Structure of PDB 7y41 Chain K Binding Site BS01

Receptor Information

>7y41 Chain K (length=146) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

PTYTPKAGDTTRSWYVIDASDVVLGRLASAAATLLRGKHKPTFTPNVDGG
DFVIVINADKIAVSGDKLTKKFAYRHSGYPGGLRKRTIGELLEKHPTRVV
ENAIIGMLPHNKLGRQIQKKLKVYAGPDHPHAAQQPIPFEIKQVAQ

Ligand information

>7y41 Chain A (length=3119)

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
acuaaccauccaaaaccaccgugaccgcaccuuucgggguguggcguugg
uggggcugcaugggaccuucguugguaguagucaagcgauggggugacgc
aggaagguagccguaccggucagugguaauaccgggguaagccuguaggg
agucagauagguaaauccgucuggcauauauccugagaggugaugcauag
ccgagugaggcgaauucggugauccuaugcugccgagaaaagccucuagc
gaggacauacacggcccguaccccaaaccaacacagguggucagguagag
aauacuaaggcguacgagugaacuaugguuaaggaacucggcaaaaugcc
cccguaacuucgggagaagggggacccacauggcguguaagccuuuacgg
cccaagcgugaguggguggcacaaaccagugagaagcgacuguuuacuaa
aaacacagguccgugcgaagucgcaagacgauguauacggacugacgccu
gcccggugcuggaagguuaagaggacccguuaacucccuuugggggugaa
gcggagaauuuaagccccaguaaacggcggugguaacuauaaccauccua
agguagcgaaauuccuugucggguaaguuccgaccugcacgaauggcgua
acgacuucucaacugucucaaccauagacucggcgaaauugcacuacgag
uaaagaugcucguuacgcgcggcaggacgaaaagaccccgggaccuucac
uacaacuugguauuggugcucgauacgguuuguguaggauaggugggaga
cugugaagcucacacgccaguguggguggagucguuguugaaauaccacu
cugaucguauugggccucuaaccucggaccguauauccgguucagggaca
gugccugguggguaguuuaacuggggcgguugccuccuaaaauguaacgg
aggcgcccaaagguucccucaaccuggacggcaaucagguguugagugua
agugcacaagggagcuugacugcgagacggacaugucgagcagggacgaa
agucgggacuagugauccggcaccucugaguggaaggggugucgcucaac
ggauaaaagguaccccggggauaacaggcugaucuuccccaagaguccau
aucgacgggaugguuuggcaccucgaugucggcucgucgcauccuggggc
uggagcaggucccaaggguugggcuguucgcccauuaaagcggcacgcga
gcuggguuuagaacgucgugagacaguucggucucuauccgccgcgcgcg
ucagaagcuugaggaaaccugucccuaguacgagaggaccgggacggacg
aaccucugguauaccaguugucccaccaggggcacggcuggauagccacg
uucggacaggauaaccgcugaaagcaucuaagcgggaaaccucuuccaag
accaggcuucucacccucuaggagggauaaggccccccgcagaccacggg
auugauagaccagaccuggaagccuaguaauaggugcagggaacuggcac
uaaccggccgaaaacuuac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7y41 Cryo-EM structures reveal a unique conformational dynamics of the Mycobacterium 23S rRNA helices
• Resolution: 4.1 Å
• Binding residue (original residue number in PDB): P2 T3 P6 W15 D22 V24 L25 G26 R27 S30 K39 N47 S65 K68 K71 K72 Y75 R76 H77 S78 Y80 L84 R85 R99 G107 M108 H111 N112 K113 L114 R116 K120 H132 Q135 Q144 Q147
• Binding residue (residue number reindexed from 1): P1 T2 P5 W14 D21 V23 L24 G25 R26 S29 K38 N46 S64 K67 K70 K71 Y74 R75 H76 S77 Y79 L83 R84 R98 G106 M107 H110 N111 K112 L113 R115 K119 H131 Q134 Q143 Q146

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7y41, PDBe:7y41, PDBj:7y41
• PDBsum: 7y41
• PubMed: 37709237
• UniProt: A0QSP8|RL13_MYCS2 Large ribosomal subunit protein uL13 (Gene Name=rplM)