Structure of PDB 8y39 Chain r Binding Site BS01

Receptor Information

>8y39 Chain r (length=64) Species: 1280 (Staphylococcus aureus)

KVCYFTANGITHIDYKDTELLKRFISERGKILPRRVTGTSAKYQRMLTTA
IKRSRHMALLPYVK

Ligand information

>8y39 Chain a (length=1479)

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

Structure summary

• PDB: 8y39 Synthetic macrolides overcoming MLS B K-resistant pathogens.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): K43 I44 R47 K55 Q57 R58 T61 K65 R66 R68 H69 Y75
• Binding residue (residue number reindexed from 1): K30 I31 R34 K42 Q44 R45 T48 K52 R53 R55 H56 Y62

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8y39, PDBe:8y39, PDBj:8y39
• PDBsum: 8y39
• PubMed: 38992047
• UniProt: P66469|RS18_STAAW Small ribosomal subunit protein bS18 (Gene Name=rpsR)