Structure of PDB 8s1p Chain Z Binding Site BS01

Receptor Information

>8s1p Chain Z (length=58) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

AKLEITLKRSVIGRPEDQRVTVRTLGLKKTNQTVVHEDNAAIRGMINKVS
HLVSVKEQ

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): R10 S11 I13 G14 R15 P16 E17 V21 T22 R24 T25 K29 K30 T31 N32 H37 A41 A42 I43 G45 M46 K49
• Binding residue (residue number reindexed from 1): R9 S10 I12 G13 R14 P15 E16 V20 T21 R23 T24 K28 K29 T30 N31 H36 A40 A41 I42 G44 M45 K48

Gene Ontology

Biological Process

• GO:0006412 translation

Cellular Component

• 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: P19947|RL30_BACSU Large ribosomal subunit protein uL30 (Gene Name=rpmD)