Structure of PDB 5aj4 Chain B2 Binding Site BS01

Receptor Information
>5aj4 Chain B2 (length=178) Species: 9823 (Sus scrofa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LEEFFDDPKNWGEEKVKSGASWTCQQLRNKSNEDLHKLWYVLLKERNMLL
TLEQEAKRQRLPMPSPERLEKVVDSMDALDKVVQEREDALRLLQTGQEKA
RPGAWRRDIFGRIIWHKFKQWPIPWYLNKKYNRKRFFAMPYVERFVRMRI
EKQARIKARKRSLERKKEKFLQEKFPHL
Ligand information
>5aj4 Chain BA (length=1515) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
accaaagcuagcucaacaacaaauacaaaaauacaccaaaauaaaauaaa
acauucaccuaacauuaaaguauaggagauagaaauuuuuauccugacgc
uauagagauaguaccguaagggaaagaugaaagaauaaaaguaaaaaaaa
gcaaagauuaccccuucuaccuuuugcauaaugguuuaaccagaaaaaau
cuaacaaagagaacuuuagcuagauaccccgaaaccagacgagcuaccca
ugagcaguuuaaaagaaccaacucaucuauguggcaaaauagugagaaga
cuuguagguagaggugaaaagccuaacgagccuggugauagcugguuguc
cgagaaagaauuuuaguucaaccuuaaaaauaccccaaaaacccuaaauu
ccaauguauuuuuaagagauagucuaaaaagguacagcuuuuuagaaacg
gauacaaccuugacuagagaguaaaucuuaauacuaccauaguaggccua
aaagcagccaucaauugagaaagcguuaaagcucaacaaauucaccaaca
uaaucccaaaaacuaauaacaaacuccuagcccaauaccggacuaaucua
uugaaacauagaagcaauaauguuaauaugaguaacaagaagccuuucuc
cucgcacacgcuuacaucaguaacuaauaauauacugauaauuaacaacc
aauaaaccaaaacaacacuaaaacguuuauuaauuacauuguuaacccaa
cacaggagugcaccaaggaaagauuaaaagaaguaaaaggaacucggcaa
acacaaaccccgccuguuuaccaaaaacaucaccucuagcauuacuagua
uuagaggcaaugccugcccagugacaaguuuaacggccgcgguacugacc
gugcaaagguagcauaaucacuuguucuccaaauaaggacuuguaugaau
ggccacacgaggguuuuacugucucuuacuuccaaucagugaaauuaacc
uucccgugaagaggcgggaauaaaaaaauaagacgagaagacccuaugga
gcuuuaauuaacuauuccaaaaguucuuaacauggacuagcaauuucggu
uggggugaccucggaguacaaaaaacccuccgagugauuuuaaucuagac
aaaccagucaaaauaaucacuuauugauccaaaauuuugaucaacggaac
aaguuacccuagggauaacagcgcaauccuguucuagaguuccuaucgac
aauaggguuuacgaccucgauguuggaucaggacacccaaauggugcagc
cgcuauuaaagguucguuuguucaacgauuaaaguccuacgugaucugag
uucagaccggagcaauccaggucgguuucuaucuauuauaaauuucuccc
aguacgaaaggacaagagaaaugggaccaaccucacaaacgcgucucaga
gauaauuaaugauuuaaucuuaaccuaauuaacucauaauaaauccagcc
cuagaacagggcaca
<<........<<<<.................................<..
....>.................<<.....>>..............>>.>>
.............<<....>>...................>>........
...<<<.......>>>...<.<........>.>..<<<<<........<<
<<<.<..<<....>>...>.>>>>>..<<.<..<<<<<.<.....<<<.<
<<<<..<<<......>>>...<<<<.<<<<........>>>>>>>>....
>>>>>.>>>...<<<.....>>>......>.>>>>...>..>.>>..<<<
<<.....<<<<....>>>>...<<<<<<<<<<<.....<<........>>
.....>>>>>>>>>>>......<<<<<<<<<......>>>>>>>>>...<
<......>>....<<<<.<<<..................<....<<<...
......>>>....>.......<<<......>>>.................
.......................>>>>>>>........>>>>>...<<<<
<......>>>>>.........>>>>>.<......<<..<<<<..>>>><<
<<.<<<<........<<<<<....<<....>>..>>>>>......<<<..
<<<<<<<.................>>>>>>>.......>>>.....<<..
....>>.>>>>....>>>>..<<<<....<<<<<<<.<<...........
....<<<<<<<<..<<<.........>>>...<<<<<<............
.>>>>>>...<<<<.<<<..<<<<<..>>>..>>>>><<<<<<....>>>
>>>........<...........<<<<<.......>>>>>.....>....
>>>.>..>>.>>>>>>......>>.>>>>>>>.>>>>.>>.....>..(.
.<<<<<.......)>>>>>.......<<<.<<<.<<......<<<<.<<<
<<<..<<<<..<<<.<<<<.<<<..>>>....>>>>.>>>.>>>>..<<<
<.....>>>><<<<<<...........>>>>>>.<<<<....<<...<<<
......>>>...>>.>>>>..........<<<<..>>>>...........
.>>>>..>>>>>>.......<<<..<.<<<<<<...<<.......>>...
>>>>>>...>.>>.>.......<<<<<.<<<<<<..<<.<<<<<<.....
.>>>>>>...>>.<<<<<.....>>>>>.....>>>>>..>...>>>.>>
....<<<<<<<....>>>.>>>>....>>..>>>>>>.<<.<<<<<<<..
...............>>>>>>><<<<<...............>>>>>.<<
<...<<<<.................>>>>...>>>.>>.........<<<
<.......>>>>...
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5aj4 The complete structure of the 55S mammalian mitochondrial ribosome.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		K122 R123 R125 R166 I174 K182 K184 P187 I188 Y191 L192 N193 K194 N197 R198 K199 R200 F202 M204 R224 K232 K234
Binding residue
(residue number reindexed from 1)		K57 R58 R60 R101 I109 K117 K119 P122 I123 Y126 L127 N128 K129 N132 R133 K134 R135 F137 M139 R159 K167 K169
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Thu Mar 13 11:28:30 2025

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 = '5aj4', asym_id = 'B2', bs = 'BS01', title = 'The complete structure of the 55S mammalian mitochondrial ribosome.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5aj4', asym_id='B2', bs='BS01', title='The complete structure of the 55S mammalian mitochondrial 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 = '0003735,0005761,0006412', uniprot = '', pdbid = '5aj4', asym_id = 'B2'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005761,0006412', uniprot='', pdbid='5aj4', asym_id='B2')
    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>