Structure of PDB 5ngm Chain A3 Binding Site BS01

Receptor Information
>5ngm Chain A3 (length=64) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PKMKTHRGAAKRVKRTASGQLKRSRAFTSHLFANKSTKQKRQLRKARLVS
KSDMKRVKQLLAYK
Ligand information
>5ngm Chain AA (length=2905) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccgauga
aggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuuga
uccagagauuuccgaauggggaaacccagcaugaguuaugucauguuauc
gauaugugaauacauagcauaucagaaggcacacccggagaacugaaaca
ucuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggc
gagcgaaaugggaagagcccaaaccaacaagcuugcuuguugggguugua
ggacacucuacggaguuacaaaggacgacauuagacgaaucaucuggaaa
gaugaaucaaagaagguaauaauccuguagucgaaaauguugucucucuu
gaguggauccugaguacgacggagcacgugaaauuccgucggaaucuggg
aggaccaucuccuaaggcuaaauacucucuagugaccgauagugaaccag
uaccgugagggaaaggugaaaagcaccccggaaggggagugaaauagaac
cugaaaccgugugcuuacaaguagucagagcccguuaaugggugauggcg
ugccuuuuguagaaugaaccggcgaguuacgauuugaugcaagguuaagc
aguaaauguggagccguagcgaaagcgagucugaauagggcguuuaguau
uuggucguagacccgaaaccaggugaucuacccuuggucagguugaaguu
cagguaacacugaauggaggaccgaaccgacuuacguugaaaagugagcg
gaugaacugaggguagcggagaaauuccaaucgaaccuggagauagcugg
uucucuccgaaauagcuuuagggcuagccucaagugaugauuauuggagg
uagagcacuguuuggacgaggggccgguuaccgaauucagacaaacuccg
aaugccaauuaauuuaacuugggagucagaacaugggugauaagguccgu
guucgaaagggaaacagcccagaccaccagcuaaggucccaaaauauaug
uuaaguggaaaaggauguggcguugcccagacaacuaggauguuggcuua
gaagcagccaucauuuaaagagugcguaauagcucacuagucgagugaca
cugcgccgaaaauguaccggggcuaaacauauuaccgaagcuguggauug
uccuuuggacaaugguaggagagcguucuaagggcguugaagcaugaucg
uaaggacauguggagcgcuuagaagugagaaugccggugugaguagcgaa
agacgggugagaaucccguccaccgauugacuaagguuuccagaggaagg
cucguccgcucuggguuagucggguccuaagcugaggccgacaggcguag
gcgauggauaacagguugauauuccuguaccaccuauaaucguuuuaauc
gauggggggacgcaguaggauaggcgaagcgugcgauuggauugcacguc
uaagcaguaaggcugaguauuaggcaaauccgguacucguuaaggcugag
cugugauggggagaagacauugugucuucgagucguugauuucacacugc
cgagaaaagccucuagauagaaaauaggugcccguaccgcaaaccgacac
agguagucaagaugagaauucuaaggugagcgagcgaacucucguuaagg
aacucggcaaaaugaccccguaacuucgggagaaggggugcucuuuaggg
uuaacgcccagaagagccgcagugaauaggcccaagcgacuguuuaucaa
aaacacaggucucugcuaaaccguaaggugauguauaggggcugacgccu
gcccggugcuggaagguuaagaggagugguuagcuucugcgaagcuacga
aucgaagccccaguaaacggcggccguauaacgguccuaagguagcgaaa
uuccuugucggguaaguuccgacccgcacgaaaggcguaacgauuugggc
acugucucaacgagagacucggugaaaucauaguaccugugaagaugcag
guuacccgcgacaggacggaaagaccccguggagcuuuacuguagccuga
uauugaaauucggcacagcuuguacaggauagguaggagccuuugaaacg
ugagcgcuagcuuacguggaggcgcuggugggauacuacccuagcugugu
uggcuuucuaacccgcaccacuuaucguggugggagacagugucaggcgg
gcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcucaaa
gguucccucagaaugguuggaaaucauucauagaguguaaaggcauaagg
gagcuugacugcgagaccuacaagucgagcagggucgaaagacggacuua
gugauccggugguuccgcauggaagggccaucgcucaacggauaaaagcu
accccggggauaacaggcuuaucucccccaagaguucacaucgacgggga
gguuuggcaccucgaugucggcucaucgcauccuggggcuguagucgguc
ccaaggguugggcuguucgcccauuaaagcgguacgcgagcuggguucag
aacgucgugagacaguucggucccuauccgucgugggcguaggaaauuug
agaggagcuguccuuaguacgagaggaccgggauggacauaccucuggug
uaccaguugucgugccaacggcauagcuggguagcuauguguggacggga
uaagugcugaaagcaucuaagcaugaagccccccucaagaugagauuucc
caacuucgguuauaagaucccucaaagaugaugagguuaauagguucgag
guggaagcauggugacauguggagcugacgaauacuaaucgaucgaagac
uuaau
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.>.......>>>>.>.........<<....>>..<<<<<......<<...
