Structure of PDB 5nd8 Chain M Binding Site BS01

Receptor Information

>5nd8 Chain M (length=145) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

MRQTFMANESNIERKWYVIDAEGQTLGRLSSEVASILRGKNKVTYTPHVD
TGDYVIVINASKIEFTGNKETDKVYYRHSNHPGGIKSITAGELRRTNPER
LIENSIKGMLPSTRLGEKQGKKLFVYGGAEHPHAAQQPENYELRG

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): M1 R2 Q3 T4 G27 R28 S31 R38 K40 H48 Y54 T66 K69 Y76 H78 S79 N80 G83 K86 R100 S105 G108 M109 T113 R114 K121 H133 A135 Q136 Q137 R144
• Binding residue (residue number reindexed from 1): M1 R2 Q3 T4 G27 R28 S31 R38 K40 H48 Y54 T66 K69 Y76 H78 S79 N80 G83 K86 R100 S105 G108 M109 T113 R114 K121 H133 A135 Q136 Q137 R144

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• 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: Q2FW38|RL13_STAA8 Large ribosomal subunit protein uL13 (Gene Name=rplM)