Structure of PDB 5nd8 Chain X Binding Site BS01

Receptor Information

>5nd8 Chain X (length=87) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

IKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVEGVNIMKKHQGGILETE
AAIHVSNVQLLDPKTNEPTRVGYKFVRIAKKSGEEIK

Ligand information

>5nd8 Chain A (length=2912)

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
cuacgaaucgaagccccaguaaacggcggccguaauaacgguccuaaggu
agcgaaauuccuugucggguaaguuccgacccgcacgaaaggcguaacga
uuugggcacugucucaacgagagacucggugaaaucauaguaccugugaa
gaugcagguuacccgcgacaggacggaaagaccccguggagcuuuacugu
agccugauauugaaauucggcacagcuuguacaggauagguaggagccuu
ugaaacgugagcgcuagcuuacguggaggcgcuggugggauacuacccua
gcuguguuggcuuucuaacccgcaccacuuaucguggugggagacagugu
caggcgggcaguuugacuggggcggucgccuccuaaaagguaacggaggc
gcucaaagguucccucagaaugguuggaaaucauucauagaguguaaagg
cauaagggagcuugacugcgagaccuacaagucgagcagggucgaaagac
ggacuuagugauccggugguuccgcauggaagggccaucgcucaacggau
aaaagcuaccccggggauaacaggcuuaucucccccaagaguucacaucg
acggggagguuuggcaccucgaugucggcucaucgcauccuggggcugua
gucggucccaaggguugggcuguucgcccauuaaagcgguacgcgagcug
gguucagaacgucgugagacaguucggucccuauccgucgugggcguagg
aaauuugagaggagcuguccuuaguacgagaggaccgggauggacauacc
ucugguguaccaguugucgugccaacggcauagcuggguagcuaugugug
gacgggauaagugcugaaagcaucuaagcaugaagccccccucaagauga
gauuucccaacuucgguuauaagaucccucaaagaugaugagguuaauag
guucgagguggaagcauggugacauguggagcugacgaauacuaaucgau
cgaagacuuaau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5nd8 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 P28 K29 I40 M41 K42 K43 H64 N76 R80 V81 V91 K96
• Binding residue (residue number reindexed from 1): K3 G12 K13 T24 P26 K27 I38 M39 K40 K41 H54 N66 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:5nd8, PDBe:5nd8, PDBj:5nd8
• PDBsum: 5nd8
• PubMed: 28645916
• UniProt: Q2FW17|RL24_STAA8 Large ribosomal subunit protein uL24 (Gene Name=rplX)