Structure of PDB 6yef Chain T Binding Site BS01

Receptor Information

>6yef Chain T (length=116) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

PRVKGGTVTRARRKKTIKLAKGYFGSKHTLYKVAKQQVMKSGQYAFRDRR
QRKRDFRKLWITRINAAARQHEMSYSRLMNGLKKAGIDINRKMLSEIAIS
DEKAFAQLVTKAKDAL

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): P2 R3 V4 K5 R11 R13 R14 K22 G23 Y24 F25 G26 S27 T30 K33 K36 Q37 Q38 K41 S42 Y45 A46 F47 R48 D49 R50 R51 R53 K54 R55 F57 R58 K59 N66 Y76 S77 N81 K84 N91 R92 K93
• Binding residue (residue number reindexed from 1): P1 R2 V3 K4 R10 R12 R13 K21 G22 Y23 F24 G25 S26 T29 K32 K35 Q36 Q37 K40 S41 Y44 A45 F46 R47 D48 R49 R50 R52 K53 R54 F56 R57 K58 N65 Y75 S76 N80 K83 N90 R91 K92

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• 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: Q2FXQ1|RL20_STAA8 Large ribosomal subunit protein bL20 (Gene Name=rplT)