Structure of PDB 8why Chain 8 Binding Site BS01

Receptor Information

>8why Chain 8 (length=63) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

PKAKTHSGASKRFRRTGTGKIVRQKANRRHLLEHKPTKRTRRLDGRTTVS
AADNSRINKLLNG

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): P2 K3 K5 T6 H7 S8 K12 R13 R15 T17 G18 T19 K21 R24 K26 A27 N28 R29 R30 H31 L32 L33 E34 H35 T38 R40 R42 R43 L44 R47 A53 D54 R57
• Binding residue (residue number reindexed from 1): P1 K2 K4 T5 H6 S7 K11 R12 R14 T16 G17 T18 K20 R23 K25 A26 N27 R28 R29 H30 L31 L32 E33 H34 T37 R39 R41 R42 L43 R46 A52 D53 R56

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• 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: A0QYU7|RL35_MYCS2 Large ribosomal subunit protein bL35 (Gene Name=rpmI)