Structure of PDB 5hd1 Chain 1n Binding Site BS01

Receptor Information
>5hd1 Chain 1n (length=60) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKG
QLPGVRKASW
Ligand information
>5hd1 Chain 1a (length=1477) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga
caugcaagucgugcgggccgcggguccguggucagcggcggacgggugag
uaacgcgugggugaccuacccggaagagggggacaacccggggaaacucg
ggcuaaucccccauguggacccgccccuugggguguguccaaagggcuuu
gcccgcuuccggaugggcccgcgucccaucagcuaguuggugggguaaug
gcccaccaaggcgacgacggguagccggucugagaggauggccggccaca
ggggcacugagacacgggccccacuccucgggaggcagcaguuaggaauc
uuccgcaaugggcgcaagccugacggagcgacgccgcuuggaggaagaag
cccuucgggguguaaacuccugaacccgggacgaaacccccgacgagggg
acugacgguaccgggguaauagcgccggccaacuccgugccagcagccgc
gguaauacggagggcgcgagcguuacccggauucacugggcguaaagggc
guguaggcggccuggggcgucccaugugaaagaccacggcucaaccgugg
gggagcgugggauacgcucaggcuagacggugggagagggugguggaauu
cccggaguagcggugaaaugcgcagauaccgggaggaacgccgauggcga
aggcagccaccugguccacccgugacgcugaggcgcgaaagcguggggag
caaaccggauuagauacccggguaguccacgcccuaaacgaugcgcgcua
ggucucugggucuccugggggccgaagcuaacgcguuaagcgcgccgccu
ggggaguacggccgcaaggcugaaacucaaaggaauugacgggggcccgc
acaagcgguggagcaugugguuuaauucgaagcaacgcgaagaaccuuac
caggccuugacaugcuagggaacccgggugaaagccugggccuagcacag
gugcugcauggccgucgucagcucgugccgugagguguuggguuaagucc
cgcaacgagcgcaacccccgccguuaguugccagcgguucggccgggcac
ucuaacgggacugcccgcgaaagcgggaggaaggaggggacgacgucugg
ucagcauggcccuuacggccugggcgacacacgugcuacaaugcccacua
caaagcgaugccacccggcaacggggagcuaaucgcaaaaaggugggccc
aguucggauuggggucugcaacccgaccccaugaagccggaaucgcuagu
aaucgcggaucagccaugccgcggugaauacguucccgggccuuguacac
accgcccgucacgccaugggagcgggcucuacccgaagucgccgggagcc
uacgggcaggcgccgaggguagggcccgugacuggggcggucguaacaag
guagcuguaccggaaggugcggcugga
.....<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<..<..<<
<.<<<..<<<..<<.<<<<<<<....>>>>>>>.>>>>>......<<...
....<<<<<<<<..<<...<<<<<<<.<<<<<...<<<<<<......>>>
>>.>...>>>>>....<<<<.<<<<<....>>>>>.>>>>...<<<<...
>>>>.>>>>>>>..>>>>>>>>>><<<....<<<..<<<<<<<<......
.>>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>>>.>>.
<<<<<.<.........>>>>>>.<<<<...>>>>...>>>>>>>......
..<<<....<<<<....>>>>..>>>..>>.>>>>>>..<<<<......<
<<<....>>>>.....>>>>....<<<<<........<<<<.....>>>>
..........>>>>>......<<<<<(((...<<<<<.....<<.)))>>
.......>>>>>>>>>>..>>>>>>>>>..........<<<((.....<<
<<...<<<.<<<<<<<.<<<<<<<<<<......<<<<<<.....>>>>>>
....>>>>>>>>..>>>>>>>>>...<<<<<<<<...<<<<<<<....<<
<<<<<.<..<<<......>>>.....>.>>>>>>>...........<<..
..>>.>>>>>>>..>>>>>.>>>...>>>...>>>>....<<<<<<...<
<...<<<<.<.....>.>>>>...>>>>>>>>..........<<<<<<..
<<<<<<<<<<...>>>>>>>>>>...<<..))>>.....>>>>>>.>>>.
<<<......<<<<....>>>>....>>>..)))).]<<<<<.<<<<<<<.
<<.<<<<<<..<<<<<<<<<<......<<........>>..........<
<<<<<<......<<<<<<<...<<<<<<<....>>>>>>>>>>>>>>.<<
<.<<<..<<<<<<.......<<<<<<<<<....>>>..<<<<......>>
>>..>>>>>>.....<<<<.<<<<<<<..<<<..<<<.....>>>>>>..
.>>>>>>>.....<<<<<....>>>>>........>>>>.........>>
>...>>>>>>>>>...>>>>>>>...>>.>>>>>>>>.....<<<<<<<.
....<<<..<<..<<<<....>>>>..>>....>>>.....>>>>>>>..
....<....<<<<<<<........>>>>>>>....>.....>>>>>>...
.<<<<<<<..........>>>>>>>......>>...>>>>>>>>>>.>>.
...<..<<.<.<<<<.<<<..<<<<<<<<<<<<<...<.<<<<....<<<
....>>>.>>>>.>..>>>>>>>>>>>>>..>>>.>>>>>.>>...>...
..<<<<<<<<<....>>>>>>>>>...
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5hd1 Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		A2 R3 K4 A5 E8 K9 K15 F16 K17 V18 R19 Y21 T22 R31 S32 Y34 R35 R41 I42 R45 S60 W61
Binding residue
(residue number reindexed from 1)		A1 R2 K3 A4 E7 K8 K14 F15 K16 V17 R18 Y20 T21 R30 S31 Y33 R34 R40 I41 R44 S59 W60
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Nov 15 17:48:05 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 = '5hd1', asym_id = '1n', bs = 'BS01', title = 'Structures of proline-rich peptides bound to the...common mechanism of protein synthesis inhibition.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5hd1', asym_id='1n', bs='BS01', title='Structures of proline-rich peptides bound to the...common mechanism of protein synthesis inhibition.')
   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 = '5hd1', asym_id = '1n'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='5hd1', asym_id='1n')
    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>