Structure of PDB 6o8x Chain C Binding Site BS01

Receptor Information

>6o8x Chain C (length=275) Species: 1351 (Enterococcus faecalis)

AIKKYKPTTNGRRNMTSSDFAEITTSTPEKSLLQPLKNNAGRNNNGRITV
RHQGGGHKRQYRVIDFKRNKDNVAAVVKTIEYDPNRSANIALVHYEDGVK
AYILAPKGLEVGMRLVSGPEADIKVGNALPLENIPVGTVIHNIEMKPGKG
GQLIRSAGTSAQVLGKEGKYVLIRLNSGEVRMILATCRATIGSVGNEQHE
LINIGKAGRSRWMRKRPTVRGSVMNPNDHPHGGGEGKTPIGRKAPVSPWG
QPAIGYKTRNKKAKSDKLIVRRRTK

Ligand information

>6o8x Chain A (length=2898)

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
caguaaacggcggccguuaacgguccuaagguagcgaaauuccuugucgg
guaaguuccgacccgcacgaaaggcguaacgauuugggcacugucucaac
gagagacucggugaaauuuuaguaccugugaagaugcagguuacccgcga
caggacggaaagaccccauggagcuuuacuguaguuugauauugaguguu
uguaccacauguacaggauagguaggagccgaugagaccggaacgcuagu
uucggaggaggcgcuggugggauacuacccuuguguuaugaacccucuaa
cccgcaccacuaaucguggugggagacagugucagaugggcaguuugacu
ggggcggucgccuccuaaaagguaacggaggcgcccaaagguucccucag
aaugguuggaaaucauucgaagaguguaaaggcagaagggagcuugacug
cgagaccuacaagucgagcagggacgaaagucgggcuuagugauccggug
guuccgcauggaagggccaucgcucaacggauaaaagcuacccuggggau
aacaggcuuaucucccccaagaguccacaucgacggggagguuuggcacc
ucgaugucggcucgucgcauccuggggcuguagucggucccaaggguugg
gcuguucgcccauuaaagcggcacgcgagcuggguucagaacgucgugag
acaguucggucccuauccgucgcgggcguuggaaauuugagaggagcugu
ccuuaguacgagaggaccgggauggacuuaccgcugguguaccaguuguu
cugccaagggcauugcuggguagcuauguagggaagggauaaacgcugaa
agcaucuaagugugaagcccaccucaagaugagauuucccauuucuuuaa
gaaaguaagaccccugagagaugaucagguagauagguuggaaguggaag
gcuagugauaguuggagcggaccaauacuaaucggucgaggacuuaac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6o8x Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis.
• Resolution: 3.68 Å
• Binding residue (original residue number in PDB): K4 K7 P8 N11 R13 R14 K31 K38 N39 N40 G42 R43 N44 N45 N46 G47 R48 I49 T50 G56 Y62 R63 K79 Y83 P85 R87 E97 D98 K101 R115 K147 K150 Q153 L154 R156 S157 A158 G159 T160 Y171 N177 R182 E198 H200 E201 G206 K207 A208 G209 R210 R212 W213 R217 P218 V220 R221 G222 V224 M225 N226 N228 D229 H230 G235 E236 G237 K238 P240 I241 R243 P249 W250 Q252 G256 Y257 K258 T259 R260 K263 K268 K276
• Binding residue (residue number reindexed from 1): K3 K6 P7 N10 R12 R13 K30 K37 N38 N39 G41 R42 N43 N44 N45 G46 R47 I48 T49 G55 Y61 R62 K78 Y82 P84 R86 E96 D97 K100 R114 K146 K149 Q152 L153 R155 S156 A157 G158 T159 Y170 N176 R181 E197 H199 E200 G205 K206 A207 G208 R209 R211 W212 R216 P217 V219 R220 G221 V223 M224 N225 N227 D228 H229 G234 E235 G236 K237 P239 I240 R242 P248 W249 Q251 G255 Y256 K257 T258 R259 K262 K267 K275

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6o8x, PDBe:6o8x, PDBj:6o8x
• PDBsum: 6o8x
• PubMed: 33004869
• UniProt: A0A1B4XKR6