Structure of PDB 6ddd Chain D Binding Site BS01

Receptor Information

>6ddd Chain D (length=100) Species: 1280 (Staphylococcus aureus)

MFAIIETGGKQIKVEEGQEIFVEKLDVNEGDTFTFDKVLFVGGDSVKVGA
PTVEGATVTATVNKQGRGKKITVFTYKRRKNSKRKKGHRQPYTKLTIDKI

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): G8 G9 K10 F21 E23 K24 R67 K70 I71 K77 R78 R79 K80 N81 K83 R84 K85 K86 G87 H88 R89 Y92
• Binding residue (residue number reindexed from 1): G8 G9 K10 F21 E23 K24 R67 K70 I71 K77 R78 R79 K80 N81 K83 R84 K85 K86 G87 H88 R89 Y92

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ddd, PDBe:6ddd, PDBj:6ddd
• PDBsum: 6ddd
• PubMed: 30667174
• UniProt: Q2FXS8|RL21_STAA8 Large ribosomal subunit protein bL21 (Gene Name=rplU)