Structure of PDB 8p2f Chain P Binding Site BS01

Receptor Information

>8p2f Chain P (length=136) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

MLLPKRVKYRRQHRPKTTGRSKGGNYVTFGEFGLQATTTSWITSRQIESA
RIAMTRYMKRGGKVWIKIFPHTPYTKKPLEVRMGAGKGAVEGWIAVVKPG
RILFEVAGVSEEVAREALRLASHKLPVKTKFVKREE

Ligand information

>8p2f Chain A (length=2844)

uuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccgauga
aggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuuga
uccagagauuuccgaauggggaaacccagcaugaguuaugucauguuauc
gauaugugaauacauagcauaucagaaggcacacccggagaacugaaaca
ucuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggc
gagcgaaacgggaagagcccaaaccaacaagcuugcuuguugggguugua
ggacacucuauacggaguuacaaaggacgacauuagacgaaucaucugga
aagaugaaucaaagaagguaauaauccuguagucgaaaauguugucucuc
uugaguggauccugaguacgacggagcacgugaaauuccgucggaaucug
ggaggaccaucuccuaaggcuaaauacucucuagugaccgauagugaacc
aguaccgugagggaaaggugaaaagcaccccggaaggggagugaaauaga
accugaaaccgugugcuuacaaguagucagagcccguuaaugggugaugg
cgugccuuuuguagaaugaaccggcgaguuacgauuugaugcaagguuaa
gcaguaaauguggagccguagcgaaagcgagucugaauagggcguuuagu
auuuggucguagacccgaaaccaggugaucuacccuuggucagguugaag
uucagguaacacugaauggaggaccgaaccgacuuacguugaaaagugag
cggaugaacugaggguagcggagaaauuccaaucgaaccuggagauagcu
gguucucuccgaaauagcuuuagggcuagccucaagugaugauuauugga
gguagagcacuguuuggacgaggggccguuaccgaauucagacaaacucc
gaaugccaauuaauuuaacuugggagucagaacaugggugauaagguccg
uguucgaaagggaaacagcccagaccaccagcuaaggucccaaaauauau
guuaaguggaaaaggauguggcguugcccagacaacuaggauguuggcuu
agaagcagccaucauuuaaagagugcguaauagcucacuagucgagugac
acugcgccgaaaauguaccggggcuaaacauauuaccgaagcuguggauu
guccuuuggacaaugguaggagagcguucuaagggcguugaagcaugauc
guaaggacauguggagcgcuuagaagugagaaugccggugugaguagcga
aagacgggugagaaucccguccaccgauugacuaagguuuccagaggaag
gcucguccgcucuggguuagucggguccuaagcugaggccgacaggcgua
ggcgauggauaacagguugauauuccuguaccaccuauaaucguuuuaau
cgauggggggacgcaguaggauaggcgaagcgugcgauuggauugcacgu
cuaagcaguaaggcugaguauuaggcaaauccgguacucguuaaggcuga
gcugugauggggagaagacauugugucuucgagucguugauuucacacug
ccgagaaaagccucuagauagaaaauaggugcccguaccgcaaaccgaca
cagguagucaagaugagaauucuaaggugagcgagcgaacucucguuaag
gaacucggcaaaaugaccccguaacuucgggagaaggggugcucuuuagg
guuaacgcccagaagagccgcagugaauaggcccaagcgacuguuuauca
aaaacacaggucucugcuaaaccguaaggugauguauaggggcugacgcc
ugcccggugcuggaagguuaagaggagugguuagcuucugcgaagcuacg
aaucgaagccccaguaaacggcggccguaacuauaacgguccuaagguag
cgaaauuccuugucggguaaguuccgacccgcacgaaaggcguaacgauu
ugggcacugucucaacgagagacucggugaaaucauaguaccugugaaga
ugcagguuacccgcgacaggacggaaagaccccguggagcuuuacuguag
ccugauauugaaauucggcacagcuugcccuagcuguguuggcuuucuaa
cccgcaccacuuaucguggugggagacagugucaggcgggcaguuugacu
ggggcggucgccuccuaaaagguaacggaggcgcucaaagguucccucag
aaugguuggaaaucauucauagaguguaaaggcauaagggagcuugacug
cgagaccuacaagucgagcagggucgaaagacggacuuagugauccggug
guuccgcauggaagggccaucgcucaacggauaaaagcuaccccggggau
aacaggcuuaucucccccaagaguucacaucgacggggagguuuggcacc
ucgaugucggcucaucgcauccuggggcuguagucggucccaaggguugg
gcuguucgcccauuaaagcgguacgcgagcuggguucagaacgucgugag
acaguucggucccuauccgucgugggcguaggaaauuugagaggagcugu
ccuuaguacgagaggaccgggauggacauaccucugguguaccaguuguc
gugccaacggcauagcuggguagcuauguguggacgggauaagugcugaa
agcaucuaagcaugaagccccccucaagaugagauuucccaacuucgguu
auaagaucccucaaagaugaugagguuaauagguucgagguggaagcaug
gugacauguggagcugacgaauacuaaucgaucgaagacuuaau

