Structure of PDB 5nd9 Chain g Binding Site BS01

Receptor Information

>5nd9 Chain g (length=143) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

VPKRDVLPDPIHNSKLVTKLINKIMLDGKRGTAQRILYSAFDLVEQRSGR
DALEVFEEAINNIMPVLEVKARSNYQVPVEVRPERRTTLGLRWLVNYARL
RGEKTMEDRLANEILDAANNTGGAVKKREDTHKMAEANKAFAH

Ligand information

>5nd9 Chain a (length=1541)

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

Structure summary

• PDB: 5nd9 Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): V7 K9 R10 N28 M31 D33 G34 K35 T38 R41 I42 K76 R78 R92 R95 T98 R102 K114 M116
• Binding residue (residue number reindexed from 1): V1 K3 R4 N22 M25 D27 G28 K29 T32 R35 I36 K70 R72 R82 R85 T88 R92 K104 M106

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5nd9, PDBe:5nd9, PDBj:5nd9
• PDBsum: 5nd9
• PubMed: 28645916
• UniProt: P48940|RS7_STAA8 Small ribosomal subunit protein uS7 (Gene Name=rpsG)