Structure of PDB 5nd9 Chain m Binding Site BS01

Receptor Information
>5nd9 Chain m (length=110) 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]
ARIAGVDIPREKRVVISLTYIYGIGTSTAQKILEEANVSADTRVKDLTDD
ELGRIREVVDGYKVEGDLRRETNLNIKRLMEISSYRGIRHRRGLPVRGQK
TKNNARTRKG
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)		R14 G24 I25 G26 T29 T43 R44 Y86 R87 R90 R93 G94 L95 V97 R98 G99 Q100 K101 T102 K103 N104 R107 T108 R109 K110
Binding residue
(residue number reindexed from 1)		R13 G23 I24 G25 T28 T42 R43 Y85 R86 R89 R92 G93 L94 V96 R97 G98 Q99 K100 T101 K102 N103 R106 T107 R108 K109
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005829 cytosol
GO:0005840 ribosome
GO:0015935 small ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5nd9, PDBe:5nd9, PDBj:5nd9
PDBsum5nd9
PubMed28645916
UniProtQ2FW30|RS13_STAA8 Small ribosomal subunit protein uS13 (Gene Name=rpsM)

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