Structure of PDB 8s1u Chain G Binding Site BS01

Receptor Information

>8s1u Chain G (length=175) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

SRVGKKLLEIPSDVTVTLNDNNTVAVKGPKGELTRTFHPDMEIKVEDNVL
TVARPSDQKEHRALHGTTRSLLGNMVEGVSKGFERGLELVGVGYRASKSG
NKLVLNVGYSHPVEIVPEEGIEIEVPSQTKVVVKGTDKERVGAIAANIRA
VRSPEPYKGKGIRYEGEVVRRKEGK

Ligand information

>8s1u Chain A (length=2789)

uuaaguuagaaagggcgcacgguggaugccuuggcacuaggagccgauga
aggacgggacgaacaccgauaugcuucggggagcuguaagcaagcuuuga
uccggagauuuccgaauggggaaacccaccacucguaauggagugguauc
cauaucugaauucauaggauaugagaaggcagacccggggaacugaaaca
ucuaaguacccggaggaagagaaagcaaaugcgauucccugaguagcggc
gagcgaaacgggaucagcccaaaccaagaggcuugccucuugggguugua
ggacacucuguaggaguuacaaaggaacgagguagaugaagaggucugga
aaggcccgccauaggagguaacagcccuguagucaaaacuucguucucuc
cugaguggauccugaguacggcggaacacgugaaauuccgucggaauccg
ggaggaccaucucccaaggcuaaauacucccuagugaccgauagugaacc
aguaccgugagggaaaggugaaaagcaccccggaaggggagugaaagaga
uccugaaaccgugugccuacaaguagucagagcccguuaacgggugaugg
cgugccuuuuguagaaugaaccggcgaguuacgaucucgugcaagguuaa
gcagaagaugcggagccgcagcgaaagcgagucugaauagggcgcaagua
cguggucguagacccgaaaccaggugaucuacccauguccagggugaagu
uaauggaggcccgaacccacgcacguugaaaagugcggggaugaggugug
gguaggggugaaaugccaaucgaaccuggagauagcugguucucuccgaa
auagcuuuagggcuagccucaagguaagagucuuggagguagagcacuga
uuggacuagggguuaccgaauucagucaaacuccgaaugccaaugacuua
uccuugggagucagacugcgagugauaagauccguagucgaaagggaaac
agcccagaccgccagcuaaggucccaaaguauacguuaaguggaaaagga
uguggaguugcuuagacaaccaggauguuggcuuagaagcagccaccauu
uaaagagugcguaauagcucacuggucgagugacucugcgccgaaaaugu
accggggcuaaacguaucaccgaagcugcggacuguucgaacagugguag
gagagcguucuaagggcugugaagccagaccggaaggacugguggagcgc
uuagaagugagaaugccgguaugaguagcgaaagaggggugagaaucccc
uccaccgaaugccuaagguuuccugaggaaggcucguccgcucaggguua
gucgggaccuaagccgaggccgaaaggcguaggcgauggacaacagguug
auauuccuguaccaccuccucaccauuugagcaauggggggacgcaggag
gauaggguaagcgcgguauuggauauccgcguccaagcaguuaggcuggg
aaauaggcaaauccguuucccaaaggcugagcugugauggcgagcgcgaa
guuccugauuccacacugccaagaaaagccucuagcgaggugagaggugc
ccguaccgcaaaccgacacagguaggcgaggagagaauccuaaggugauc
gagagaacucucguuaaggaacucggcaaaaugaccccguaacuucggga
gaaggggugcucuguagggugcaagcccgagagagccgcagugaauaggc
ccaggcgacuguuuagcaaaaacacaggucucugcgaagccguaaggcga
aguauaggggcugacgccugcccggugcuggaagguuaagaggagcgcuu
agcguaagcgaaggugcgaauugaagccccaguaaacggcggccgcgguc
cuaagguagcgaaauuccuugucggguaaguuccgacccgcacgaaaggc
gcaacgaucugggcacugucucaacgagagacucggugaaauuauaguac
cugugaagaugcagguuacccgcgacaggacggaaagaccccguggagcu
uuacugcagccugauauugaauguugguaauugaccuucuaacccgccgc
ccuuaucgggcggggagacagugucaggugggcaguuugacuggggcggu
cgccuccuaaaagguaacggaggcgcccaaagguucccucagaaugguug
gaaaucauucgcagaguguaaaggcacaagggagcuugacugcgagaccu
acaagucgagcagggacgaaagucgggcuuagugauccggugguuccgca
uggaagggccaucgcucaacggauaaaagcuaccccggggauaacaggcu
uaucucccccaagaguccacaucgacggggagguuuggcaccucgauguc
ggcucaucgcauccuggggcuguagucggucccaaggguugggcuguucg
cccauuaaagcgguacgcgagcuggguucagaacgucgugagacaguucg
gucccuauccgucgcgggcgcaggaaauuugagaggagcuguccuuagua
cgagaggaccgggauggacgcaccgcugguguaccaguuguucugccaag
ggcaucgcuggguagcuaugugcggacgggauaagugcugaaagcaucua
agcaugaagccccccucaagaugagauuucccauuccgcaaggaaguaag
aucccugaaagaugaucagguugauaggucugagguggaaguguggcgac
acauggagcugacagauacuaaucgaucgaggacuuaac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8s1u A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): S2 R3 R36 K60 R63 A64 G67 T68 S71 N75 G109 Y110 S111 H112 K139 E140 G143 Y158 K159 K161 K173 K176
• Binding residue (residue number reindexed from 1): S1 R2 R35 K59 R62 A63 G66 T67 S70 N74 G108 Y109 S110 H111 K138 E139 G142 Y157 K158 K160 K172 K175

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• 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:8s1u, PDBe:8s1u, PDBj:8s1u
• PDBsum: 8s1u
• PubMed: 38811035
• UniProt: P46898|RL6_BACSU Large ribosomal subunit protein uL6 (Gene Name=rplF)