Structure of PDB 8s1p Chain C Binding Site BS01

Receptor Information

>8s1p Chain C (length=273) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

AIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTV
RHQGGGHKRQYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEK
RYILAPKGIQVGTEIMSGPEADIKVGNALPLINIPVGTVVHNIELKPGKG
GQLVRSAGTSAQVLGKEGKYVLVRLNSGEVRMILSACRASIGQVGNEQHE
LINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAPIGRKSPMSPWG
KPTLGFKTRKKKNKSDKFIVRRR

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): K7 P8 T9 S10 N11 G12 R13 R14 K31 L37 H38 K39 K40 G41 G42 R43 N44 N45 Q46 G47 K48 L49 T50 V51 R52 H53 Q54 G56 H58 K59 R60 Q61 Y62 R63 I74 Y83 P85 N86 R87 D98 G99 E100 K101 L146 K147 G149 K150 Q153 L154 V155 R156 S157 A158 G159 T160 K170 Y171 L176 N177 S178 E180 R182 E198 H200 E201 N204 I205 G206 K207 A208 G209 R210 S211 R212 W213 R217 P218 T219 V220 R221 G222 S223 V224 M225 N226 P227 N228 D229 H230 H232 G234 G235 E236 G237 R238 P240 I241 G242 R243 K244 P246 M247 S248 P249 W250 T254 L255 G256 F257 K258 T259 R260 K263 K265 S266 K268 R273 R274
• Binding residue (residue number reindexed from 1): K6 P7 T8 S9 N10 G11 R12 R13 K30 L36 H37 K38 K39 G40 G41 R42 N43 N44 Q45 G46 K47 L48 T49 V50 R51 H52 Q53 G55 H57 K58 R59 Q60 Y61 R62 I73 Y82 P84 N85 R86 D97 G98 E99 K100 L145 K146 G148 K149 Q152 L153 V154 R155 S156 A157 G158 T159 K169 Y170 L175 N176 S177 E179 R181 E197 H199 E200 N203 I204 G205 K206 A207 G208 R209 S210 R211 W212 R216 P217 T218 V219 R220 G221 S222 V223 M224 N225 P226 N227 D228 H229 H231 G233 G234 E235 G236 R237 P239 I240 G241 R242 K243 P245 M246 S247 P248 W249 T253 L254 G255 F256 K257 T258 R259 K262 K264 S265 K267 R272 R273

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• 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: P42919|RL2_BACSU Large ribosomal subunit protein uL2 (Gene Name=rplB)