Structure of PDB 8y39 Chain p Binding Site BS01

Receptor Information
>8y39 Chain p (length=87) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVKIRLTRLGSKRNPFYRIVVADARSPRDGRIIEQIGTYNPTSANAPEIK
VDEALALKWLNDGAKPTDTVHNILSKEGIMKKFDEQK
Ligand information
>8y39 Chain a (length=1479) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
auggagaguuugauccuggcucaggaugaacgcuggcggcgugccuaaua
caugcaagucgagcgaacggacugauguuagcggcggacgggugaguaac
acguggauaaccuaccuauaagacugggauaacuucgggaaaccggagcu
aauaccggauaauauuuugacgcaugguucaaaagugaaagacggcuguc
acuuauagauggauccgcgcugcauuagcuaguugguaagguaacggcuu
accaaggcaacgaugcauagccgaccugagagggugaucggccacacugg
aacugagacacgguccagacuccuacgggaggcagcaguagggaaucuuc
cgcaaugggcgaaagccugacggagcaacgccgcgugagugaugaagguc
uucggaucguaaaacucuguuauuagggaagaacauauguguaaguaacu
gugcacaucuugacgguaccuaaucagaaagccacggcuaacuacgugcc
agcagccgcgguaauacguagguggcaagcguuauccggaauuauugggc
guaaagcgcgcguaggcgguuuuuuaagucugaugugaaagcccacggcu
caaccguggagggucauuggaaacuggaaaacuugagugcagaagaggaa
aguggaauuccauguguagcggugaaaugcgcagagauauggaggaacac
caguggcgaaggcgacuuucuggucuguaacugacgcugaugugcgaaag
cguggggaucaaacaggauuagauacccugguaguccacgccguaaacga
ugagugcuaaguguuaggggggccccuuagugcugcagcuaacgcauuaa
gcacuccgccuggggaguacgaccgcaagguugaaacucaaaggaauuga
cggggacccgcacaagcgguggagcaugugguuuaauucgaagcaacgcg
aagaaccuuaccaaaucuugacauccucuagagauagaggacagguggug
caugguugucgucagcucgugucgugagauguuggguuaagucccgcaac
gagcgcaacccuuaagcuuaguugccaucaugggcacucuaaguugacug
ccggugacaaaccggaggaagguggggaugacgucaaaucaucaugcccc
uuaugauuugggcuacacacgugcuacaauggacaauacaaagggcagcg
aaaccgcgaggucaagcaaaucccauaaaguuguucucaguucggauugu
agucugcaacucgacuacaugaagcuggaaucgcuaguaaucguagauca
gcaugcuacggugaauacguucccgggucuuguacacaccgcccgucaca
ccacgagaguuuguaacacccgaagccgguggaguaaccuaggagcuagc
cgucgaaggugggacaaaugauuggggugaagucguaacaagguagccgu
aucggaaggugcggcuggaucaccuccuu
.....<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<.....<<
<.<<<..<<<..<<...<<......>>...>>>>>......<<.......
.<<<<<<<..<<...<<<<<<<.<<<<.....<<<<<<....>>>>>>..
....>>>>......<<<.<.........>.>>>.......<..<.>..>.
.>>>>>>>..>>>>>>>>>.<<<....<<<..<<<<<<<<.......>>>
>>>>>>>>......>>>..<<<<<<<<....>>>>...>>>>.>>.<<<<
<.<.........>>>>>>.<<<<....>>>>...>>>>>>.........<
<<....<<<<....>>>>..>>>..>>.>>>>>>..<<<<......<<<<
....>>>>.....>>>>...<<<<<<<.......<.<<<<<<<.......
.>>>>>>>.>........>>>>>>...>..<<<<<(((...<<<<<....
.<<.)))>>.......>>>>>>>>>>..>>>>>>>>>..........<<<
((.....<<<<<..<<<.<<<<<<<.<<<<<<<<<.......<<<<<<..
...>>>>>>.....>>>>>>>..>>>>>>>>>...<<<<<<<<...<<<<
<<<....<<<<<<<<...<<<......>>>......>>>>>>>>......
.....<<....>>.>>>>>>>..>>>>>.>>>...>>>..>>>>>....<
<<<<<<...<...<<<<.<.....>.>>>>...>>>>>>>>.........
.<<<<<<..<<<<<<<<<<<<.>>>>>>>>>>>>...<<..))>>.....
>>>>>>.>>>.<<<......<<<<....>>>>....>>>..)))).]<<<
<<.<<<<<<<.<<.<<<.<<..<<<<<<<<<<......<<........>>
..........<<<<<<<......<<.<<<<....>>>>.>>.<<<.<<<.
.<<<<<<.......<<<<<<<<<....>>>..<<<<......>>>>..>>
>>>>.....<<<<.<<<<<<...<<<..<..>>>>....>>>>>>.....
<<<<<.....>>>>>........>>>>.........>>>...>>>>>>>>
>...>>>>>>>...>>.>>>>>>>>.....<<<<<<<.....<<<..<<.
..<<<....>>>...>>....>>>.....>>>>>>>......<....<<<
<<<<........>>>>>>>....>.....>>.>>>....<<<<<<<....
.....>>>>>>>......>>...>>>>>>>>>>.>>....<..<<.<.<<
<<.<<<..<<<<<<..<<<<....<.<<<<..<<<..<<..>>.>>>.>>
>>.>...>>>>..>>>>>>..>>>.>>>>..>.>>...>.....<<<<<<
<<<....>>>>>>>>>.............
Receptor-Ligand Complex Structure
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PDB8y39 Synthetic macrolides overcoming MLS B K-resistant pathogens.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		A2 V3 K4 R6 L7 R9 L10 S12 K13 R14 F17 Y18 R19 D24 A25 R26 R29 G31 R32 W60 D63 G64 K66 T68 T70 H72 N73 S76 K77 M81 K82 D85 K88
Binding residue
(residue number reindexed from 1)		A1 V2 K3 R5 L6 R8 L9 S11 K12 R13 F16 Y17 R18 D23 A24 R25 R28 G30 R31 W59 D62 G63 K65 T67 T69 H71 N72 S75 K76 M80 K81 D84 K87
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:8y39, PDBe:8y39, PDBj:8y39
PDBsum8y39
PubMed38992047
UniProtP66441|RS16_STAAW Small ribosomal subunit protein bS16 (Gene Name=rpsP)

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