Structure of PDB 8s1p Chain J Binding Site BS01

Receptor Information

>8s1p Chain J (length=143) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

TTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTG
DHVIIINAEKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKML
ELAIKGMLPKGSLGRQMFKKLNVYRGSEHPHEAQKPEVYELRG

Ligand information

>8s1p Chain A (length=2733)

uuaaguuagaaagggcgcacgguggaugccuuggcacuaggagccgauga
aggacgggacgaacaccgauaugcuucggggagcuguaagcaagcuuuga
uccggagauuuccgaauggggaaacccaccacucguaauggagugguauc
cauaucugaauucauaggauaugagaaggcagacccggggaacugaaaca
ucuaaguacccggaggaagagaaagcaaaugcgauucccugaguagcggc
gagcgaaacgggaucagcccaaaccaagaggcuugccucuugggguugua
ggacacucuguaggaguuacaaaggaacgagguagaugaagaggucugga
aaggcccgccauaggagguaacagcccuguagucaaaacuucguucucuc
cugaguggauccugaguacggcggaacacgugaaauuccgucggaauccg
ggaggaccaucucccaaggcuaaauacucccuagugaccgauagugaacc
aguaccgugagggaaaggugaaaagcaccccggaaggggagugaaagaga
uccugaaaccgugugccuacaaguagucagagcccguuaacgggugaugg
cgugccuuuuguagaaugaaccggcgaguuacgaucucgugcaagguuaa
gcagaagaugcggagccgcagcgaaagcgagucugaauagggcgcaagua
cguggucguagacccgaaaccaggugaucuacccauguccagggugaagu
uaauggaggcccgaacccacgcacguugaaaagugcggggaugaggugug
gguaggggugaaaugccaaucgaaccuggagauagcugguucucuccgaa
auagcuuuagggcuagccucaagguaagagucuuggagguagagcacuga
uuggacuagggguuaccgaauucagucaaacuccgaaugccaaugacuua
uccuugggagucagacugcgagugauaagauccguagucgaaagggaaac
agcccagaccgccagcuaaggucccaaaguauacguuaaguggaaaagga
uguggaguugcuuagacaaucgagugacucugcgccgaaaauguaccggg
gcuaaacguaucaccgaagcugcggacuguucgaacagugguaggagagc
guucuaagggcugugaagccagaccggaaggacugguggagcgcuuagaa
gugagaaugccgguaugaguagcgaaagaggggugagaauccccuccacc
gaaugccuaagguuuccugaggaaggcucguccgcucaggguuagucggg
accuaagccgaggccgaaaggcguaggcgauggacaacagguugauauuc
cuguaccaccuccucaccauuugagcaauggggggacgcaggaggauagg
guaagcgcgguauuggauauccgcguccaagcaguuaggcugggaaauag
gcaaauccguuucccaaaggcugagcugugauggcgagcgcgaaguuccu
gauuccacacugccaagaaaagccucuagcgaggugagaggugcccguac
cgcaaaccgacacagguaggcgaggagagaauccuaaggugaucgagaga
acucucguuaaggaacucggcaaaaugaccccguaacuucgggagaaggg
gugcucuguagggugcaagcccgagagagccgcagugaauaggcccaggc
gacuguuuagcaaaaacacaggucucugcgaagccguaaggcgaaguaua
ggggcugacgccugcccggugcuggaagguuaagaggagcgcuuagcgua
agcgaaggugcgaauugaagccccaguaaacggcggccgcgguccuaagg
uagcgaaauuccuugucggguaaguuccgacccgcacgaaaggcgcaacg
aucugggcacugucucaacgagagacucggugaaauuauaguaccuguga
agaugcagguuacccgcgacaggacggaaagaccccguggagcuuuacug
cagccugauauugaauguugguaauugaccuucuaacccgccgcccuuau
cgggcggggagacagugucaggugggcaguuugacuggggcggucgccuc
cuaaaagguaacggaggcgcccaaagguucccucagaaugguuggaaauc
auucgcagaguguaaaggcacaagggagcuugacugcgagaccuacaagu
cgagcagggacgaaagucgggcuuagugauccggugguuccgcauggaag
ggccaucgcucaacggauaaaagcuaccccggggauaacaggcuuaucuc
ccccaagaguccacaucgacggggagguuuggcaccucgaugucggcuca
ucgcauccuggggcuguagucggucccaaggguugggcuguucgcccauu
aaagcgguacgcgagcuggguucagaacgucgugagacaguucggucccu
auccgucgcgggcgcaggaaauuugagaggagcuguccuuaguacgagag
gaccgggauggacgcaccgcugguguaccaguuguucugccaagggcauc
gcuggguagcuaugugcggacgggauaagugcugaaagcaucuaagcaug
aagccccccucaagaugagauuucccauuccgcaaggaaguaagaucccu
gaaagaugaucagguugauaggucugagguggaaguguggcgacacaugg
agcugacagauacuaaucgaucgaggacuuaac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8s1p A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis.
• Resolution: 1.96 Å
• Binding residue (original residue number in PDB): T4 M6 N8 W16 T25 G27 R28 S31 R38 K40 H48 H54 T66 K68 K69 K73 Y76 R77 H78 T79 H81 P82 G83 L85 R88 K100 E103 A105 G108 M109 K112 S114 L115 R117 K121 H133 A135 Q136 K137 G145
• Binding residue (residue number reindexed from 1): T2 M4 N6 W14 T23 G25 R26 S29 R36 K38 H46 H52 T64 K66 K67 K71 Y74 R75 H76 T77 H79 P80 G81 L83 R86 K98 E101 A103 G106 M107 K110 S112 L113 R115 K119 H131 A133 Q134 K135 G143

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:8s1p, PDBe:8s1p, PDBj:8s1p
• PDBsum: 8s1p
• PubMed: 38811035
• UniProt: P70974|RL13_BACSU Large ribosomal subunit protein uL13 (Gene Name=rplM)