Structure of PDB 6ddd Chain F Binding Site BS01

Receptor Information

>6ddd Chain F (length=87) Species: 1280 (Staphylococcus aureus)

RDILKRPVITEKSSEAMAEDKYTFDVDTRVNKTQVKMAVEEIFNVKVASV
NIMNYKPKKKRMGRYQGYTNKRRKAIVTLKEGSIDLF

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): T13 E14 K15 R32 N34 K35 T36 Q37 N54 I55 M56 Y58 K59 K61 K63 M65 Y68 Q69 G70 Y71 N73 I79
• Binding residue (residue number reindexed from 1): T10 E11 K12 R29 N31 K32 T33 Q34 N51 I52 M53 Y55 K56 K58 K60 M62 Y65 Q66 G67 Y68 N70 I76

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: Q2FW08|RL23_STAA8 Large ribosomal subunit protein uL23 (Gene Name=rplW)