Structure of PDB 5nd9 Chain X Binding Site BS01

Receptor Information

>5nd9 Chain X (length=87) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

IKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVEGVNIMKKHQGGILETE
AAIHVSNVQLLDPKTNEPTRVGYKFVRIAKKSGEEIK

Ligand information

>5nd9 Chain A (length=2914)

uuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccgauga
aggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuuga
uccagagauuuccgaauggggaaacccagcaugaguuaugucauguuauc
gauaugugaauacauagcauaucagaaggcacacccggagaacugaaaca
ucuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggc
gagcgaaaugggaagagcccaaaccaacaagcuugcuuguugggguugua
ggacacucuauacggaguuacaaaggacgacauuagacgaaucaucugga
aagaugaaucaaagaagguaauaauccuguagucgaaaauguugucucuc
uugaguggauccugaguacgacggagcacgugaaauuccgucggaaucug
ggaggaccaucuccuaaggcuaaauacucucuagugaccgauagugaacc
aguaccgugagggaaaggugaaaagcaccccggaaggggagugaaauaga
accugaaaccgugugcuuacaaguagucagagcccguuaaugggugaugg
cgugccuuuuguagaaugaaccggcgaguuacgauuugaugcaagguuaa
gcaguaaauguggagccguagcgaaagcgagucugaauagggcguuuagu
auuuggucguagacccgaaaccaggugaucuacccuuggucagguugaag
uucagguaacacugaauggaggaccgaaccgacuuacguugaaaagugag
cggaugaacugaggguagcggagaaauuccaaucgaaccuggagauagcu
gguucucuccgaaauagcuuuagggcuagccucaagugaugauuauugga
gguagagcacuguuuggacgaggggccccucggguaccgaauucagacaa
acuccgaaugccaauuaauuuaacuugggagucagaacaugggugauaag
guccguguucgaaagggaaacagcccagaccaccagcuaaggucccaaaa
uauauguuaaguggaaaaggauguggcguugcccagacaacuaggauguu
ggcuuagaagcagccaucauuuaaagagugcguaauagcucacuagucga
gugacacugcgccgaaaauguaccggggcuaaacauauuaccgaagcugu
ggauuguccuuuggacaaugguaggagagcguucuaagggcguugaagca
ugaucguaaggacauguggagcgcuuagaagugagaaugccggugugagu
cgcgaaagacgggugagaaucccguccaccgauugacuaagguuuccaga
ggaaggcucguccgcucuggguuagucggguccuaagcugaggccgacag
gcguaggcgauggauaacagguugauauuccuguaccaccuauaaucguu
uuaaucgauggggggacgcaguaggauaggcgaagcgugcgauuggauug
cacgucuaagcaguaaggcugaguauuaggcaaauccgguacucguuaag
gcugagcugugauggggagaagacauugagucuucgagucguugauuuca
cacugccgagaaaagccucuagauagaaaauaggugcccguaccgcaaac
cgacacagguagucaagaugagaauucuaaggugagcgagcgaacucucg
uuaaggaacucggcaaaaugaccccguaacuucgggagaaggggugcucu
uuaggguuaacgcccagaagagccgcagugaauaggcccaagcgacuguu
uaucaaaaacacaggucucugcuaaaccguaaggugauguauaggggcug
acgccugcccggugcuggaagguuaagaggagugguuagcuucugcgaag
cuacgaaucgaagccccaguaaacggcggccguacuauaacgguccuaag
guagcgaaauuccuugucggguaaguuccgacccgcacgaaaggcguaac
gauuugggcacugucucaacgagagacucggugaaaucauaguaccugug
aagaugcagguuacccgcgacaggacggaaagaccccguggagcuuuacu
guagccugauauugaaauucggcacagcuuguacaggauagguaggagcc
uuugaaacgugagcgcuagcuuacguggaggcgcuggugggauacuaccc
uagcuguguuggcuuucuaacccgcaccacuuaucguggugggagacagu
gucaggcgggcaguuugacuggggcggucgccuccuaaaagguaacggag
gcgcucaaagguucccucagaaugguuggaaaucauucauagaguguaaa
ggcauaagggagcuugacugcgagaccuacaagucgagcagggucgaaag
acggacuuagugauccggugguuccgcauggaagggccaucgcucaacgg
auaaaagcuaccccggggauaacaggcuuaucucccccaagaguucacau
cgacggggagguuuggcaccucgaugucggcucaucgcauccuggggcug
uagucggucccaaggguugggcuguucgcccauuaaagcgguacgcgagc
uggguucagaacgucgugagacaguucggucccuauccgucgugggcgua
ggaaauuugagaggagcuguccuuaguacgagaggaccgggauggacaua
ccucugguguaccaguugucgugccaacggcauagcuggguagcuaugug
uggacgggauaagugcugaaagcaucuaagcaugaagccccccucaagau
gagauuucccaacuucgguuauaagaucccucaaagaugaugagguuaau
agguucgagguggaagcauggugacauguggagcugacgaauacuaaucg
aucgaagacuuaau

