Structure of PDB 6sj6 Chain E Binding Site BS01

Receptor Information

>6sj6 Chain E (length=216) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

TKGILGRKIGMTQVFGENGELIPVTVVEAKENVVLQKKTVEVDGYNAIQV
GFEDKKAYKKDAKSNKYANKPAEGHAKKADAAPKRFIREFRNVDVDAYEV
GQEVSVDTFVAGDVIDVTGVSKGKGFQGAIKRHGQSRGPMSHGSHFHRAP
GSVGMASDASRVFKGQKMPGRMGGNTVTVQNLEVVQVDTENKVILVKGNV
PGPKKGLVEIRTSIKK

Ligand information

>6sj6 Chain A (length=2585)

uuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccgauga
aggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuuga
uccagagauuuccgaauggggaaacccagcaugaguuaugucauguuauc
gauaugugaauacauagcauaucagaaggcacacccggagaacugaaaca
ucuuaguacccggaggaagagaaagaaaucgauucccuuaguagcggcga
gcgaaacgggaagagcccaaaccaacaagcuugcuuguugggguuguagg
acacucuauacggaguuacaaaggacgacauuagacgaaucaucuggaaa
gaugaaucaaagaagguaauaauccuguagucgaaaauguugucucucuu
gaguggauccugaguacgacggagcacgugaaauuccgucggaaucuggg
aggaccaucuccuaaggcuaaauacucucuagugaccgauagugaaccag
uaccgugagggaaaggugaaaagcaccccggaaggggagugaaauagaac
cugaaaccgugugcuuacaaguagucagagcccguuaaugggugauggcg
ugccuuuuguagaaugaaccggcgaguuacgauuugaugcaagguuaagc
aguaaauguggagccguagcgaaagcgagucuguagggcguuuaguauuu
ggucguagacccgaaaccaggugaucuacccuuggucagguugaaguuca
gcugaauggaggaccgaaccgacuuacguugaaaagugagcggaugaacu
gaggguagcggagaaauuccaaucgaaccuggagauagcugguucucucc
gaaauagcuuuagggcuagccucaagugaugauuauuggagguagagcac
uguuuggacgaggggccgguuaccgaauucagacaaacuccgaaugccaa
uuaauuuaacuugggagucagaacaugggugauaagguccguguucgaaa
gggaaacagcccagaccaccagcuaaggucccaaaauauauguuaagugg
aaaaggauguggcguugccgugacacugcgccgaaaauguaccggggcua
aacauauuaccgaagcuguggauuguccuuuggacaaugguaggagagcg
uucuaagggcguugaagcaugaucguaaggacauguggagcgcuuagaag
ugagaaugccggugugaguagcgaaagacgggugagaaucccguccaccg
auugacuaagguuuccagaggaaggcucguccgcucuggguuagucgggu
ccuaagcugaggccgacaggcguaggcgauggauaacagguugauauucc
uguaccaccuauaaucguuuuaaucgauggggggacgcaguaggauaggc
gaagcgugcgauuggauucguugauuucacacugccgagaaaagccucua
gauagaaaauaggugcccguaccgcaaaccgacacagguagucaagauga
gaauucuaaggugagcgagcgaacucucguuaaggaacucggcaaaauga
ccccguaacuucgggagaaggggugcucuuuaggguuaacgcccagaaga
gccgcagugaauaggcccaagcgacuguuuaucaaaaacacaggucucug
cuaaaccguaaggugauguauaggggcugacgccugcccggugaguaaac
ggcgaagguagcgaaauuccuugucggguaaguuccgacccgcacgaaag
gcguaacgauuugggcacugucucaacgagagacucggugaaaucauagu
accugugaagaugcagguuacccgcgacaggacggaaagaccccguggag
cuuuacuguagccugauauugaaauucggcacacuguguuggcuuucuaa
cccgcaccacucguggugggagacagugucaggcgggcaguuugacuggg
gcggucgccuccuaaaagguaacggaggcgcucaaagguucccucagaau
gguuggaaaucauucauagaguguaaaggcauaagggagcuugacugcga
gaccuacaagucgagcagggucgaaagacggacuuagugauccggugguu
ccgcauggaagggccaucgcucaacggauaaaagcuaccccggggauaac
aggcuuaucucccccaagaguucacaucgacggggagguuuggcaccucg
augucggcucaucgcauccuggggcuguagucggucccaaggguugggcu
guucgcccauuaaagcgguacgcgagcuggguucagaacgucgugagaca
guucggucccuauccgucgugggcguaggaaauuugagaggagcuguccu
uaguacgagaggaccgggauggacauaccucugguguaccaguugucgug
ccaacggcauagcuggguagcuauguguggacgggauaagugcugaaagc
aucuaagcaugaagccccccucaagaugagauuucccaauuauaagaucc
cucaaagaugaugagguuaauagguucgagguggaagcauggugacaugu
ggagcugacgaauacuaaucgaucgaagacuuaau

