Structure of PDB 5ngm Chain Ap Binding Site BS01

Receptor Information
>5ngm Chain Ap (length=89) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVKIRLTRLGSKRNPFYRIVVADARSPRDGRIIEQIGTYNPTSANAPEIK
VDEALALKWLNDGAKPTDTVHNILSKEGIMKKFDEQKKA
Ligand information
>5ngm Chain Aa (length=1539) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
auggagaguuugauccuggcucaggaugaacgcuggcggcgugccuaaua
caugcaagucgagcgaacggacgagaagcuugcuucucugauguuagcgg
cggacgggugaguaacacguggauaaccuaccuauaagacugggauaacu
ucgggaaaccggagcuaauaccggauaauauuuugaaccgcaugguucaa
aagugaaagacggucuugcugucacuuauagauggauccgcgcugcauua
gcuaguugguaagguaacggcuuaccaaggcaacgaugcauagccgaccu
gagagggugaucggccacacuggaacugagacacgguccagacuccuacg
ggaggcagcaguagggaaucuuccgcaaugggcgaaagccugacggagca
acgccgcgugagugaugaaggucuucggaucguaaaacucuguuauuagg
gaagaacauauguguaaguaacugugcacaucuugacgguaccuaaucag
aaagccacggcuaacuacgugccagcagccgcgguaauacguagguggca
agcguuauccggaauuauugggcguaaagcgcgcguaggcgguuuuuuaa
gucugaugugaaagcccacggcucaaccguggagggucauuggaaacugg
aaaacuugagugcagaagaggaaaguggaauuccauguguagcggugaaa
ugcgcagagauauggaggaacaccaguggcgaaggcgacuuucuggucug
uaacugacgcugaugugcgaaagcguggggaucaaacaggauuagauacc
cugguaguccacgccguaaacgaugagugcuaaguguuaggggguuuccg
ccccuuagugcugcagcuaacgcauuaagcacuccgccuggggaguacga
ccgcaagguugaaacucaaaggaauugacggggacccgcacaagcggugg
agcaugugguuuaauucgaagcaacgcgaagaaccuuaccaaaucuugac
auccuuugacaacucuagagauagagccuuccccuucgggggacaaagug
acagguggugcaugguugucgucagcucgugucgugagauguuggguuaa
gucccgcaacgagcgcaacccuuaagcuuaguugccaucauuaaguuggg
cacucuaaguugacugccggugacaaaccggaggaagguggggaugacgu
caaaucaucaugccccuuaugauuugggcuacacacgugcuacaauggac
aauacaaagggcagcgaaaccgcgaggucaagcaaaucccauaaaguugu
ucucaguucggauuguagucugcaacucgacuacaugaagcuggaaucgc
uaguaaucguagaucagcaugcuacggugaauacguucccgggucuugua
cacaccgcccgucacaccacgagaguuuguaacacccgaagccgguggag
uaaccuuuuaggagcuagccgucgaaggugggacaaaugauuggggugaa
gucguaacaagguagccguaucggaaggugcggcuggau
.....<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<.....<<
<.<<<..<<<..<<.<<<<......................>>>>.>>>>
>......<<........<<<<<<<..<<...<<<<<<<.<<<<.....<<
<<<<....>>>>>>......>>>>......<<<.<...........>.>>
>.......<....<...>...>..>>>>>>>..>>>>>>>>>.<<<....
<<<..<<<<<<<<.......>>>>>>>>>>>......>>>..<<<<<<<<
....>>>>...>>>>.>>.<<<<<.<.........>>>>>>.<<<<....
>>>>...>>>>>>.........<<<....<<<<....>>>>..>>>..>>
.>>>>>>..<<<<.......<<<....>>>......>>>>....<<<<<<
.......<.<<<<<<<........>>>>>>>.>........>>>>>>...
...<<<<<(((...<<<<<.....<<.)))>>.......>>>>>>>>>>.
.>>>>>>>>>..........<<<((.....<<<<<..<<<.<<<<<<<.<
<<<<<<<<.......<<<<<<.....>>>>>>.....>>>>>>>..>>>>
>>>>>...<<<<<<<<...<<<<<<<....<<<<<<<<...<<<......
>>>......>>>>>>>>...........<<....>>.>>>>>>>..>>>>
>.>>>...>>>..>>>>>....<<<<<<<...<...<<<<.........>
>>>...>>>>>>>>..........<<<<<<..<<<<<<<<<<<<<....>
>>>>>>>>>>>>...<<..))>>.....>>>>>>.>>>.<<<......<<
<<....>>>>....>>>..)))).]<<<<<.<<<<<<<.<<..<<<<<..
<<<<<<<<<<......<<........>>..........<<<<<<<.....
..<<<<......<<<<<....>>>>>.....<<<<..>>>>....>>>.>
..<<<.<<<..<<<<<<.......<<<<<<<<<....>>>..<<<<....
..>>>>..>>>>>>.....<<<<..<.<<.........<<......>>..
.......>>>......<<<<.......>>>>........>>>>.......
..>>>...>>>>>>>>>...>>>>>>>...>>.>>>>>>>>......<<<
<<<.....<<<..<<...<<<....>>>...>>....>>>.....>>>>>
>.......<..<.<<<..<<........>>..>>>>...>.....>>>>>
.....<<<<<<<.........>>>>>>>......>>...>>>>>>>>>>.
>>....<..<<.<.<<<<.<<<..<<<<<<..<<<<....<.<<<<..<<
<..<<<...>>>.>>>.>>>>.>...>>>>..>>>>>>..>>>.>>>>..
>.>>...>.....<<<<<<<<<....>>>>>>>>>....
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5ngm The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		A2 K4 R6 L7 L10 G11 S12 K13 R14 F17 R19 D24 R26 P28 R29 G31 R32 W60 D63 G64 D69 T70 H72 N73 S76 M81 K82 D85
Binding residue
(residue number reindexed from 1)		A1 K3 R5 L6 L9 G10 S11 K12 R13 F16 R18 D23 R25 P27 R28 G30 R31 W59 D62 G63 D68 T69 H71 N72 S75 M80 K81 D84
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
GO:0005840 ribosome
GO:0015935 small 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
UniProtW8U6K4

[Back to BioLiP]