DH')
    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>