Structure of PDB 6ddd Chain Z Binding Site BS01

Receptor Information

>6ddd Chain Z (length=114) Species: 1280 (Staphylococcus aureus)

YRKLGRTSDQRKAMLRDLATSLIISERIETTEARAKEVRSVVEKLITLGK
KGDLASRRNAAKTLRNVEITQTALQKLFGEIAERYTERQGGYTRILKQGP
RRGDGAESVIIELV

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): Y3 R4 K5 G7 R8 S10 Q12 R13 K14 L17 R18 L20 I30 E31 A35 K38 E39 R41 E45 K46 T49 L56 R59 R60 K64 R67 N68 V69 Q83 R96 Q97 G98 G99 T101 R102 K105 R109 R110 G111 D112
• Binding residue (residue number reindexed from 1): Y1 R2 K3 G5 R6 S8 Q10 R11 K12 L15 R16 L18 I28 E29 A33 K36 E37 R39 E43 K44 T47 L54 R57 R58 K62 R65 N66 V67 Q75 R88 Q89 G90 G91 T93 R94 K97 R101 R102 G103 D104

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

External links

• PDB: RCSB:6ddd, PDBe:6ddd, PDBj:6ddd
• PDBsum: 6ddd
• PubMed: 30667174
• UniProt: Q2FW33|RL17_STAA8 Large ribosomal subunit protein bL17 (Gene Name=rplQ)