Structure of PDB 6ddd Chain C Binding Site BS01

Receptor Information

>6ddd Chain C (length=116) Species: 1280 (Staphylococcus aureus)

PRVKGGTVTRARRKKTIKLAKGYFGSKHTLYKVAKQQVMKSGQYAFRDRR
QRKRDFRKLWITRINAAARQHEMSYSRLMNGLKKAGIDINRKMLSEIAIS
DEKAFAQLVTKAKDAL

Ligand information

>6ddd Chain 1 (length=2646)

uaaguuauuaagggcgcacgguggaugccuuggcacuagaagccgaugaa
ggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuugau
ccagagauuuccgaauggggaaacccagcaugaguuaugucauguuaucg
auaugugaauacauagcauaucagaaggcacacccggagaacugaaacau
cuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggcg
agcgaaacgggaagagcccaaaccaugggguuguaggacacucucaaagg
acgacauuagacgaaucaucuggaaagaugaaucaaagaagguaauaauc
cuguagucgaaaauguugucucucuugaguggauccugaguacgacggag
cacgugaaauuccgucggaaucugggaggaccaucuccuaaggcuaaaua
cucucuagugaccgauagugaaccaguaccgugagggaaaggugaaaagc
accccggaaggggagugaaauagaaccugaaaccgugugcuuacaaguag
ucagagcccguuaaugggugauggcgugccuuuuguagaaugaaccggcg
aguuacgauuugaugcaagguuaagcaguaaauguggagccguagcgaaa
gcgagucugaauagggcguuuaguauuuggucguagacccgaaaccaggu
gaucuacccuuggucagguugaaguucaggacugaauggaggaccgaacc
gacuuacguugaaaagugagcggaugaacugaggguagcggagaaauucc
aaucgaaccuggagauagcugguucucuccgaaauagcuuuagggcuagc
cucaagugaugauuauuggagguagagcacuguuuggacuucagacaaac
uccgaaugccaauuaauuuaacuugggagucagaacaugggugauaaggu
ccguguucgaaagggaaacagcccagaccaccagcuaaggucccaaaaua
uauguuaaguggaaaaggauguggcguugugacacugcgccgaaaaugua
ccggggcuaaacauauuaccgaagcuguggauuguccuuuggacaauggu
aggagagcguucuaagggcguugaagcaugaucguaaggacauguggagc
gcuuagaagugagaaugccggugugaguagcgaaagacgggugagaaucc
cguccaccgauugacuaagguuuccagaggaaggcucguccgcucugggu
uagucggguccuaagcugaggccgacaggcguaggcgauggauaacaggu
ugauauuccuguaccaccuauaaucguaucgauggggggacgcaguagga
uaggcgaagcgugcgauuggauugcacgucuaagcaguaaggcgcugagc
ugugauggggagaaguucgagucguugauuucacacugccgagaaaagcc
ucuagauagaaaauaggugcccguaccgcaaaccgacacagguagucaag
augagaauucuaaggugagcgagcgaacucucguuaaggaacucggcaaa
augaccccguaacuucgggagaaggggugcucuuuaggguuaacgcccag
aagagccgcagugaauaggcccaagcgacuguuuaucaaaaacacagguc
ucugcuaaaccguaaggugauguauaggggcugacgccugcccggugcug
gaagguuaagaggagugguuagcuucugcgaagcuacgaaucgaagcccc
aguaaacggcggccguaacuauaacgguccuaagguagcgaaauuccuug
ucggguaaguuccgacccgcacgaaaggcguaacgauuugggcacugucu
caacgagagacucggugaaaucauaguaccugugaagaugcagguuaccc
gcgacaggacggaaagaccccguggagcuuuacuguagccugauauugaa
auugcuuucuaacccgcaccacuuaucguggugggagacagugucaggcg
ggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcucaa
agguucccucagaauggucauucauagaguguaaaggcauaagggagcuu
gacugcgagaccuacaagucgagcagggucgaaagacggacuuagugauc
cggugguuccgcauggaagggccaucgcucaacggauaaaagcuaccccg
gggauaacaggcuuaucucccccaagaguucacaucgacggggagguuug
gcaccucgaugucggcucaucgcauccuggggcuguagucggucccaagg
guugggcuguucgcccauuaaagcgguacgcgagcuggguucagaacguc
gugagacaguucggucccuauccgucgugggcguaggaaauuugagagga
gcuguccuuaguacgagaggaccgggauggacauaccucugguguaccag
uugucgugccaacggcauagcuggguagcuauguguggacgggauaagug
cugaaagcaucuaagcaugaagccccccucaagaugagauuucccaacug
guuauaagaucccucaaagaugaugagguuaauagguucgagguggaagc
auggugacauguggagcugacgaauacuaaucgaucgaagacuuaa

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ddd cryoEM-Guided Development of Antibiotics for Drug-Resistant Bacteria.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): P2 R3 V4 G6 T8 T10 R11 R13 R14 K15 K19 K22 G23 Y24 F25 G26 T30 L31 K33 V34 K36 Q37 Q38 K41 S42 Y45 F47 R48 D49 R50 R51 Q52 R53 K54 R55 F57 R58 W61 I62 N66 R70 Y76 S77 N81 K84 N91 R92 K93
• Binding residue (residue number reindexed from 1): P1 R2 V3 G5 T7 T9 R10 R12 R13 K14 K18 K21 G22 Y23 F24 G25 T29 L30 K32 V33 K35 Q36 Q37 K40 S41 Y44 F46 R47 D48 R49 R50 Q51 R52 K53 R54 F56 R57 W60 I61 N65 R69 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:6ddd, PDBe:6ddd, PDBj:6ddd
• PDBsum: 6ddd
• PubMed: 30667174
• UniProt: Q2FXQ1|RL20_STAA8 Large ribosomal subunit protein bL20 (Gene Name=rplT)