Structure of PDB 5nrg Chain R Binding Site BS01

Receptor Information

>5nrg Chain R (length=102) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

IKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVEGVNIMKKHQKPTQLNP
EGGILETEAAIHVSNVQLLDPKTNEPTRVGYKFVDGKKVRIAKKSGEEIK
SN

Ligand information

>5nrg Chain X (length=2710)

uuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccaauga
aggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuuga
uccagagauuuccgaauggggaaacccagcaugaguuaugucauguuauc
gauauguauacauagcauaucagaaggcacacccggagaacugaaacauc
uuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggcga
gcgaaacgggaagagcccaaaccaacaagcuugcuuguugggguugagga
cacucuaugaguuacaaaggacgacauuagacgaaucaucuggaaagaug
aaucaaagaagguaauaauccuguagucgaaaauguugucucucuugagu
ggauccugaguacgacggagcacgugaaauuccgucggaaucugggagga
ccaucuccuaaggcuaaauacucucuagugaccgauagugaaccaguacc
gugagggaaaggugaaaagcaccccggaaggggagugaaauagaaccuga
aaccgugugcuuacaaguagucagagcccguuaaugggugauggcgugcc
uuuuguagaaugaaccggcgaguuacgauuugaugcaagguuaagcagua
aauguggagccguagcgaaagcgagucugaauagggcguuuaguauuugg
ucguagacccgaaaccaggugaucuacccuuggucagguugaaguucagg
cugaauggaggaccgaaccgacuuacguugaaaagugagcggaugaacug
aggguagcggagaaauuccaaucgaaccuggagauagcugguucucuccg
aaauagcuuuagggcuagccucaagugaugauuauuggagguagagcacu
guuuggacgaggggguuaccgaauucagacaaacuccgaaugccaauuaa
uuuaacuugggagucagaacaugggugauaagguccguguucgaaaggga
aacagcccagaccaccagcuaaggucccaaaauauauguuaaguggaaaa
ggauguggcguugcccagacaacuagcucauagucgagugacacugcgcc
gaaaauguaccggggcuaaacauauuaccgaagcuguggauuguccuugg
acaaugguaggagagcguucuaagggcguugaagcaugaucguaaggaca
uguggagcgcuuagaagugagaaugccggugugaguagcgaaagacgggu
gagaaucccguccaccgauugacuaagguuuccagaggaaggcucguccg
cucuggguuagucggguccuaagcugaggccgacaggcguaggcgaugga
uaacagguugauauuccuguaccaccuauaaucguaaucgauggggggac
gcaguaggauaggcgaagcgugcgauuggaugcacgucuaagcaguaagg
cugaguauccgguacucgaggcugagcugugauggggagagagucguuga
uuucacacugccgagaaaagccucuagauagauaggugcccguaccgcaa
accgacacagguagucaagaugagaauucuaaggugagcgagcgaacucu
cguuaaggaacucggcaaaaugaccccguaacuucgggagaaggggugcu
cuuuaggguuaacgcccagaagagccgcagugaauaggcccaagcgacug
uuuaucaaaaacacaggucucugcuaaaccguaaggugauguauaggggc
ugacgccugcccggugcuggaagguuaagaggagugguuagcugcgaagc
uacgaaucgaagccccaguaaacggcggcccuaagguagcgaaauuccuu
gucggguaaguuccgacccgcacgaaaggcguaacgauuugggcacuguc
ucaacgagagacucggugaaaucauaguaccugugaagaugcagguuacc
cgcgacaggacggaaagaccccguggagcuuuacuguagccugauauuga
aauucuggcuuucuaacccgcaccacuuaucguggugggagacaguguca
agcgggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgc
ucaaagguucccucagaaugguuggaaaucauucauagaguguaaaggca
uaagggagcuugacugcgagaccuacaagucgagcagggucgaaagacgg
acuuagugauccggugguuccgcauggaagggccaucgcucaacggauaa
aagcuaccccggggauaacaggcuuaucucccccaagaguucacaucgac
ggggagguuuggcaccucgaugucggcucaucgcauccuggggcuguagu
cggucccaaggguugggcuguucgcccauuaaagcgguacgcgagcuggg
uucagaacgucgugagacaguucggucccuauccgucgugggcguaggaa
auuugagaggagcuguccuuaguacgagaggaccgggauggacauaccuc
ugguguaccaguugucgugccaacggcauagcuggguagcuaugugugga
cgggauaagugcugaaagcaucuaagcaugaagccccccucaagaugaga
uuucccaacuugguuauaagaucccucaaagaugaugagguuaauagguu
cgagguggaagcauggugacauguggagcugacgaauacuaaucgaucga
agacuuaauc

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5nrg Structural insights of lincosamides targeting the ribosome of Staphylococcus aureus.
• Resolution: 3.442 Å
• Binding residue (original residue number in PDB): D7 K15 D16 L27 K42 K43 Q45 G55 R80 V81
• Binding residue (residue number reindexed from 1): D5 K13 D14 L25 K40 K41 Q43 G53 R78 V79

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5nrg, PDBe:5nrg, PDBj:5nrg
• PDBsum: 5nrg
• PubMed: 28973455
• UniProt: Q2FW17|RL24_STAA8 Large ribosomal subunit protein uL24 (Gene Name=rplX)