Structure of PDB 8kab Chain P Binding Site BS01

Receptor Information
>8kab Chain P (length=126) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AHKPVGQNISEVRRNARLRRHARLRKKVAGTAEVPRLVVNRSARHIHVQL
VNDLNGTTLAAASSIEADVRAIDGDKKAHSVRVGQLIAERAKAAGVETVV
FDRGGYTYGGRIAALADAAREAGLKF
Ligand information
>8kab Chain A (length=3111) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
aaguguuuaagggcgcaugguggaugccuuggcacugggagccgaugaag
gacguaggaggcugcgauaagccucggggagcugucaaccgagcguugau
ccgaggauguccgaauggggaaacccggcacgagugaugucgugucacca
ggcgcugaauauauaggcgucuggggggaacgcggggaagugaaacaucu
caguacccguaggaagagaaaacaaaaugugauuccgugaguaguggcga
gcgaaagcggaggauggcuaaaccguaugcaugugauaccggguaggggu
ugugugugcgggguugugggaccuaucuuuccggcucuaccuggcuggag
ggcagugagaaaauguugugguuagcggaaauggcuugggauggccugcc
guagacggugagagcccgguacgugaaaacccgacgucugucuugauggu
guucccgaguagcagcgggcccguggaaucugcugugaaucugccgggac
cacccgguaagccugaauacuucccagugaccgauagcggauuaguaccg
ugagggaauggugaaaaguaccccgggaggggagugaaagaguaccugaa
accgugcgcuuacaauccgucagagcccucgacgugucguggggugaugg
cgugccuuuugaagaaugagccugcgagucagggacaugucgcgagguua
acccgggugggguagccgcagcgaaagcgagucugaauagggcguaucca
cacaagagugugugguguagugguguguucuggacccgaagcggagugau
cuacccauggccagggugaagcgcggguaagaccgcguggaggcccgaac
ccacuuagguugaagacugaggggaugagcuguggguaggggugaaaggc
caaucaaacuccgugauagcugguucuccccgaaaugcauuuaggugcag
cgucgcauguuucuugccggagguagagcuacuggauggccgaugggccc
cacaggguuacugacgucagccaaacuccgaaugccgguaaguccaagag
ugcggcagugagacggcgggggauaagcuccgugcgucgagagggaaaca
gcccagaucgccggcuaaggccccuaagcgugugcuaaguggaaaaggau
gugcagucgcgaagacaaccaggagguuggcuuagaagcagccacccuug
aaagagugcguaauagcucacuggucaagugauugugcgccgauaaugua
gcggggcucaagcacaccgccgaagccgcggcagccaacguguuggcugg
guaggggagcguccugcauccggugaagccgccgagugaucgaguggugg
agggugugggagugagaaugcaggcaugaguagcgauuaggcaagugaga
accuugcccgccgaaagaccaaggguuccugggccaggccaguccgccca
gggugagucgggaccuaaggcgaggccgacaggcguagucgauggacaac
ggguugauauucccguacccguguaugugcguccaugaugaaucagcggu
acuaaccauccaaaaccaccgugaccgcaccuuucgggguguggcguugg
uggggcugcaugggaccuucguugguaguagucaagcgauggggugacgc
aggaagguagccguaccggucagugguaauaccgggguaagccuguaggg
agucagauagguaaauccgucuggcauauauccugagaggugaugcauag
ccgagugaggcgaauucggugauccuaugcugccgagaaaagccucuagc
gaggacauacacggcccguaccccaaaccaacacagguggucagguagag
aauacuaaggcguacgagugaacuaugguuaaggaacucggcaaaaugcc
cccguaacuucgggagaagggggacccacauggcguguaagccuuuacgg
cccaagcgugaguggguggcacaaaccagugagaagcgacuguuuacuaa
aaacacagguccgugcgaagucgcaagacgauguauacggacugacgccu
gcccggugcuggaagguuaagaggacccguuaacucccuuugggggugaa
gcggagaauuuaagccccaguaaacggcggugguacauccuaagguagcg
aaauuccuugucggguaaguuccgaccugcacgaauggcguaacgacuuc
ucaacugucucaaccauagacucggcgaaauugcacuacgaguaaagaug
cucguuacgcgcggcaggacgaaaagaccccgggaccuucacuacaacuu
gguauuggugcucgauacgguuuguguaggauaggugggagacugugaag
cucacacgccaguguggguggagucguuguugaaauaccacucugaucgu
auugggccucuaaccucggaccguauauccgguucagggacagugccugg
uggguaguuuaacuggggcgguugccuccuaaaauguaacggaggcgccc
aaagguucccucaaccuggacggcaaucagguguugaguguaagugcaca
agggagcuugacugcgagacggacaugucgagcagggacgaaagucggga
cuagugauccggcaccucugaguggaaggggugucgcucaacggauaaaa
gguaccccggggauaacaggcugaucuuccccaagaguccauaucgacgg
gaugguuuggcaccucgaugucggcucgucgcauccuggggcuggagcag
gucccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguu
uagaacgucgugagacaguucggucucuauccgccgcgcgcgucagaagc
uugaggaaaccugucccuaguacgagaggaccgggacggacgaaccucug
guauaccaguugucccaccaggggcacggcuggauagccacguucggaca
ggauaaccgcugaaagcaucuaagcgggaaaccucuuccaagaccaggcu
ucucacccucuaggagggauaaggccccccgcagaccacgggauugauag
accagaccuggaagccuaguaauaggugcagggaacuggcacuaaccggc
cgaaaacuuac
<<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<<......<
<<<<<.[[.(((.>>>.....<<<<<<<..<<<)))..]].>>>.....>
>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<<
<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>>.
