Structure of PDB 8s1p Chain N Binding Site BS01

Receptor Information

>8s1p Chain N (length=119) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

SYRKLGRTSAQRKAMLRDLTTDLIINERIETTETRAKELRSVVEKMITLG
KRGDLHARRQAAAYIRNEVANEENNQDALQKLFSDIATRYEERQGGYTRI
MKLGPRRGDGAPMAIIELV

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): S2 Y3 R4 K5 G7 R8 S10 Q12 R13 K14 L17 R18 D19 L20 D23 N27 I30 E31 T32 T33 T35 R36 K38 E39 R41 S42 E45 K46 T49 R53 L56 H57 R59 R60 Q61 A64 N68 E69 R94 Q95 G96 G97 T99 R100 K103 R107 R108 G109 D110 A112
• Binding residue (residue number reindexed from 1): S1 Y2 R3 K4 G6 R7 S9 Q11 R12 K13 L16 R17 D18 L19 D22 N26 I29 E30 T31 T32 T34 R35 K37 E38 R40 S41 E44 K45 T48 R52 L55 H56 R58 R59 Q60 A63 N67 E68 R93 Q94 G95 G96 T98 R99 K102 R106 R107 G108 D109 A111

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:8s1p, PDBe:8s1p, PDBj:8s1p
• PDBsum: 8s1p
• PubMed: 38811035
• UniProt: P20277|RL17_BACSU Large ribosomal subunit protein bL17 (Gene Name=rplQ)