Structure of PDB 5nd9 Chain k Binding Site BS01

Receptor Information
>5nd9 Chain k (length=115) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKNIENGVAHIRSTFNNTIVTITDEFGNALSWSSAGALGFKGSKKSTPFA
AQMASETASKSAMEHGLKTVEVTVKGPGPGRESAIRALQSAGLEVTAIRD
VTPVPHNGCRPPKRR
Ligand information
>5nd9 Chain a (length=1541) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ggagaguuugauccuggcucaggaugaacgcuggcggcgugccuaauaca
ugcaagucgagcgaacggacgagaagcuugcuucucugauguuagcggcg
gacgggugaguaacacguggauaaccuaccuauaagacugggauaacuuc
gggaaaccguagcuaauaccggauaauauuuugaaccgcaugguucaaaa
gugaaagacggucuugcugucacuuauagauggauccgcgcugcauuagc
uaguugguaagguaacggcuuaccaaggcaacgaugcauagccgaccuga
gagggugaucggccacacuggaacugagacacgguccagacuccuacggg
aggcagcaguagggaaucuuccgcaaugggcgaaagccugacggagcaac
gccgcgugagugaugaaggucuucggaucguaaaacucuguuauuaggga
agaacauauguguaaguaacugugcacaucuugacgguaccuaaucagaa
agccacggcuaacuacgugccagcagccgcgguaauacguagguggcaag
cguuauccggaauuauugggcguaaagcgcgcguaggcgguuuuuuaagu
cugaugugaaagcccacggcucaaccguggagggucauuggaaacuggaa
aacuugagugcagaagaggaaaguggaauuccauguguagcggugaaaug
cgcagagauauggaggaacaccaguggcgaaggcgacuuucuggucugua
acugacgcugaugugcgaaagcguggggaucaaacaggauuagauacccu
gguaguccacgccguaaacgaugagugcuaaguguuaggggguuucccgc
cccuuagugcugcagcuaacgcauuaagcacuccgccuggggaguacgac
cgcaagguugaaacucaaaggaauugacggggacccgcacaagcggugga
gcaugugguuuaauucgaagcaacgcgaagaaccuuaccaaaucuugaca
uccuuugacaacucuagagauagagccuuccccuucgggggacaaaguga
cagguggugcaugguugucgucagcucgugucgugagauguuggguuaag
ucccgcaacgagcgcaacccuuaagcuuaguugccaucauuaaguugggc
acucuaaguugacugccggugacaaaccggaggaagguggggaugacguc
aaaucaucaugccccuuaugauuugggcuacacacgugcuacaauggaca
auacaaagggcagcgaaaccgcgaggucaagcaaaucccauaaaguuguu
cucaguucggauuguagucugcaacucgacuacaugaagcuggaaucgcu
aguaaucguagaucagcaugcuacggugaauacguucccgggucuuguac
acaccgcccgucacaccacgagaguuuguaacacccgaagccgguggagu
aaccuuuuaggagcuagccgucgaaggugggacaaaugauuggggugaag
ucguaacaagguagccguaucggaaggugcggcuggaucac
...<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<.....<<<.
<<<..<<<..<<.<<<<...<<<<........>>>>...>>>>.>>>>>.
.....<<........<<<<<<<..<<...<<<<<<<.<<<<.....<<.<
<<....>>>.>>......>>>>......<<<<<<<<<<..>>>>>>>>>>
......<<<<<<...>>>>>>.>>>>>>>..>>>>>>>>>.<<<....<<
<..<<<<<<<<.......>>>>>>>>>>>......>>>..<<<<<<<<..
..>>>>...>>>>.>>.<<<<<.<.........>>>>>>.<<<<....>>
>>...>>>>>>.......<.<<<....<<<<....>>>>..>>>>.>>.>
>>>>>..<<<<......<<<<....>>>>.....>>>>...<<<<<<<..
............<.<.......>>...............>>>>>>...>.
.<<<<<(((...<<<<<.....<<.)))>>.......>>>>>>>>>>..>
>>>>>>>>..........<<<((.....<<<<<..<<<.<<<<<<<.<<<
<<<<<<.......<<<<<<.....>>>>>>.....>>>>>>>..>>>>>>
>>>...<<<<<<<<...<<<<<<<....<<<<<<<<...<<<......>>
>......>>>>>>>.>..........<<....>>.>>>>>>>..>>>>>.
>>>...>>>..>>>>>....<<<<<<<...<...<<<<.<.....>.>>>
>...>>>>>>>>..........<<<<<<..<<<<<<<<<<<<<.....>>
>>>>>>>>>>>...<<..))>>.....>>>>>>.>>>.<<<......<<<
<....>>>>....>>>..)))).].<<<<.<<<<<<<.<<.<<<<<<..<
<<<<<<<<.......<<........>>..........<<<<<<<......
<<<<.......<<<<<....>>>>>.....<<<....>>>.....>>.>>
.<<<.<<<..<<<<<<.......<<<<<<<<<....>>>..<<<<.....
.>>>>..>>>>>>.....<<<<.<<<<<<...<<...<<......>>.>>
....>>>>>>.....<<<<<.....>>>>>........>>>>........
.>>>...>>>>>>>>>...>>>>>>>....>.>>>>>>>>.....<<<<<
<<.....<<<..<<...<<<....>>>...>>....>>>.....>>>>>>
>.........<.<<<<<<<........>>>>>>>>.........>>>>>>
....<<<<<<<.........>>>>>>>......>>...>>>>>>>>>>.>
.....<..<<...<<<<.<<<..<<<<<<..<<<<....<.<<<<..<<<
..<<<...>>>.>>>.>>>>.>...>>>>..>>>>>>..>>>.>>>>...
.>>...>.....<<<<<<<<<....>>>>>>>>>.......
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5nd9 Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF.
Resolution3.7 Å
Binding residue
(original residue number in PDB)		R24 N28 N29 N40 A41 W44 S46 A49 G54 P117 H118 N119 G120 K125 R126
Binding residue
(residue number reindexed from 1)		R12 N16 N17 N28 A29 W32 S34 A37 G42 P105 H106 N107 G108 K113 R114
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:1990904 ribonucleoprotein complex

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Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:5nd9, PDBe:5nd9, PDBj:5nd9
PDBsum5nd9
PubMed28645916
UniProtQ2FW31|RS11_STAA8 Small ribosomal subunit protein uS11 (Gene Name=rpsK)

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