Structure of PDB 8why Chain X Binding Site BS01

Receptor Information

>8why Chain X (length=93) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

MKVHKGDTVLVISGKDKGAKGKVLVAYPDRNKVLVEGVNRIKKHTGIVTQ
EAPIHVSNVMVVDSDGKPTRVGYRIDDETGKKVRIAKTNGKDI

Ligand information

>8why Chain A (length=3017)

aaguguuuaagggcgcaugguggaugccuuggcacugggagccgaugaag
gacguaggaggcugcgauaagccucggggagcugucaaccgagcguugau
ccgaggauguccgaauggggaaacccggcacgagugaugucgugucacca
ggcgcugaauauauaggcgucuggggggaacgcggggaagugaaacaucu
caguacccguaggaagagaaaacaaaaugugauuccgugaguaguggcga
gcgaaagcggaggauggcuaaaccguaugcaugugauaccggguaggggu
ugugugugcgggguugugggaccuaucuuuccggcucuaccuggcuggag
ggcagugagaaaauguugugguuagcggaaauggcuugggauggccugcc
guagacggugagagcccgguacgugaaaacccgacgucugucuugauggu
guucccgaguagcagcgggcccguggaaucugcugugaaucugccgggac
cacccgguaagccugaauacuucccagugaccgauagcggauuaguaccg
ugagggaauggugaaaaguaccccgggaggggagugaaagaguaccugaa
accgugcgcuuacaauccgucagagcccucgacgugucguggggugaugg
cgugccuuuugaagaaugagccugcgagucagggacaugucgcgagguua
acccgggugggguagccgcagcgaaagcgagucugaauagggcguaucca
cacaagagugugugguguagugguguguucuggacccgaagcggagugau
cuacccauggccagggugaagcgcggguaagaccgcguggaggcccgaac
ccacuuagguugaagacugaggggaugagcuguggguaggggugaaaggc
caaucaaacuccgugauagcugguucuccccgaaaugcauuuaggugcag
cgucgcauguuucuugccggagguagagcuacuggauggccgaugggccc
cacaggguuacugacgucagccaaacuccgaaugccgguaaguccaagag
ugcggcagugagacggcgggggauaagcuccgugcgucgagagggaaaca
gcccagaucgccggcuaaggccccuaagcgugugcuaaguggaaaaggau
gugcagucgcgaagacaacuggucaagugauugugcgccgauaauguagc
ggggcucaagcacaccgccgaagccgcggcagccaacguguuggcugggu
aggggagcguccugcauccggugaagccgccgagugaucgagugguggag
ggugugggagugagaaugcaggcaugaguagcgauuaggcaagugagaac
cuugcccgccgaaagaccaaggguuccugggccaggccaguccgcccagg
gugagucgggaccuaaggcgaggccgacaggcguagucgauggacaacgg
guugauauucccguacccguguaugugcguccaugaugaaucagcgguac
uaaccauccugcaugggaccuucguugguaguagucaagcgaugggguga
cgcaggaagguagccguaccggucagugguaauaccgggguaagccugua
gggagucagauagguaaauccgucuggcauauauccugagaggugaugca
uagccgagugaggcgaauucggugauccuaugcugccgagaaaagccucu
agcgaggacauacacggcccguaccccaaaccaacacagguggucaggua
gagaauacuaaggcguacgagugaacuaugguuaaggaacucggcaaaau
gcccccguaacuucgggagaagggggacccacauggcguguaagccuuua
cggcccaagcgugaguggguggcacaaaccagugagaagcgacuguuuac
uaaaaacacagguccgugcgaagucgcaagacgauguauacggacugacg
ccugcccggugcuggaagguuaagaggacccguuaacucccuuugggggu
gaagcggagaauuuaagccccaguaaacggcggugguaacuauaaccauc
cuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaauggc
guaacgacuucucaacugucucaaccauagacucggcgaaauugcacuac
gaguaaagaugcucguuacgcgcggcaggacgaaaagaccccgggaccuu
cacuacaacuugguauuggugcucgauacgguuuguguaggauagguggg
agacugugaagcucacacgccaguguggguggagucguuguugaaauacc
acucugaucguauugggccucuaaccucggaccguauauccgguucaggg
acagugccugguggguaguuuaacuggggcgguugccuccuaaaauguaa
cggaggcgcccaaagguucccucaaccuggacggcaaucagguguugagu
guaagugcacaagggagcuugacugcgagacggacaugucgagcagggac
gaaagucgggacuagugauccggcaccucugaguggaaggggugucgcuc
aacggauaaaagguaccccggggauaacaggcugaucuuccccaagagau
cgacgggaugguuuggcaccucgaugucggcucgucgcauccuggggcug
gagcaggucccaaggguugggcuguucgcccauuaaagcggcacgcgagc
uggguuuagaacgucgugagacaguucggucucuauccgccgcgcgcguc
agaagcuugaggaaaccugucccuaguacgagaggaccgggacggacgaa
ccucugguauaccaguugucccaccaggggcacggcuggauagccacguu
cggacaggauaaccgcugaaagcaucuaagcgggaaaccucuuccaagac
caggcuucucacccucuaggagggauaaggccccccgcagaccacgggau
ugauagaccagaccuggaagccuaguaauaggugcagggaacuggcacua
accggccgaaaacuuac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8why Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): K2 H4 G14 K15 A26 I41 K42 K43 H44 T45 H67 S69 N70 K79 P80 R82 Y85 K93 K94 K99
• Binding residue (residue number reindexed from 1): K2 H4 G14 K15 A26 I41 K42 K43 H44 T45 H55 S57 N58 K67 P68 R70 Y73 K81 K82 K87

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8why, PDBe:8why, PDBj:8why
• PDBsum: 8why
• PubMed: 38245551
• UniProt: A0QSG0|RL24_MYCS2 Large ribosomal subunit protein uL24 (Gene Name=rplX)