Structure of PDB 6yef Chain W Binding Site BS01

Receptor Information

>6yef Chain W (length=89) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

EARDILKRPVITEKSSEAMAEDKYTFDVDTRVNKTQVKMAVEEIFNVKVA
SVNIMNYKPKKKRMGRYQGYTNKRRKAIVTLKEGSIDLF

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): T13 K15 K24 N34 K35 T36 Q37 K39 M40 N54 I55 M56 Y58 K61 M65 Y68 N73 I79
• Binding residue (residue number reindexed from 1): T12 K14 K23 N33 K34 T35 Q36 K38 M39 N53 I54 M55 Y57 K60 M64 Y67 N72 I78

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: Q2FW08|RL23_STAA8 Large ribosomal subunit protein uL23 (Gene Name=rplW)