Structure of PDB 6ddg Chain K Binding Site BS01

Receptor Information
>6ddg Chain K (length=56) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IRDLTTSEIEEQIKSSKEELFNLRFQLATGQLEETARIRTVRKTIARLKT
VARERE
Ligand information
>6ddg Chain 1 (length=2646) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
Global viewLocal viewStructure summary

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PDB6ddg cryoEM-Guided Development of Antibiotics for Drug-Resistant Bacteria.
Resolution3.1 Å
Binding residue
(original residue number in PDB)
E39 T40 R44 R47 K48 K54 T55 R58
Binding residue
(residue number reindexed from 1)
E34 T35 R39 R42 K43 K49 T50 R53
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

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Biological Process

View graph for
Cellular Component
External links
PDB RCSB:6ddg, PDBe:6ddg, PDBj:6ddg
PDBsum6ddg
PubMed30667174
UniProtQ2FW14|RL29_STAA8 Large ribosomal subunit protein uL29 (Gene Name=rpmC)

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