Structure of PDB 8p2f Chain I Binding Site BS01

Receptor Information

>8p2f Chain I (length=204) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

NYDVLKLDGTKSGSIELSDAVFGIEPNNSVLFEAINLQRASLRQGTHAVK
NRSAVSGGGRKPWKQKGTGRARQGTIRAPQWRGGGIVFGPTPRSYAYKMP
KKMRRLALRSALSFKAQENGLTVVDAFNFEAPKTKEFKNVLSTLEQPKKV
LVVTENEDVNVELSARNIPGVQVTTAQGLNVLDITNADSLVITEAAAKKV
EEVL

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): N29 V32 L39 Q40 R41 S43 R45 Q46 T48 H49 A50 V51 K52 N53 R54 S55 V57 S58 G59 R62 K63 K66 Q67 K68 G69 G71 R72 A73 R74 Q75 G76 R79 P81 Q82 W83 R84 G85 I88 V89 F90 P92 R95 Y99 K100 P102 K103 K104 M105 R106 P134 T136 K151 L165 R168 N169 P171
• Binding residue (residue number reindexed from 1): N27 V30 L37 Q38 R39 S41 R43 Q44 T46 H47 A48 V49 K50 N51 R52 S53 V55 S56 G57 R60 K61 K64 Q65 K66 G67 G69 R70 A71 R72 Q73 G74 R77 P79 Q80 W81 R82 G83 I86 V87 F88 P90 R93 Y97 K98 P100 K101 K102 M103 R104 P132 T134 K149 L163 R166 N167 P169

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8p2f, PDBe:8p2f, PDBj:8p2f
• PDBsum: 8p2f
• PubMed: 38902339
• UniProt: Q2FW07|RL4_STAA8 Large ribosomal subunit protein uL4 (Gene Name=rplD)