.....>>>>>.>.........<<.....>>..<<<<<<.....<<.....
>>....>>>>>>...<<<....<<<<<<<<<<.........(((((....
.>>>>>>>>>>......<<<<<.<<<<..<<<<<<<))))).>>>>>>><
<<<<<........<<<<<.<<<<.<<<.....<<<<......>>>>.((.
.....<<<.....))>>>...>>>...>>>>>>>>>.>>>>>>.>>>>..
>.>>>>.....<<<<<<<<.........>>>>>>>>......<<<<<..<
<<<>>>>>..>>>......>>.>>>>>>>.>>...............<<.
...>>....>>.........<<<<....>>>>..................
>>>>>>>>>>>.......<<<<..<<<<<<<<<..>>>>.>>>>>..>>>
>...<.<........>.>.<<<<<<....<<<.<<<<<<<<<<..<<<..
.<<<....>>>...>>>...<<....>>..<<<<.....>>>>....<<<
<<<<....>>>>>>>....>>>>>>>>>>>>>..<<.<..<<<<<<<...
..<<<<<<<<<..<<<....<<<<<<......>>>>>>.....>>>...<
<<.<<<<<........>>>>>>>>....>>>>>>>>>...<<<.....>>
>......>>>>>>...>..>.>>..<<<<<<....<<<<<....>>>>><
<<<<<<<<....<<<<<<<<.....<<<....<<<.<<<<......<<<.
.....>>>.......>>>>.>>>..>>.>.....>>>>>>>>.......>
>>>>>>.>>..<<<<<<<<<<......>>>>>>.>>>>....<<<.....
.>>>...<<<<.<<<...<<<(((.....<<<<<<...........<<..
<<<<<<<<<<.......<<<...<<<..<<<.........>>>..>>>..
.......<<......>>.....>>>...>>>>>>>>>>.>>.........
..)))......>>>>>>.>>>...>>>>>>><<<<<<<<..>>>>>>>>.
...>>>>>><.<<<<<<<<<<......<<<<<<<<....>>>.>>>>>..
.>>>>>>>>>>..>.....>>>>>><......<<.....<<<<<<.....
..>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....>>.>>>>
>>....((<<<<.<<...<<<...<<<....>>>...>>>...>>...<<
<<<........>>>>>))<<<<<<<<<<........<<.....<<.<<<.
.....<<<<.<<...<<<<<....<<<<<<<<....>>>>>>>>....>>
>>>...>>.>>>>.....>>>.>>.......>>..<<...<<<<<...<<
<<..<<<..<<<<..<<<<<...((((...>>>>>.<<..<<<<...<<<
<<<<<<<<.<<.....>>>>>>>>>.....>>>>...>>>>...>>...<
<<......>>>.....>>>>...>>>...>>>>........>>>>>..>>
....>>>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<...
..>>>>..>>>>..<<<<<...<<<<<<<<.<<.........<.....<<
<<<....<<..>>.....>>>>><<<<<<...<<<<....<<<.....>>
>....>>>>..>>>>>>............<<<<<<<<<..<<<.......
..>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.<<<<<.
.<<..<<<<<<<..<<<...<.....<<<<<.<<<<<.....>>>>>..>
>>>>......>..>>>>>>>>..>>>>.......................
...........<.<.......>.>............>>>>>..>>.>>>>
>>>..>..>>.>>>>>>>>>>>>>>>.....>.((..<<<<<......))
>>>>>..<<<<<<<<.<<<.<<......<<<<<<<<<<..<<<<<.<<<.
<<<<<.<<.<<<<<<<<<<<<<.........(.<<<<<..<<.......<
...<<<......>>>...>....>>.........)..>>>>>..>>>>>>
>>>>>>>.>>...<<<.<<<<<<......>>>>>>>>>....>>>>>.>>
>..>>>>>..<<<<.....>>>><<<<<<...........>>>>>>..<<
...<<<<<<<...<<<<<<.......>>>>>>.....<<.[.(((>>...
.>>>>>>>...<<<<..<<<<....>>>>..>>>>.<<<....>>>.>>)
))]......<<<<<<<.<<..>>>>..>>>>>>>>>.............>
>>>..>>>>>>.......<<<<.<.<.<<<<...<<.......>>...>>
>>.>...>>>>.>.......<<<<<.<<<<<<..<<<<<<<<<......>
>>>>>..>>>.<<<<<.....>>>>>.....>>>>>..>...>>>.>>..
..<<<<<<<....>>>.>>>>....>>..>>>>>>>>>>>....<<<<<<
<...<<<<..<<<<<<<...............>>>>>>>.<<<<<...<<
<<...<<<<<<<<<<<))))>>>>>>..>>>>>...>>>>.>>>>>...<
<<....<<<<<...........>>>>>....>>>.>>>>.......>>>>
>>>..<<<<<...>>>>>....<<<<.<<<<.......>>>>.....<<<
.<<<<.<<<....<<<<<....>>>>>...>>>..>>>>..>>>...>>>
>....>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8kab Cryo-EM structures reveal the molecular mechanism of HflX-mediated erythromycin resistance in mycobacteria.
Resolution3.3 Å
Binding residue
(original residue number in PDB)
R20 R21 R24 K27 F102 R104 Y109 R121 F127
Binding residue
(residue number reindexed from 1)
R19 R20 R23 K26 F101 R103 Y108 R120 F126
Gene Ontology
Molecular Function
GO:0008097 5S rRNA binding
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8kab, PDBe:8kab, PDBj:8kab
PDBsum8kab
PubMed39029461
UniProtA0QSG5

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