<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<.....
.<<<<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....
>>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<
<<<<<<<.........>>>>>>>.>>.>>....<<<<<......<<....
>>.......>>>>.>.........<<....>>..<<<<<......<<...
..>>.....>>>>>..(((....<<<<<<<<....>>>>>>>>......<
<<<<<<<<.....<..........<<<<<<<<<<.<<<...<<<<<....
..>>>>>((......<<<.....))>>>...>>>...>>>>>>>>>>...
>.>>>>>..>>>>.....<<<<<<<<.........>>>>>>>>......<
<<<<..<<<<>>>>>..)))......]].>>>>>>>.]]...........
....<<....>>....]].........<<<<....>>>>...........
.......>>>>>>>>>>>.......<<<<..<<<<......>>>>..>>>
>...<.<........>.>.<<<<<<....<<<<<<<.<<<<<..<<<...
<<<.....>>>...>>>...<<....>>..<<<<.....>>>>.....>>
>>>.>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<....<
<<<<<......>>>>>>.....>>>...<<<.<<<<<........>>>>>
>>>....>>>>>>>>>...<<<.....>>>......>>>>>>......>.
>>..<<<<<<....<<<<<....>>>>><<<<<<<<<...<<<<<<<<<.
....<<<...<<<<<<<<...<<...<<...>>...>>...>>>>>>>>.
.>>.>.....>>>>.>>>>>..>>>>>>>.>>..<<<<<<<<<<......
>>>>>>>>>>....<<<......>>>...<<<<.<<<...<<<(((....
.<<<<<<...........<<..<<<<.<<<<........<<<<<.<<...
<<...........>>...>>......................>>>>>...
.>>>>.>>>>.>>...........))).....>>>>>>.>>>...>>>>>
>><<<<<<<...>>>>>>>....>>>>>>..<<<<<<<.<<......<<<
<<.<<....>>.>>>>>...>>.>>>>>>>........>>>>>><.....
<<<....<<<<<<.......>>>>>><<<<....<<<<<.<<...<<<<<
<...<<.....>>.>>>>>>....((<<<<.<<...<<<...<<<....>
>>...>>>...>>...<<<<<........>>>>>))<<<<<<<.......
...<<<...<<<<....<<<<...<<...<....<.<<......{....>
>.>.<....<<<<...<<<.<<<<<<..<<.....>>.>>>>>>......
>>>...>>>>.....>..........................>....>>.
..>>>>.........>>>>..>>>.....>>>>>>>>>>>..>>.....<
<......>>>>>>>.<<<.......>>>..>>>>..<<<<....<<<<<<
<<.<<...............<<<<<.....<..>......>>>>><<<<<
<<.<<<<....>>>>.>>>>>>>............<<<<<<<<<..<<<.
........>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.
<<<<<.<<<..<<<<<<<..<<<...<<...<<<<<..<<....>>...>
>>>>...>>...>>>>>>>>..>>>>><<<<<........>>>>>.....
...<...........<<<<<<.....>>>>>>.....>....>>>>>..>
>.>>>>>>>.....>>.>>>>>>>>.>>>>>>>....>.....<<<<<..
......>>>>>..<<<<<<<<.(((.[[......<<<<.[[<<<<..<<<
<<.<<<<<<<<<.<<<<.<<<<<<<<<<<...........<<<<<..<<<
......<<<<<<<<....>>>>>>>>...>>>............>>>>>.
.>>>>>>>>>>>.>>>>....<<.<<<<<<.....>>>>>>>>.....>>
>>>>>>>..>>>>>..<<<<.....>>>><<<<<<...........>>>>
>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.[.((
(>>....>>>>>>>...<<<<..<<<......>>>..>>>>.<<<....>
>>.>>)))]......<<<<<<<.((..>>>>..))>>>>>>>........
.....>>>>..]]>>>>.......<<<<...<<<<<<...<<.......>
>...>>>>>>....>>>.>.......<<<<<.<<<<<<..<<<<<<<<<.
.....>>>>>>..>>>.<<<<<.....>>>>>.....>>>>>..>...>>
>.>>....<<<<<<<....>>>.>>>>....]]..)))>>>>>>>>....
<<<<<<<...<<<<..<<<<<<<...............>>>>>>>.<<<<
<...<<<<...<<<<<<<<<<<.}..>>>>>>..>>>>>...>>>>.>>>
>>...<<<.<..<<<<<...........>>>>>...>>>>.>>>>.....
..>>>>>>>.<<<....>>>....<<<<<<<<<.......>>>>>....<
<<<<<<<.<<<....<<<<<....>>>>>...>>>..>>>>>.>>>...>
>>>....>>>>>>.

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): K5 G14 K15 T26 K29 M41 K42 K43 H64 R80 V81 V91 K96
• Binding residue (residue number reindexed from 1): K3 G12 K13 T24 K27 M39 K40 K41 H54 R70 V71 V76 K81

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5nd9, PDBe:5nd9, PDBj:5nd9
• PDBsum: 5nd9
• PubMed: 28645916
• UniProt: Q2FW17|RL24_STAA8 Large ribosomal subunit protein uL24 (Gene Name=rplX)