<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<.....
.<<<.<<.((..((.>>......<<<<<<<..<<<))..)).>>>.....
>>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<
<<<.<<<.........>>>.>>>.>.>>>....<<<<<......<.....
.>.......>>>>.>.........<<..>>...<<<<......<<.....
>>.....>>>>...(((....<<.<<<<<....>>>>>.>>......<<<
<...<..................<<<<<<<<..<<<...<<<<<......
>>>>><<......((......>>.))...>>>....>>>>>>>>......
>......>>>>.....<<<<<<<<.........>>>>>>>>......<<<
<<..<<<<>>>>>..)))......]].>>>>>>>.]].............
..<<....>>....]].........<<<......>>>.............
.....>>>>>>>>>>>.......<<<<..<<<<......>>>>..>>>>.
..<............>.<<<<<<....<<<<<<<.<.<<...<<<...<<
<.....>>>...>>>...<......>....<<...>.>.......>>>..
>>>>>>>..<<....<<<<<<<.....<<<<<<<<<..<<<....<<<<<
..>>>>>.....>>>...<<<.<<<<<........>>>>>>>>....>>>
>>>>>>...<<<.....>>>......>>>>>>...>....>>..<<<<<<
....<<<<<....>>>>><<<<<<<<<...<<<<<<<<<...........
.<<<<<<<...................>>>>>>>............>>>>
.>>>>>..>>>>>>>.>>..<<<<<<<<<<......>>>>>>>>>>....
<<<......>>>...<<<<.<<<...<<<<<<.....(((.((.......
....<<...<<<.<.<.....>.>.>>>..>>...........>>>....
.)).))).>>>...>>>>>>>.<<<<<<...>>>>>>.....>>>>>><.
<<<<<<<.........<<<<<.<......>.>>>>>......>>>>>>>.
.>.....>>>>>><......<.....<<<<<.........>>>>><<<<.
...<<<<<.<<...<<<<<<...<<.....>>.>>>>>>.....(<<<<.
<.<<.<<<...<<<....>>>...>>>..>>>...<<<<<........>>
>>>).<<<<<.............<<...<<<<....<.....<<<.....
..........................>>.>.....>........>>>.>.
>>........>>>>>>>>>..>>.....<<......>>>>>>>.<<<...
....>>>..>>>>..<<<<....<<<<<<<<..<................
<<<<....<....>.....>>>>.<<<<<<<.<<........>>.>>>>>
>>............<<<<<<<<<..<<<.........>>>..<<<<<<<.
....<<......>>.......>>>>>>>..<<<<.<<<............
>>>.....................<<<.......>>>............>
>>>...>>.>>>>>>>.....>..>>>>>>>>.>>>>.>.....>.....
<<<<<........>>>>>..<<<<<<<<.(((.[[......<<<<.[[<<
<<..<<<<..<<<<<<<<<..<<<.<.<<<.......>>>>..>>>....
.<<.<<<<<....>>>>>>>.....>>>>>>>>>...>>>>..<<<<...
..>>>><<<.<<...........>>.>>>..<<...<<<<<<<....<<.
............>>......<<.[.(((>>....>>>>>>>...<<<<..
<<<......>>>..>>>>.<<<....>>>.>>)))]......<<<<<<<.
((..>>>>..))>>>>>>>.............>>>>..]]>>>>......
.<<<<...<<<<<<...<<.......>>...>>>>>>....>>>.>....
...<.<<<.<.<<<...<<<<<<<<<......>>>>>>>..>>.<<<<<.
....>>>>>......>>>...>...>>>..>....<<<<<<<....>>>.
>>>>....]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<<<<<
.....<....>....>>>>>>>.<<<<<...<<.<...<<<<<<<<<...
.....>>>>..>>>>>...>.>>.>>>>>...<<<.<..<<<<.......
......>>>>...>>>>.>>>>.......>>>>>>>.........<<<.<
<<<.........>>>>....<<<<<<<<.<<<.....<<<<....>>>>.
...>>>..>>>>>.>>>....>>>....>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6sj6 Mechanism of ribosome shutdown by RsfS in Staphylococcus aureus revealed by integrative structural biology approach.
• Resolution: 3.23 Å
• Binding residue (original residue number in PDB): Y46 Q50 K60 K64 S65 K67 K71 P72 G75 R86 R89 E90 R92 K123 G124 K125 G126 F127 G129 K132 Q136 S137 R138 S142 H143 G144 H146 F147 H148 R149 S153 M156 S158 D159 A160 S161 R162 V163 K165 M169 R172 T177 Q181 N200 P202 K216 K217
• Binding residue (residue number reindexed from 1): Y45 Q49 K59 K63 S64 K66 K70 P71 G74 R85 R88 E89 R91 K122 G123 K124 G125 F126 G128 K131 Q135 S136 R137 S141 H142 G143 H145 F146 H147 R148 S152 M155 S157 D158 A159 S160 R161 V162 K164 M168 R171 T176 Q180 N199 P201 K215 K216

Gene Ontology

Molecular Function

• 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:6sj6, PDBe:6sj6, PDBj:6sj6
• PDBsum: 6sj6
• PubMed: 32245971
• UniProt: Q2FW06|RL3_STAA8 Large ribosomal subunit protein uL3 (Gene Name=rplC)