Structure of PDB 7xam Chain G Binding Site BS01

Receptor Information

>7xam Chain G (length=176) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

SRIGKQPVPVPSGVDVTINGQNLSVKGPKGTLTLDVAEPISVSRAEDGAI
VVTRPDDERRSRSLHGLSRTLIANLVTGVTEGYTQKMEIFGVGYRVQLKG
QNLEFALGYSHPVLIEAPEGITFAVESPTKFSVSGIDKQKVGQISAVIRR
LRRPDPYKGKGVRYEGEQIRRKVGKT

Ligand information

>7xam Chain A (length=3062)

aaguguuuaagggcgcaugguggaugccuuggcacugggagccgaugaag
gacguaggaggcugcgauaagccucggggagcugucaaccgagcguugau
ccgaggauguccgaauggggaaacccggcacgagugaugucgugucacca
ggcgcugaauauauaggcgucuggggggaacgcggggaagugaaacaucu
caguacccguaggaagagaaaacaaaaugugauuccgugaguaguggcga
gcgaaagcggaggauggcuaaaccguaugcaugugauaccggguaggggu
ugugugugcgggguugugggaccuaucuuuccggcucuaccuggcuggag
ggcagugagaaaauguugugguuagcggaaauggcuugggauggccugcc
guagacggugagagcccgguacgugaaaacccgacgucugucuugauggu
guucccgaguagcagcgggcccguggaaucugcugugaaucugccgggac
cacccgguaagccugaauacuucccagugaccgauagcggauuaguaccg
ugagggaauggugaaaaguaccccgggaggggagugaaagaguaccugaa
accgugcgcuuacaauccgucagagcccucgacgugucguggggugaugg
cgugccuuuugaagaaugagccugcgagucagggacaugucgcgagguua
acccgggugggguagccgcagcgaaagcgagucugaauagggcguaucca
cacaagagugugugguguagugguguguucuggacccgaagcggagugau
cuacccauggccagggugaagcgcggguaagaccgcguggaggcccgaac
ccacuuagguugaagacugaggggaugagcuguggguaggggugaaaggc
caaucaaacuccgugauagcugguucuccccgaaaugcauuuaggugcag
cgucgcauguuucuugccggagguagagcuacuggauggccgaugggccc
cacaggguuacugacgucagccaaacuccgaaugccgguaaguccaagag
ugcggcagugagacggcgggggauaagcuccgugcgucgagagggaaaca
gcccagaucgccggcuaaggccccuaagcgugugcuaaguggaaaaggau
gugcagucgcgaagacaaccaggagguuggcuuagaagcagccacccuug
aaagagugcguaauagcucacuggucaagugauugugcgccgauaaugua
gcggggcucaagcacaccgccgaagccgcggcagccaacguguuggcugg
guaggggagcguccugcauccggugaagccgccgagugaucgaguggugg
agggugugggagugagaaugcaggcaugaguagcgauuaggcaagugaga
accuugcccgccgaaagaccaaggguuccugggccaggccaguccgccca
gggugagucgggaccuaaggcgaggccgacaggcguagucgauggacaac
ggguugauauucccguacccguguaugugcguccaugaugaaucagcggu
acuaaccauccaugggaccuucguugguaguagucaagcgauggggugac
gcaggaagguagccguaccggucagugguaauaccgggguaagccuguag
ggagucagauagguaaauccgucuggcauauauccugagaggugaugcau
agccgagugaggcgaauucggugauccuaugcugccgagaaaagccucua
gcgaggacauacacggcccguaccccaaaccaacacagguggucagguag
agaauacuaaggcguacgagugaacuaugguuaaggaacucggcaaaaug
cccccguaacuucgggagaagggggacccacauggcguguaagccuuuac
ggcccaagcgugaguggguggcacaaaccagugagaagcgacuguuuacu
aaaaacacagguccgugcgaagucgcaagacgauguauacggacugacgc
cugcccggugcuggaagguuaagaggacccguuaacucccuuugggggug
aagcggagaauuuaagccccaguaaacggcgguggucauccuaagguagc
gaaauuccuugucggguaaguuccgaccugcacgaauggcguaacgacuu
cucaacugucucaaccauagacucggcgaaauugcacuacgaguaaagau
gcucguuacgcgcggcaggacgaaaagaccccgggaccuucacuacaacu
ugguauuggugcucgauacgguuuguguaggauaggugggagacugugaa
gcucacacgccaguguggguggagucguuguugaaauaccacucugaucg
uauugggccucuaaccucggaccguauauccgguucagggacagugccug
guggguaguuuaacuggggcgguugccuccuaaaauguaacggaggcgcc
caaagguucccucaaccuggacggcaaucagguguugaguguaagugcac
aagggagcuugacugcgagacggacaugucgagcagggacgaaagucggg
acuagugauccggcaccucugaguggaaggggugucgcucaacggauaaa
agguaccccggggauaacaggcugaucuuccccaagaguccauaucgacg
ggaugguuuggcaccucgaugucggcucgucgcauccuggggcuggagca
ggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcugggu
uuagaacgucgugagacaguucggucucuauccgccgcgcgcgucagaag
cuugaggaaaccugucccuaguacgagaggaccgggacggacgaaccucu
gguauaccaguugucccaccaggggcacggcuggauagccacguucggac
aggauaaccgcugaaagcaucuaagcgggaaaccucuuccaagaccaggc
uucucacccucuaggagggauaaggccccccgcagaccacgggauugaua
gaccagaccuggaagccuaguaauaggugcagggaacuggcacuaaccgg
ccgaaaacuuac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7xam Cryo-EM structures reveal a unique conformational dynamics of the Mycobacterium 23S rRNA helices
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): S2 R3 I4 R60 R63 S64 G67 L68 T71 N75 Y110 S111 H112 K139 Q140 G143 Q144 A147 R151 R154 Y158 K161 T177
• Binding residue (residue number reindexed from 1): S1 R2 I3 R59 R62 S63 G66 L67 T70 N74 Y109 S110 H111 K138 Q139 G142 Q143 A146 R150 R153 Y157 K160 T176

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:7xam, PDBe:7xam, PDBj:7xam
• PDBsum: 7xam
• PubMed: 37709237
• UniProt: A0QSG4|RL6_MYCS2 Large ribosomal subunit protein uL6 (Gene Name=rplF)