Structure of PDB 6yef Chain X Binding Site BS01

Receptor Information

>6yef Chain X (length=87) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

IKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVEGVNIMKKHQGGILETE
AAIHVSNVQLLDPKTNEPTRVGYKFVRIAKKSGEEIK

Ligand information

>6yef Chain A (length=2881)

uuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccgauga
aggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuuga
uccagagauuuccgaauggggaaacccagcaugaguuaugucauguuauc
gauaugugaauacauagcauaucagaaggcacacccggagaacugaaaca
ucuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggc
gagcgaaacgggaagagcccaaaccaacaaguuguugggguuguaggaca
cucggaguuacaaaggacgacauuagacgaaucaucuggaaagaugaauc
aaagaagguaauaauccuguagucgaaaauguugucucucuugaguggau
ccugaguacgacggagcacgugaaauuccgucggaaucugggaggaccau
cuccuaaggcuaaauacucucuagugaccgauagugaaccaguaccguga
gggaaaggugaaaagcaccccggaaggggagugaaauagaaccugaaacc
gugugcuuacaaguagucagagcccguuaaugggugauggcgugccuuuu
guagaaugaaccggcgaguuacgauuugaugcaagguuaagcaguaaaug
uggagccguagcgaaagcgagucugaauagggcguuuaguauuuggucgu
agacccgaaaccaggugaucuacccuuggucagguugaaguucagguaac
acugaauggaggaccgaaccgacuuacguugaaaagugagcggaugaacu
gaggguagcggagaaauuccaaucgaaccuggagauagcugguucucucc
gaaauagcuuuagggcuagccucaagugaugauuauuggagguagagcac
uguuuggacgaggggccccucggguaccgaauucagacaaacuccgaaug
ccaauuaauuuaacuugggagucagaacaugggugauaagguccguguuc
gaaagggaaacagcccagaccaccagcuaaggucccaaaauauauguuaa
guggaaaaggauguggcguugcccagacaacuaggauguuggcuuagaag
cagccaucauuuaaagagugcguaauagcucacuagucgagugacacugc
gccgaaaauguaccggggcuaaacauauuaccgaagcuguggauuguccu
ggacaaugguaggagagcguucuaagggcguugaagcaugaucguaagga
cauguggagcgcuuagaagugagaaugccggugugaguagcgaaagacgg
gugagaaucccguccaccgauugacuaagguuuccagaggaaggcucguc
cgcucuggguuagucggguccuaagcugaggccgacaggcguaggcgaug
gauaacagguugauauuccuguaccaccuauaaaucgauggggggacgca
guaggauaggcgaagcgugcgauuggauugcacgucuaagcaguaaggcu
gaguauuaggcaaauccgguacucguuaaggcugagcugugauggggaga
aguucgagucguugauuucacacugccgagaaaagccucuagauagaaaa
uaggugcccguaccgcaaaccgacacagguagucaagaugagaauucuaa
ggugagcgagcgaacucucguuaaggaacucggcaaaaugaccccguaac
uucgggagaaggggugcucuuuaggguuaacgcccagaagagccgcagug
aauaggcccaagcgacuguuuaucaaaaacacaggucucugcuaaaccgu
aaggugauguauaggggcugacgccugcccggugcuggaagguuaagagg
agugguuagcuucugcgaagcuacgaaucgaagccccaguaaacggcggc
cguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguucc
gacccgcacgaaaggcguaacgauuugggcacugucucaacgagagacuc
ggugaaaucauaguaccugugaagaugcagguuacccgcgacaggacgga
aagaccccguggagcuuuacuguagccugauauugaaauucggcacagcu
uguacaggauagguaggagccuuugaaacgugagcgcuagcuuacgugga
ggcgcuggugggauacuacccuagcuguguuggcuuucuaacccgcacca
cuuaucguggugggagacagugucaggcgggcaguuugacuggggcgguc
gccuccuaaaagguaacggaggcgcucaaagguucccucagaaugguugg
aucauucauagaguguaaaggcauaagggagcuugacugcgagaccuaca
agucgagcagggucgaaagacggacuuagugauccggugguuccgcaugg
aagggccaucgcucaacggauaaaagcuaccccggggauaacaggcuuau
cucccccaagaguucacaucgacggggagguuuggcaccucgaugucggc
ucaucgcauccuggggcuguagucggucccaaggguugggcuguucgccc
auuaaagcgguacgcgagcuggguucagaacgucgugagacaguucgguc
ccuauccgucgugggcguaggaaauuugagaggagcuguccuuaguacga
gaggaccgggauggacauaccucugguguaccaguugucgugccaacggc
auagcuggguagcuauguguggacgggauaagugcugaaagcaucuaagc
augaagccccccucaagaugagauuucccaacugguuauaagaucccuca
aagaugaugagguuaauagguucgagguggaagcauggugacauguggag
cugacgaauacuaaucgaucgaagacuuaau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6yef Cryo-EM structure of the ribosome functional complex of the human pathogen Staphylococcus aureus at 3.2 angstrom resolution.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): K4 A13 G14 K15 M41 K42 K43 Q45 G55 H64 R80 V81
• Binding residue (residue number reindexed from 1): K2 A11 G12 K13 M39 K40 K41 Q43 G45 H54 R70 V71

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:6yef, PDBe:6yef, PDBj:6yef
• PDBsum: 6yef
• PubMed: 32852796
• UniProt: Q2FW17|RL24_STAA8 Large ribosomal subunit protein uL24 (Gene Name=rplX)