Structure of PDB 8why Chain T Binding Site BS01

Receptor Information

>8why Chain T (length=124) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

ARVKRALNAQKKRRTVLKASKGYRGQRSRLYRKAKEQQLHSLTYAYRDRR
ARKGEFRKLWISRINAAARANDITYNRLIQGLKAAGVEVDRKNLAELAVS
DPAAFTALVDVARAALPEDVNAPS

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): A2 R3 V4 K5 R6 A7 N9 A10 K12 K13 R14 R15 G23 Y24 R25 Q27 R28 R30 L31 R33 K34 K36 E37 Q38 H41 S42 Y45 A46 Y47 R48 D49 R50 R51 R53 K54 F57 R58 N66 R70 Y76 N77 R78 Q81 D91 R92 V121 N122 A123 P124
• Binding residue (residue number reindexed from 1): A1 R2 V3 K4 R5 A6 N8 A9 K11 K12 R13 R14 G22 Y23 R24 Q26 R27 R29 L30 R32 K33 K35 E36 Q37 H40 S41 Y44 A45 Y46 R47 D48 R49 R50 R52 K53 F56 R57 N65 R69 Y75 N76 R77 Q80 D90 R91 V120 N121 A122 P123

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8why, PDBe:8why, PDBj:8why
• PDBsum: 8why
• PubMed: 38245551
• UniProt: A0QYU6|RL20_MYCS2 Large ribosomal subunit protein bL20 (Gene Name=rplT)