Structure of PDB 4wf9 Chain D Binding Site BS01

Receptor Information

>4wf9 Chain D (length=160) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

KEKFNTEVTENLMKKFNYSSVMEVPKIDKIVVNMGVGDAVQNSKVLDNAV
EEQKPLVTKAKKSIATFRLREGMPIGAKVTLRGERMYEFLDKLISVSLPR
VRDFQGVSKKAFDGRGNYTLGVKEQLIFPEIDYDKVSKVRGMDIVIVTTA
NTDEEARELL

Ligand information

>4wf9 Chain X (length=2712)

uuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccaauga
aggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuuga
uccagagauuuccgaauggggaaacccagcaugaguuaugucauguuauc
gauauguauacauagcauaucagaaggcacacccggagaacugaaacauc
uuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggcga
gcgaaacgggaagagcccaaaccaacaagcuugcuuguugggguuguagg
acacucuaugaguuacaaaggacgacauuagacgaaucaucuggaaagau
gaaucaaagaagguaauaauccuguagucgaaaauguugucucucuugag
uggauccugaguacgacggagcacgugaaauuccgucggaaucugggagg
accaucuccuaaggcuaaauacucucuagugaccgauagugaaccaguac
cgugagggaaaggugaaaagcaccccggaaggggagugaaauagaaccug
aaaccgugugcuuacaaguagucagagcccguuaaugggugauggcgugc
cuuuuguagaaugaaccggcgaguuacgauuugaugcaagguuaagcagu
aaauguggagccguagcgaaagcgagucugaauagggcguuuaguauuug
gucguagacccgaaaccaggugaucuacccuuggucagguugaaguucag
gcugaauggaggaccgaaccgacuuacguugaaaagugagcggaugaacu
gaggguagcggagaaauuccaaucgaaccuggagauagcugguucucucc
gaaauagcuuuagggcuagccucaagugaugauuauuggagguagagcac
uguuuggacgaggggguuaccgaauucagacaaacuccgaaugccaauua
auuuaacuugggagucagaacaugggugauaagguccguguucgaaaggg
aaacagcccagaccaccagcuaaggucccaaaauauauguuaaguggaaa
aggauguggcguugcccagacaacuagcucacuagucgagugacacugcg
ccgaaaauguaccggggcuaaacauauuaccgaagcuguggauuguccuu
ggacaaugguaggagagcguucuaagggcguugaagcaugaucguaagga
cauguggagcgcuuagaagugagaaugccggugugaguagcgaaagacgg
gugagaaucccguccaccgauugacuaagguuuccagaggaaggcucguc
cgcucuggguuagucggguccuaagcugaggccgacaggcguaggcgaug
gauaacagguugauauuccuguaccaccuauaaucguaucgaugggggga
cgcaguaggauaggcgaagcgugcgauuggauugcacgucuaagcaguag
gcugaguauauccgguacucguggcugagcugugauggggagaagaaguc
guugauuucacacugccgagaaaagccucuagauagaauaggugcccgua
ccgcaaaccgacacagguagucaagaugagaauucuaaggugagcgagcg
aacucucguuaaggaacucggcaaaaugaccccguaacuucgggagaagg
ggugcucuuuaggguuaacgcccagaagagccgcagugaauaggcccaag
cgacuguuuaucaaaaacacaggucucugcuaaaccgaaggugauguaua
ggggcugacgccugcccgugcuggaagguuaagaggagugguuagcugcg
aagcuacgaaucgaagccccaguaaacggcggccccuaagguagcgaaau
uccuugucggguaaguuccgacccgcacgaaaggcguaacgauuugggca
cugucucaacgagagacucggugaaaucauaguaccugugaagaugcagg
uuacccgcgacaggacggaaagaccccguggagcuuuacuguagccugau
auugaaauucggcuuucuaacccgcaccacuuaucguggugggagacagu
gucaagcgggcaguuugacuggggcggucgccuccuaaaagguaacggag
gcgcucaaagguucccucagaaugguugaaaucauucauagaguguaaag
gcauaagggagcuugacugcgagaccuacaagucgagcagggucgaaaga
cggacuuagugauccggugguuccgcauggaagggccaucgcucaacgga
uaaaagcuaccccggggauaacaggcuuaucucccccaagaguucacauc
gacggggagguuuggcaccucgaugucggcucaucgcauccuggggcugu
agucggucccaaggguugggcuguucgcccauuaaagcgguacgcgagcu
ggguucagaacgucgugagacaguucggucccuauccgucgugggcguag
gaaauuugagaggagcuguccuuaguacgagaggaccgggauggacauac
cucugguguaccaguugucgugccaacggcauagcuggguagcuaugugu
ggacgggauaagugcugaaagcaucuaagcaugaagccccccucaagaug
agauuucccaacuugguuauaagaucccucaaagaugaugagguuaauag
guucgagguggaagcauggugacauguggagcugacgaauacuaaucgau
cgaagacuuaau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4wf9 Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus.
• Resolution: 3.427 Å
• Binding residue (original residue number in PDB): M38 P65 T68 E81 Q115 D123 Y143
• Binding residue (residue number reindexed from 1): M34 P55 T58 E71 Q105 D113 Y133

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• 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:4wf9, PDBe:4wf9, PDBj:4wf9
• PDBsum: 4wf9
• PubMed: 26464510
• UniProt: Q2FW18|RL5_STAA8 Large ribosomal subunit protein uL5 (Gene Name=rplE)