Structure of PDB 8v9k Chain I Binding Site BS01

Receptor Information

>8v9k Chain I (length=126) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

MAKADKATAVADIAEQFKASTATVVTEYRGLTVANLAELRRALGDSATYT
VAKNTLVKRAASEAGIEGLDELFAGPTAIAFVKGEAVDAAKAIKKFAKDN
KALVIKGGYMDGKALSVADVEKIADL

Ligand information

>8v9k Chain A (length=3081)

aaguguuuaagggcgcaugguggaugccuuggcacugggagccgaugaag
gacguaggaggcugcgauaagccucggggagcugucaaccgagcguugau
ccgaggauguccgaauggggaaacccggcacgagugaugucgugucacca
ggcgcugaauauauaggcgucuggggggaacgcggggaagugaaacaucu
caguacccguaggaagagaaaacaaaaugugauuccgugaguaguggcga
gcgaaagcggaggauggcuaaaccguaugcaugugauaccggguaggggu
ugugugugcgggguugugggaccuaucuuuccggcucuaccuggcuggag
ggcagugagaaaauguugugguuagcggaaauggcuugggauggccugcc
guagacggugagagcccgguacgugaaaacccgacgucugucuugauggu
guucccgaguagcagcgggcccguggaaucugcugugaaucugccgggac
cacccgguaagccugaauacuucccagugaccgauagcggauuaguaccg
ugagggaauggugaaaaguaccccgggaggggagugaaagaguaccugaa
accgugcgcuuacaauccgucagagcccucgacgugucguggggugaugg
cgugccuuuugaagaaugagccugcgagucagggacaugucgcgagguua
acccgggugggguagccgcagcgaaagcgagucugaauagggcguaucca
cacaagagugugugguguagugguguguucuggacccgaagcggagugau
cuacccauggccagggugaagcgcggguaagaccgcguggaggcccgaac
ccacuuagguugaagacugaggggaugagcuguggguaggggugaaaggc
caaucaaacuccgugauagcugguucuccccgaaaugcauuuaggugcag
cgucgcauguuucuugccggagguagagcuacuggauggccgaugggccc
cacaggguuacugacgucagccaaacuccgaaugccgguaaguccaagag
ugcggcagugggacggcgggggauaagcuccgugcgucgagagggaaaca
gcccagaucgccggcuaaggccccuaagcgugugcuaaguggaaaaggau
gugcagucgcgaagacaaccaggagguuggcuuagaagcagccacccuug
aaagagugcguaauagcucacuggucaagugauugugcgccgauaaugua
gcggggcucaagcacaccgccgaagccgcggcagccaacguguuggcugg
guaggggagcguccugcauccggugaagccgccgagugaucgaguggugg
agggugugggagugagaaugcaggcaugaguagcgauuaggcaagugaga
accuugcccgccgaaagaccaaggguuccugggccaggccaguccgccca
gggugagucgggaccuaaggcgaggccgacaggcguagucgauggacaac
ggguugauauucccguacccguguaugugcguccaugaugaaucagcggu
acuaaccauccaaaaggcugcaugggaccuucguugguaguagucaagcg
auggggugacgcaggaagguagccguaccggucagugguaauaccggggu
aagccuguagggagucagauagguaaauccgucuggcauauauccugaga
ggugaugcauagccgagugaggcgaauucggugauccuaugcugccgaga
aaagccucuagcgaggacauacacggcccguaccccaaaccaacacaggu
ggucagguagagaauacuaaggcguacgagugaacuaugguuaaggaacu
cggcaaaaugcccccguaacuucgggagaagggggacccacauggcgugu
aagccuuuacggcccaagcgugaguggguggcacaaaccagugagaagcg
acuguuuacuaaaaacacagguccgugcgaagucgcaagacgauguauac
ggacugacgccugcccggugcuggaagguuaagaggacccguuaacuccc
uuugggggugaagcggagaauuuaagccccaguaaacggcggugguaacu
auaaccauccuaagguagcgaaauuccuugucggguaaguuccgaccugc
acgaauggcguaacgacuucucaacugucucaaccauagacucggcgaaa
uugcacuacgaguaaagaugcucguuacgcgcggcaggacgaaaagaccc
cgggaccuucacuacaacuugguauuggugcucgauacgguuuguguagg
auaggugggagacugugaagcucacacgccaguguggguggagucguugu
ugaaauaccacucugaucguauugggccucuaaccucggaccguauaucc
gguucagggacagugccugguggguaguuuaacuggggcgguugccuccu
aaaauguaacggaggcgcccaaagguucccucaaccuggacggcaaucag
guguugaguguaagugcacaagggagcuugacugcgagacggacaugucg
agcagggacgaaagucgggacuagugauccggcaccucugaguggaaggg
gugucgcucaacggauaaaagguaccccggggauaacaggcugaucuucc
ccaagaguccauaucgacgggaugguuuggcaccucgaugucggcucguc
gcauccuggggcuggagcaggucccaaggguugggcuguucgcccauuaa
agcggcacgcgagcuggguuuagaacgucgugagacaguucggucucuau
ccgccgcgcgcgucagaagcuugaggaaaccugucccuaguacgagagga
ccgggacggacgaaccucugguauaccaguugucccaccaggggcacggc
uggauagccacguucggacaggauaaccgcugaaagcaucuaagcgggaa
accucuuccaagaccaggcuucucacccucuaggagggauaaggcccccc
gcagaccacgggauugauagaccagaccuggaagccuaguaauaggugca
gggaacuggcacuaaccggccgaaaacuuac

