Structure of PDB 8v9l Chain L Binding Site BS01

Receptor Information

>8v9l Chain L (length=146) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

PTYTPKAGDTTRSWYVIDASDVVLGRLASAAATLLRGKHKPTFTPNVDGG
DFVIVINADKIAVSGDKLTKKFAYRHSGYPGGLRKRTIGELLEKHPTRVV
ENAIIGMLPHNKLGRQIQKKLKVYAGPDHPHAAQQPIPFEIKQVAQ

Ligand information

>8v9l Chain A (length=3073)

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
acuaaccauccgcaugggaccuucguugguaguagucaagcgauggggug
acgcaggaagguagccguaccggucagugguaauaccgggguaagccugu
agggagucagauagguaaauccgucuggcauauauccugagaggugaugc
auagccgagugaggcgaauucggugauccuaugcugccgagaaaagccuc
uagcgaggacauacacggcccguaccccaaaccaacacagguggucaggu
agagaauacuaaggcguacgagugaacuaugguuaaggaacucggcaaaa
ugcccccguaacuucgggagaagggggacccacauggcguguaagccuuu
acggcccaagcgugaguggguggcacaaaccagugagaagcgacuguuua
cuaaaaacacagguccgugcgaagucgcaagacgauguauacggacugac
gccugcccggugcuggaagguuaagaggacccguuaacucccuuuggggg
ugaagcggagaauuuaagccccaguaaacggcggugguaacuauaaccau
ccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaaugg
cguaacgacuucucaacugucucaaccauagacucggcgaaauugcacua
cgaguaaagaugcucguuacgcgcggcaggacgaaaagaccccgggaccu
ucacuacaacuugguauuggugcucgauacgguuuguguaggauaggugg
gagacugugaagcucacacgccaguguggguggagucguuguugaaauac
cacucugaucguauugggccucuaaccucggaccguauauccgguucagg
gacagugccugguggguaguuuaacuggggcgguugccuccuaaaaugua
acggaggcgcccaaagguucccucaaccuggacggcaaucagguguugag
uguaagugcacaagggagcuugacugcgagacggacaugucgagcaggga
cgaaagucgggacuagugauccggcaccucugaguggaaggggugucgcu
caacggauaaaagguaccccggggauaacaggcugaucuuccccaagagu
ccauaucgacgggaugguuuggcaccucgaugucggcucgucgcauccug
gggcuggagcaggucccaaggguugggcuguucgcccauuaaagcggcac
gcgagcuggguuuagaacgucgugagacaguucggucucuauccgccgcg
cgcgucagaagcuugaggaaaccugucccuaguacgagaggaccgggacg
gacgaaccucugguauaccaguugucccaccaggggcacggcuggauagc
cacguucggacaggauaaccgcugaaagcaucuaagcgggaaaccucuuc
caagaccaggcuucucacccucuaggagggauaaggccccccgcagacca
cgggauugauagaccagaccuggaagccuaguaauaggugcagggaacug
gcacuaaccggccgaaaacuuac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8v9l A new family of bacterial ribosome hibernation factors
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): P2 T3 P6 D22 G26 R27 S30 R37 K39 N47 S65 K68 K72 Y75 R76 H77 S78 Y80 G82 L84 R85 R87 R99 E102 A104 G107 M108 N112 K113 L114 R116 K120 H132 A134 Q135 Q144 Q147
• Binding residue (residue number reindexed from 1): P1 T2 P5 D21 G25 R26 S29 R36 K38 N46 S64 K67 K71 Y74 R75 H76 S77 Y79 G81 L83 R84 R86 R98 E101 A103 G106 M107 N111 K112 L113 R115 K119 H131 A133 Q134 Q143 Q146

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8v9l, PDBe:8v9l, PDBj:8v9l
• PDBsum: 8v9l
• PubMed: 38355796
• UniProt: A0QSP8|RL13_MYCS2 Large ribosomal subunit protein uL13 (Gene Name=rplM)