Structure of PDB 8v9l Chain P Binding Site BS01

Receptor Information

>8v9l Chain P (length=118) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

PKPTKGPRLGGSSSHQSALLANLATSLFEHGRIKTTEPKARALRPYAEKL
ITHAKKGALHNRREVMKKIRDKDVVHTLFAEIGPFYADRNGGYTRIIKVE
NRKGDNAPMAVIELVREK

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 K3 P4 T5 K6 G7 P8 R9 S14 H16 I34 T36 P39 R42 R45 K50 T53 L60 H61 R64 M67 K68 K73 H77 R90 N91 G92 G93 R96 R103 G105 D106 N107
• Binding residue (residue number reindexed from 1): P1 K2 P3 T4 K5 G6 P7 R8 S13 H15 I33 T35 P38 R41 R44 K49 T52 L59 H60 R63 M66 K67 K72 H76 R89 N90 G91 G92 R95 R102 G104 D105 N106

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:8v9l, PDBe:8v9l, PDBj:8v9l
• PDBsum: 8v9l
• PubMed: 38355796
• UniProt: A0QSL9|RL17_MYCS2 Large ribosomal subunit protein bL17 (Gene Name=rplQ)