<<<<......<<<<<<<<<<<....{<<..<<<<<<<<<<<<<......<
<<<<<.[[.(((.>>>.....<<<<<<<..<<<)))..]].>>>.....>
>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<<
<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>>.
.....>>>>>.>.........<<.....>>..<<<<<<.....<<.....
>>....>>>>>>...<<<....<<<<<<<<<<.........(((((....
.>>>>>>>>>>......<<<<.<<.....<<<<<<<))))).>>>>>>><
<<<<<.......<<<<<<.<<<<.<<<.....<<<<......>>>>.((.
.....<<<.....))>>>...>>>...>>>>>>>>>>>>>>>>.....>.
>.>>>>.....<<<<<<<<.........>>>>>>>>......<<<<<..<
<<<>>>>>..>>>......>>.>>>>>>>.>>...............<<.
...>>....>>.........<<<<....>>>>.............}....
>>>>>>>>>>>.......<<<<..<<<<<<<<<..>>>>.>>>>>..>>>
>...<.<........>.>.<<<<<<....<<<.<<<<<<<<<<..<<<..
.<<<....>>>...>>>...<<....>>..<<<<.....>>>>....<<<
<<<<....>>>>>>>....>>>>>>>>>>>>>..<<.<..<<<<<<<...
..<<<<<<<<<..<<<....<<<<<<......>>>>>>.....>>>...<
<<.<<<<<........>>>>>>>>....>>>>>>>>>...<<<.....>>
>......>>>>>>...>..>.>>..<<<<<<....<<<<<....>>>>><
<<<<<<<<....<<<<<<<<.....<<<....<<<.<<<<....<<<<<.
.....>>>>.>....>>>>.>>>..>>.>.....>>>>>>>>.......>
>>>>>>.>>..<<<<<<<<<<......>>>>>>.>>>>....<<<.....
.>>>...<<<<.<<<...<<<(((.....<<<<<<...........<<..
<<<<<<<<<........<<<<<.<<<..<<<<.......>>>>..>>>..
.......<<......>>...>>>>>....>>>>>>>>>.>>.........
..)))......>>>>>>.>>>...>>>>>>><<<<<<<<..>>>>>>>>.
...>>>>>><.<<<<<<<<<<......<<<<<<<<....>>>.>>>>>..
.>>>>>>>>>>..>.....>>>>>><......<<.....<<<<<<.....
..>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....>>.>>>>
>>....((<<<<.<<...<<<...<<<....>>>...>>>...>>...<<
<<<........>>>>>))<<<<<<<<<<.......<<<<..<<<<<<<<.
.....<<<<.<<......>>.>>>>.....>>>>>>>>....>>>>.<<.
..<<<<<...<<<<..<<<..<<<<..<<<<<...((((...>>>>>.<<
..<<<<...<<<<<<<<<<<.<<.....>>>>>>>>>.....>>>>...>
>>>...>>...<<<......>>>.....>>>>...>>>...>>>>.....
...>>>>>..>>....>>>>>>>>>>>>>>..>>.....<<......>>>
>>>>.<<<<.....>>>>..>>>>..<<<<<...<<<<<<<<.<<.....
....<.....<<<<<.....<..>......>>>>><<<<<<...<<<<..
..<<<.....>>>....>>>>..>>>>>>............<<<<<<<<<
..<<<.........>>>..<<<<<<<.....<<<....>>>.......>>
>>>>>.<<<<<.<<<..<<<<<<<..<<<<.<<<....<<<<<.<<<<<<
...>>>>>>..>>>>>....>>>.>>>>>>>>>..>>>>><<<<<<....
...>>>>>>........<...........<<<<<.......>>>>>....
.>....>>>>>..>>.>>>>>>>..>..>>.>>>>>>>>>>>>>>>....
.>.((..<<<<<......))>>>>>..<<<<<<<<.<<<.<<......<<
<<<<<<<<..<<<<<.<<<.<<<<<.<<.<<<<<<<<<<<<<........
...<<<<<..<........<<<<<<<<....>>>>>>>>....>......
.......>>>>>..>>>>>>>>>>>>>.>>...<<<.<<<<<<......>
>>>>>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>><<<<<<.
..........>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>
>>.....<<.[.(((>>....>>>>>>>...<<<<..<<<<....>>>>.
.>>>>.<<<....>>>.>>)))]......<<<<<<<.<<..>>>>..>>>
>>>>>>.............>>>>..>>>>>>.......<<<<...<.<<<
<...<<.......>>...>>>>.>....>>>.>.......<<<<<.<<<<
<<..<<<<<<<<<......>>>>>>..>>>.<<<<<.....>>>>>....
.>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>....>>..>
>>>>>>>>>>....<<<<<<<...<<<<..<<<<<<<.............
..>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<))))>>>>>>..>>
>>>...>>>>.>>>>>...<<<.<..<<<<<...........>>>>>...
>>>>.>>>>.......>>>>>>>..<<<<<...>>>>>....<<<<.<<<
<.......>>>>.....<<<.<<<<.<<<....<<<<<....>>>>>...
>>>..>>>>..>>>...>>>>....>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8v9k A new family of bacterial ribosome hibernation factors
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): K3 K6 A7 Y28 R29 G30 T32 V33 R40 T50 V51 K53 N54 R59 G75 P76
• Binding residue (residue number reindexed from 1): K3 K6 A7 Y28 R29 G30 T32 V33 R40 T50 V51 K53 N54 R59 G75 P76

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8v9k, PDBe:8v9k, PDBj:8v9k
• PDBsum: 8v9k
• PubMed: 38355796
• UniProt: A0QS62|RL10_MYCS2 Large ribosomal subunit protein uL10 (Gene Name=rplJ)