<<<<<<......<<<<<<<<<<<.....[[.(((<<<<<<<[[<<.....
.<<<<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....
>>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<
<<<<<<<.........>>>>>>>.>>.>>....<<<<<......<<....
>>.......>>>>.>.........<<....>>..<<<<<......<<...
..>>.....>>>>>..(((....<<<<<<<<....>>>>>>>>......<
<<<<<<<<.....<<<<.......<<<<<<<<<<.<<<...<<<<<....
..>>>>>((......<<<.....))>>>...>>>...>>>>>>>>>>>>>
>.>>>>>..>>>>.....<<<<<<<<.........>>>>>>>>......<
<<<<..<<<<>>>>>..)))......]].>>>>>>>.)))..........
....<<....>>....]].........<<<<....>>>>...........
.......>>>>>>>>>>>.......<<<<..<<<<......>>>>..>>>
>...<.<........>.>.<<<<<<....<<<<<<<.<<<<<..<<<...
<<<.....>>>...>>>...<<....>>..<<<<.....>>>>.....>>
>>>.>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<....<
<<<<<......>>>>>>.....>>>...<<<.<<<<<........>>>>>
>>>....>>>>>>>>>...<<<.....>>>......>>>>>>......>.
>>..<<<<<<....<<<<<....>>>>><<<<<<<<<...<<<<<<<<<.
....<<<...<<<<<<<<..................>>>>>>>>..>>.>
.....>>>>.>>>>>..>>>>>>>.>>..<<<<<<<<<<......>>>>>
>>>>>....<<<......>>>...<<<<.<<<...<<<(((.....<<<<
<<...........<<..<<<<.<<<<........<<<<<.<<...<<<<.
......>>>>...>>.........<<......>>...>>>>>....>>>>
.>>>>.>>...........))).....>>>>>>.>>>...>>>>>>><<<
<<<<...>>>>>>>....>>>>>>..<<<<<<<.<<......<<<<<.<<
....>>.>>>>>...>>.>>>>>>>........>>>>>><......<<..
..<<<<<<.......>>>>>><<<<....<<<<<.<<<..<<<<<<...<
<.....>>.>>>>>>....((<<<<.<<...<<<...<<<....>>>...
>>>...>>...<<<<<........>>>>>))<<<<<<<..<<......<<
<...<<<<....<<<<..<<<..<<<<<.<<<<<<...(((...>>>>>>
<<..<<<<<..<<<<<<<<<<..<<.....>>.>>>>>>.....>>>>..
>>>>>...>>...<<<<<<.....>>>>>>...>>>>>...>>>...>>>
>.........>>>>..>>>.>>..>>>>>>>>>>>.>>>.....<<....
..>>>>>>>.<<<<....>.>>>..>>>>..<<<<....<<<<<<<<.<<
...............<<<<<...............>>>>><<<<<<<.<<
<<....>>>>.>>>>>>>............<<<<<<<<<..<<<......
...>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.<<<<<
.<<<..<<<<<<<..<<<<..<<...<<<<<..<<....>>...>>>>>.
..>>..>>>>>>>>>..>>>>><<<<<<.......>>>>>>........<
...........<<<<<<.....>>>>>>.....>....>>>>>..>>.>>
>>>>>.....>>.>>>>>>>>.>>>>>>.....>.....<<<<<......
..>>>>>..<<<<<<<<.(((.[[......<<<<.[[<<<<..<<<<<.<
<<<<<<<<.<<<<.<<<<<<<<<<<......>>>>>>>>>>>.>>>>...
.<<.<<<<<<.....>>>>>>>>.....>>>>>>>>>..>>>>>..<<<<
.....>>>><<<<<<...........>>>>>>..<<...<<<<<<<...<
<<<<<.......>>>>>>.....<<.[.(((>>....>>>>>>>...<<<
<..<<<......>>>..>>>>.<<<....>>>.>>)))]......<<<<<
<<.((..>>>>..))>>>>>>>.............>>>>..]]>>>>...
....<<<<.<.<<<<<<...<<.......>>...>>>>>>...>>>>.>.
......<<<<<.<<<<<<..<<<<<<<<<......>>>>>>>..>>.<<<
<<.....>>>>>.....>>>>>..>...>>>.>>....<<<<<<<....>
>>.>>>>....]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<<
<<<...............>>>>>>>.<<<<<...<<<<...<<<<<<<<<
<<.)))>>>>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<...
........>>>>>....>>>.>>>>.......>>>>>>>.<<<....>>>
....<<<<<<<<<.......>>>>>....<<<<<<<<.<<<....<<<<<
....>>>>>...>>>..>>>>>.>>>...>>>>....>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p2f Cryo-EM structures of Staphylococcus aureus 70S ribosomes in complex with elongation factor G and fusidic acid
• Resolution: 2.44 Å
• Binding residue (original residue number in PDB): P4 K5 R6 K8 Y9 R11 Q12 H13 R14 K16 K22 G24 T28 F29 W41 R45 Q46 S49 R56 K63 W65 F69 H71 K77 E80 V81 R82 M83 G84 A85 G86 K87 R101 R119 H123 K124 P126 K128
• Binding residue (residue number reindexed from 1): P4 K5 R6 K8 Y9 R11 Q12 H13 R14 K16 K22 G24 T28 F29 W41 R45 Q46 S49 R56 K63 W65 F69 H71 K77 E80 V81 R82 M83 G84 A85 G86 K87 R101 R119 H123 K124 P126 K128

Gene Ontology

Molecular Function

• GO:0000049 tRNA 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:8p2f, PDBe:8p2f, PDBj:8p2f
• PDBsum: 8p2f
• PubMed: 38902339
• UniProt: Q2FW13|RL16_STAA8 Large ribosomal subunit protein uL16 (Gene Name=rplP)