Structure of PDB 6sw9 Chain Y Binding Site BS01

Receptor Information
>6sw9 Chain Y (length=50) Species: 272844 (Pyrococcus abyssi GE5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MGQKWKLYIVKDGKVIRKNKFCPRCGPGVFMADHGDRWACGRCGYTEWKK
Ligand information
>6sw9 Chain 2 (length=1497) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
auuccgguugauccugccggaggccacugcuauggggguccgacuaagcc
augcgagucaagggggcgucccuucugggacgccaccggcggacggcuca
guaacacgucgguaaccuacccucgggagggggauaaccccgggaaacug
gggcuaaucccccauaggccugggguacuggaagguccccaggccgaaag
ggagccguaaggcuccgcccgaggaugggccggcggccgauuagguaguu
ggugggguaacggcccaccaagccgaagaucgguacgggccgugagagcg
ggagcccggagauggacacugagacacggguccaggcccuacggggcgca
gcaggcgcgaaaccuccgcaaugcgggaaaccgcgacggggggaccccca
gugccgugccucuggcacggcuuuuccggaguguaaaaagcuccgggaau
aagggcugggcaaggccgguggcagccgccgcgguaauaccggcggcccg
agugguggccacuauuauugggccuaaagcggccguagccgggcccguaa
gucccuggcgaaaucccacggcucaaccguggggcucgcuggggauacug
cgggccuugggaccgggagaggccggggguacccccgggguaggggugaa
auccuauaaucccggggggaccgccaguggcgaaggcgcccggcuggaac
ggguccgacggugagggccgaaggccaggggagcgaaccggauuagauac
ccggguaguccuggcuguaaaggaugcgggcuaggugucgggcgagcuuc
gagcucgcccggugccguagggaagccguuaagcccgccgccuggggagu
acggccgcaaggcugaaacuuaaaggaauuggcgggggagcacuacaagg
gguggagcgugcgguuuaauuggauucaacgccgggaaccucaccggggg
cgacggcaggaugaaggccaggcugaaggucuugccggacgcgccgagag
gaggugcauggccgccgucagcucguaccgugaggcguccacuuaagugu
gguaacgagcgagacccgcgcccccaguugccagucccucccgcucggga
gggaggcacucuggggggacugccggcgauaagccggaggaaggggcggg
cgacgguaggucaguaugccccgaaacccccgggcuacacgcgcgcuaca
augggcgggacaaugggugccgaccccgaaagggggagguaauccccuaa
acccgcccucaguucggaucgcgggcugcaacucgcccgcgugaagcugg
aaucccuaguacccgcgcgucaucaucgcgcggcgaauacgucccugcuc
cuugcacacaccgcccgucacuccacccgagcggggccuaggugaggccc
gaucuccuucgggaggucgggucgagccuaggcuccgugaggggggagaa
gucguaacaagguagccguaggggaaccuacggcucgaucaccuccu
...<<<<<.[.((((>>>>>.<<<<<<<<<..<<<<<<.<<......<<<
.<<<..<<<..<<.<<<<<<<<....>>>>>>>>.>>>>>......<<..
......<<<<<<<..<<...<<<<<<<.<<<<<....<<<<<<....>>>
>>>.....>>>>>...<<<<<<<<<.<<......>>>>>>>>>>>.....
<<<<<<....>>>>>>.>>>>>>>..>>>>>>>>>.<<<....<<<...<
<<<<<.........>>>>>>.>>>......>>>..<<<<<<<<....>>>
>...>>>>.>>.<<<<<............>>>>>.<<<<<..>>>>>...
>>>>>>.........<<<....<<<<....>>>>..>>>..>>.>>>>>>
..<<<<<<<<...>>>>>>>>...<<<<<<<<.......>>>>>>>>...
..<<<<<((......<<<<.....<<..))>>.......>>>>.>>>>>.
.>>>>>>>>>..........<<<((.....<<<<...<<<.<<<<<<<.<
<<<<<<<<<....<<<<<<<<.....>>>>>>>>...>>>>>>>>..>>>
>>>>>>...<<<<<.<....<<<<<<<.<..<<<<<<<<<..<<<.....
.>>>.....>>>>>>>>>..>........<<....>>.>>>>>>>....>
>>.>>>...>>>...>>>>...<<<<<<<...<<...<<<<.<.....>.
>>>>...>>>>>>>>>.........<<<<<<..<<<<<<<<<<<<<<...
..>>>>>>>>>>>>>>...<<..))>>.....>>>>>>.>>>.<<<....
..<<<<....>>>>....>>>..)))).]<<<<<.<<<<<<<..<<.<<<
<<<..<<<<<<<<<<......<<........>>..........<<<<<<<
...<<<<........<<<.<<<.......>>>.>>>......>>>>...<
<.<<<..<<<<<<<<.....<<<<<<.<<....>>...<<<<......>>
>>..>>>>>>....<<<<<.<<<<<<<..<<<..<<<<<<<<....>>>>
>>>>>>>...>>>>>>>.....<<<<<.....>>>>>........>>>>>
.....>>.>>>...>>>>>>>>....>>>>>>>...>>.>>>>>>>>...
..<<<<<<<.....<<<..<...<<<<....>>>>...>....>>>....
.>>>>>>>......<....<<<<<<<........>>>>>>>....>....
.>>>>>>.....<<<<<<<.......>>>>>>>.......>>...>>>>>
>>>>>.>>.......<<.<.<<<<.<<...<...<<<<<<<<<..<<<<<
<<<<<<<....>>>>>>>>>>>>..>>>>>>>>>...>...>.>>>>>..
>.>>..........<<<<<<<<....>>>>>>>>.............
Receptor-Ligand Complex Structure
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PDB6sw9 Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation.
Resolution4.2 Å
Binding residue
(original residue number in PDB)		M1 G2 Q3 V29 F30 M31 A32 D33 H34 R37 A39 G41 R42 T46
Binding residue
(residue number reindexed from 1)		M1 G2 Q3 V29 F30 M31 A32 D33 H34 R37 A39 G41 R42 T46
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0008270 zinc ion binding
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6sw9, PDBe:6sw9, PDBj:6sw9
PDBsum6sw9
PubMed32029867
UniProtP61238|RS27A_PYRAB Small ribosomal subunit protein eS31 (Gene Name=rps27ae)

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