Structure of PDB 6o8z Chain R Binding Site BS01

Receptor Information

>6o8z Chain R (length=118) Species: 1351 (Enterococcus faecalis)

ARVKGGTVTRKRRKKVLKLAKGYYGSKHTLFKSAKEQVMNSYYYAFRDRR
QKKRDFRKLWIARINAAARMNGLSYSKLMHGLKLAEIDINRKMLADLAVN
DAAAFTALAEQAKDALSK

Ligand information

>6o8z Chain A (length=2903)

uuaagugaauaagggcgcacgguggaugccuuggcacuaggagccgauga
aggacgggacuaacaccgauaugcuuuggggagcuguaaguaagcuauga
uccagagauuuccgaaugggggaacccaauaucuuuuauaggauauuacu
uuucagugaauacauagcugauuagagguagacgcagagaacugaaacau
cuuaguaccugcaggaagagaaagaaaauucgauucccugaguagcggcg
agcgaaacgggaagagcccaaaccaacaagcuugcuuguugggguuguag
gacuccgauaugguagucuguuaguauaguugaaggauuuggaaaauucc
gcuaaagagggugaaagccccguagacgaaaugcugacaacaccuaggag
gauccugaguacggcggaacacgagaaauuccgucggaauccgcggggac
caucccgcaaggcuaaauacucccuagugaccgauagugaaccaguaccg
ugagggaaaggugaaaagcaccccggaaggggagugaaauagauccugaa
accgugugccuacaacaagucaaagcucguuaaugagugauggcgugccu
uuuguagaaugaaccggcgaguuacgauugcaugcgagguuaagucgaag
agacggagccgcagcgaaagcgagucugaauagggcgaaugaguauguag
ucguagacccgaaaccaugugaucuacccauguccagguugaaggugcgg
uaaaacgcacuggaggaccgaacccacguacguugaaaagugcggggaug
agguguggguagcggagaaauuccaaacgaacuuggagauagcugguucu
cuccgaaauagcuuuagggcuagccucggaauugagaaugauggagguag
agcacuguuuggacuaggggcccaucggguuaccgaauucagauaaacuc
cgaaugccauucauuuauauccgggagucagacugcgagugauaagaucc
guagucgaaagggaaacagcccagaccaccagcuaaggucccaaaauaua
uguuaaguggaaaaggaugugggguugcacagacaacuaggauguuggcu
uagaagcagccaccauuuaaagagugcguaauagcucacuagucgaguga
cccugcgccgaaaauguaccggggcuaaacauauuaccgaagcuguggac
uacaccauuagguguagugguaggagagcguucuaagggcguugaagguc
gaucgugaggacggcuggagcgcuuagaagugagaaugccgguaugagua
gcgaaagacaggugagaauccuguccaccguaugacuaagguuuccuggg
gaaggcucguccgcccaggguuagucgggaccuaagccgaggccgauagg
cguaggcgauggacaacagguugauauuccuguaccaguuguuuuuguuu
gagcaauggagggacgcaguaggcuaaggaaugcaugcgauuggaagugc
auguccaagcaaugagucuugaguagaguuaaaugcuuuacucuuuaagg
acaaguugugacggggagcgaaauaguagcgaaguuccugacgucacacu
gccaagaaaagcuucuagugagaaaacaacugcccguaccguaaaccgac
acagguagucgaggagaguauccuaaggugagcgagcgaacucucguuaa
ggaacucggcaaaaugaccccguaacuucgggagaaggggugcugacuuc
ggucagccgcagugaauaggcccaagcgacuguuuaucaaaaacacaggu
cucugcaaaaucguaagaugaaguauaggggcugacgccugcccggugcu
ggaagguuaagaggauggguuagcuucggcgaagcucagaauugaagccc
caguaaacggcggccguaacuauaacgguccuaagguagcgaaauuccuu
gucggguaaguuccgacccgcacgaaaggcguaacgauuugggcacuguc
ucaacgagagacucggugaaauuuuaguaccugugaagaugcagguuacc
cgcgacaggacggaaagaccccauggagcuuuacuguaguuugauauuga
guguuuguaccacauguacaggauagguaggagccgaugagaccggaacg
cuaguuucggaggaggcgcuggugggauacuacccuuguguuaugaaccc
ucuaacccgcaccacuaaucguggugggagacagugucagaugggcaguu
ugacuggggcggucgccuccuaaaagguaacggaggcgcccaaagguucc
cucagaaugguuggaaaucauucgaagaguguaaaggcagaagggagcuu
gacugcgagaccuacaagucgagcagggacgaaagucgggcuuagugauc
cggugguuccgcauggaagggccaucgcucaacggauaaaagcuacccug
gggauaacaggcuuaucucccccaagaguccacaucgacggggagguuug
gcaccucgaugucggcucgucgcauccuggggcuguagucggucccaagg
guugggcuguucgcccauuaaagcggcacgcgagcuggguucagaacguc
gugagacaguucggucccuauccgucgcgggcguuggaaauuugagagga
gcuguccuuaguacgagaggaccgggauggacuuaccgcugguguaccag
uuguucugccaagggcauugcuggguagcuauguagggaagggauaaacg
cugaaagcaucuaagugugaagcccaccucaagaugagauuucccauuuc
uuuaagaaaguaagaccccugagagaugaucagguagauagguuggaagu
ggaaggcuagugauaguuggagcggaccaauacuaaucggucgaggacuu
aac

