Structure of PDB 5nrg Chain 3 Binding Site BS01

Receptor Information

>5nrg Chain 3 (length=65) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

PKMKTHRGAAKRVKRTASGQLKRSRAFTSHLFANKSTKQKRQLRKARLVS
KSDMKRVKQLLAYKK

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): P2 K3 M4 T6 H7 T17 A18 S19 R26 A27 F28 S30 H31 L32 F33 N35 Q40 S53 D54 R57 Q60 Y64
• Binding residue (residue number reindexed from 1): P1 K2 M3 T5 H6 T16 A17 S18 R25 A26 F27 S29 H30 L31 F32 N34 Q39 S52 D53 R56 Q59 Y63

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

External links

• PDB: RCSB:5nrg, PDBe:5nrg, PDBj:5nrg
• PDBsum: 5nrg
• PubMed: 28973455
• UniProt: Q2FXQ0|RL35_STAA8 Large ribosomal subunit protein bL35 (Gene Name=rpmI)