..>>.....>>>>>..(((....<<<<<<<<....>>>>>>>>......<
<<<<<<<<...<<<<........<<<<<<<<<.<<<...<<<<<......
>>>>>((......<<<.....))>>>...>>>...>>>>>>>>>.>>>>.
>>>>>..>>>>.....<<<<<<<<.........>>>>>>>>......<<<
<<..<<<<>>>>>..)))......]].>>>>>>>.]].............
..<<....>>....]].........<<<<....>>>>.............
.....>>>>>>>>>>>.......<<<<..<<<<......>>>>..>>>>.
..<.<........>.>.<<<<<<....<<<<<<<.<<<<<..<<<...<<
<.....>>>...>>>...<<....>>..<<<<.....>>>>.....>>>>
>.>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<
<<<......>>>>>>.....>>>...<<<.<<<<<........>>>>>>>
>....>>>>>>>>>...<<<.....>>>......>>>>>>......>.>>
..<<<<<<....<<<<<....>>>>><<<<<<<<<...<<<<<<<<<...
..<<<...<<<<<<<<...<...........>...>>>>>>>>..>>.>.
....>>>>.>>>>>..>>>>>>>.>>..<<<<<<<<<<......>>>>>>
>>>>....<<<......>>>...<<<<.<<<...<<<(((.....<<<<<
<...........<<.<<<<<.<<<<........<<....<<.........
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<<<...>>>>>>>....>>>>>>..<<<<<<<.<<......<<<<<.<<.
...>>.>>>>>...>>.>>>>>>>........>>>>>><......<<...
.<<<<<<.......>>>>>><<<<....<<<<<.<<<..<<<<<<...<<
.....>>.>>>>>>....((<<<<.<<...<<<...<<<....>>>...>
>>...>>....<<<<........>>>>.))<<<<<<<..........<<<
...<<<<....<<<<...<<...<....<.<<....{.{....>>.>.<.
...<<<<...<<<..<<<<<..<<.....>>.>>>>>.......>>>...
>>>>.....>..........................>....>>...>>>>
.........>>>>..>>>.....>>>>>>>>>>>.>>>.....<<.....
.>>>>>>>.<<<<....>.>>>..>>>>..<<<<....<<<<<<<<.<<.
..............<<<<<...............>>>>><<<<<<.....
...........>>>>>>............<<<<<<<<<..<<<.......
..>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.<<<<<.
<<<..<<<<<<<..<<<...<<...<<<<<<...........>>>>>>..
.>>...>>>>>>>>..>>>>><<<<<.....>>>>>........<.....
......<<<<<<.....>>>>>>.....>....>>>>>..>>.>>>>>>>
.....>>.>>>>>>>>.>>>>>>.....>.(...<<<<<.......)>>>
>>..<<<<<<<<.(((.[[......<<<<.[[<<<<..<<<<..<<<<<<
<<<.<<<<.<<<<<<...<.............<<...............<
<<<<......>>>>>......................>>....>...>>>
>>>.>>>>....<<.<<<<<<.....>>>>>>>>.....>>>>>>>>>..
.>>>>..<<<<.....>>>><<<<<<...........>>>>>>..<<...
<<<<<<<...<<<<<<.......>>>>>>.....<<.[.(((>>....>>
>>>>>...<<<<..<<<......>>>..>>>>.<<<....>>>.>>)))]
......<<<<<<<.((..>>>>..))>>>>>>>.............>>>>
..]]>>>>.......<<<<...<<<<<<...<<.......>>...>>>>>
>....>>>.>.......<.<<<.<<<<<<..<<<<<<<<<......>>>>
>>..>>>.<<<<<.....>>>>>.....>>>>>..>...>>>..>....<
<<<<<<....>>>.>>>>....]]..)))>>>>>>>>....<<<<<<<..
.<<<<..<<<<<<<...............>>>>>>>.<<<<<...<<<<.
..<<<<<<<<<<<.}.}>>>>>>..>>>>>...>>>>.>>>>>...<<<.
...<<<<<...........>>>>>....>>>.>>>>.......>>>>>>>
.<<<....>>>....<<<<<<<<<.......>>>>>....<<<<<<<<.<
<<....<<<<<....>>>>>...>>>..>>>>>.>>>...>>>>....>>
>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5ngm The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		P2 K3 M4 K5 T6 H7 R8 K12 R13 K15 T17 A18 K23 R24 A27 F28 T29 S30 H31 F33 N35 K39 R42 Q43 R45 K46 S51 K52 S53 D54 R57 Q60 Y64
Binding residue
(residue number reindexed from 1)		P1 K2 M3 K4 T5 H6 R7 K11 R12 K14 T16 A17 K22 R23 A26 F27 T28 S29 H30 F32 N34 K38 R41 Q42 R44 K45 S50 K51 S52 D53 R56 Q59 Y63
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ngm, PDBe:5ngm, PDBj:5ngm
PDBsum5ngm
PubMed28959035
UniProtA0A077UL47

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