<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<.....
.<<<<<<.[...((.>>>.....<<<<<<<..<<<))...].>>>.....
>>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<
..<<<<<.........>>>>>..>>.>>....<<<<<......<......
>.......>>>>.>.........<<....>>..<<<<<......<<....
.>>.....>>>>>..(((....<<<<<<<<....>>>>>>>>......<<
<<<<<<.....<<<.<<.<<<<<<<<<.<<<...<<<.<......>.>>>
((......<<<.....))>>>...>>>...>>>>>>>>>>>>>>..>>>>
..>>>>.....<<<<<<<<.........>>>>>>>>......<<<<<..<
<<<>>>>>..)))......]].>>>>>>>.]]...............<<.
...>>....]].........<<<<....>>>>.............}....
>>>>>>>>>>>.......<<<<..<<<<......>>>>..>>>>...<.<
........>.>.<<<<<<....<<<<<<<<<<<<<..<<<...<<.....
..>>...>>>...<<....>>..<<<<.....>>>>......>>>>>>>>
>>>>>..<<.<..<<<<.<<.....<<<<<<<<<..<<<....<<<<<<.
.....>>>>>>.....>>>...<<<.<<<<<........>>>>>>>>...
.>>>>>>>>>...<<<.....>>>......>>.>>>...>..>.>>..<<
<<<<....<<<<<....>>>>><<<<<<<<..<..<<<<<<<<<.....<
<<...<<.<<<<....<<...<.....>....>>....>>>>.>>..>>.
>.....>>>>.>>>>>..>>>>>>>.>>..<<<<<<<.<<......>>.>
>>>>>>....<<<......>>>...<<<<.<<<...<<<(((.....<<<
<<<...........<<..<<<<<<<<<........<<.....<...<<<.
........>>>...>..........................>>....>>>
>>>>>>.>>...........))).....>>>>>>.>>>...>>>>>>><<
<<<<<......>>>>>>>....>>>>>><.<<<<<<<.<<......<<<<
<.<<....>>.>>>>>...>>.>>>>>>>..>.....>>>>>><......
<<....<<<<<<.......>>>>>><<<<....<<<<<.<<<..<<<<<<
...<<.....>>.>>>>>>....((<<<<.<<...<<<...<<<....>>
>...>>>...>>...<<<<<........>>>>>))<<<<<<<........
...<...<<<<....<<<<..<<...<<<<<.....<...{.{......>
....<<..<<<<<..<<<<.<<<<<<<<<.....>>>>>>>>>.....>>
>>..>>>>>...>>...<<.........>>....>>>>>....>>...>>
>>.........>>>>..>.......>>>>>>>>>>>.>>>.....<<...
...>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<
<...............<<<<<....<<..>>.....>>>>><<<<<<...
.>>>>>>............<<<<<<<<<..<<<.........>>>..<<<
<<<<.....<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<<
<<..<<<<..<<...<<<<<<.<<....>>..>>>>>>...>>..>>>>>
>>>>..>>>>><<<<<<.......>>>>>>........<...........
<<<<<<.....>>>>>>.....>....>>>>>..>>.>>>>>>>.....>
>.>>>>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<
<<<<<<.(((.[[......<<<<.[[<<<<..<<<<<.<<<<<<<<<.<<
<.<<<<<<<.<<<<...........<<<<<.............<<<<<<.
...>>>>>>....................>>>>>..>>>>.>>>>>>>.>
>>....<<.<<<<<<.....>>>>>>>>.....>>>>>>>>>..>>>>>.
.<<<<.....>>>><<<<<<...........>>>>>>..<<...<<<<<<
<...<<<<<<.......>>>>>>.....<<.[.(((>>....>>>>>>>.
..<<<<..<<<......>>>..>>>>.<<<....>>>.>>)))]......
<<<<<<<.((..>>>>..))>>>>>>>.............>>>>..]]>>
>>.......<<<<.<.<<<<<<...<<.......>>...>>>>>>...>>
>>.>.......<<<<<.<.<<<<..<<<<<<<<<......>>>>>>..>>
>.<<<<<.....>>>>>.....>>>>...>...>>>.>>....<<<<<<<
....>>>.>>>>....]]..)))>>>>>>>>....<<<<<<<...<<<<.
.<<<<<<<...............>>>>>>>.<<<<<...<<<<...<<<<
<<<<<<<.}.}>>>>>>..>>>>>...>>>>.>>>>>...<<<.<..<<<
<<...........>>>>>...>>>>.>>>>.......>>>>>>>..<<<.
.....>>>.....<<<<<<<<<.......>>>>>....<<<<<<<<..<<
....<<<<<....>>>>>...>>...>>>>>.>>>...>>>>....>>>>
>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6o8z Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis.
• Resolution: 3.49 Å
• Binding residue (original residue number in PDB): A2 R3 V4 G7 T8 T10 R11 R13 R14 K15 K16 K19 K22 G23 Y24 Y25 G26 K28 H29 T30 L31 F32 K33 E37 Q38 Y45 R48 D49 R50 R51 K53 K54 R55 F57 R58 N66 Y76 H81 K84 N91 R92 K93
• Binding residue (residue number reindexed from 1): A1 R2 V3 G6 T7 T9 R10 R12 R13 K14 K15 K18 K21 G22 Y23 Y24 G25 K27 H28 T29 L30 F31 K32 E36 Q37 Y44 R47 D48 R49 R50 K52 K53 R54 F56 R57 N65 Y75 H80 K83 N90 R91 K92

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:6o8z, PDBe:6o8z, PDBj:6o8z
• PDBsum: 6o8z
• PubMed: 33004869
• UniProt: A0A1B4XM76