Structure of PDB 5xym Chain 2 Binding Site BS01

Receptor Information

>5xym Chain 2 (length=46) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

AKGKRTFQPNNRRRARVHGFRLRMRTRAGRAIVANRRSKGRRALTA

Ligand information

>5xym Chain A (length=2665)

aguguuuaagggcgcaugguggaugccuuggcacugggagccgaugaagg
acguaggaggcugcgauaagccucggggagcugucaaccgagcguugauc
cgaggauguccgaauggggaaacccggcacgagugaugucgugucaccag
gcgcuaauauauaggcgucuggggggaacgcggggaagugaaacaucuca
guacccguaggaagagaaaacaaaaugugauuccgugaguaguggcgagc
gaaagcggaggauggcuaaaccggcgggguugugggaugguuagcggaaa
uggcuugggauggccugccguagacggugagagcccgguacgugaaaacc
cgaccccgaguagcagcgggcccguggaaucugcugugaaucugccggga
ccacccgguaagccugaauacuucccagugaccgauagcggauuaguacc
gugagggaauggugaaaaguaccccgggaggggagugaaagaguaccuga
aaccgugcgcuuacaauccgucagagcccucgacuggggugauggcgugc
cuuuugaagaaugagccugcgagucagggacaugucgcgagguuaacccg
ggugggguagccgcagcgaaagcgagucugaauagggcguauccacacaa
gagugugugguguagugguguguucuggacccgaagcggagugaucuacc
cauggccagggugaagcgcggguaagaccgcguggaggcccgaacccacu
uagguugaagacugaggggaugagcuguggguaggggugaaaggccaauc
aaacuccgugauagcugguucuccccgaaaugcauuuaggugcagcgucg
cauguuucuugccggagguagagcuacuggauggccacgucagccaaacu
ccgaaugccgguaaguccaagagugcggcagugggacggcgggggauaag
cuccgugcgucgagagggaaacagcccagaucgccggcuaaggccccuaa
gcgugugcuaaguggaaaaggaugugcagucgugauugugcgccgauaau
guagcggggcucaagcacaccgccgaagccgcggcagccaauuggcuggg
uaggggagcguccugcauccggugaagccgccgagugaucgaguggugga
gggugugggagugagaaugcaggcaugaguagcgauuaggcaagugagaa
ccuugcccgccgaaagaccaaggguuccugggccaggccaguccgcccag
ggugagucgggaccuaaggcgaggccgacaggcguagucgauggacaacg
gguugauauucccguacccguguagcgauggggugacgcaggaagguagc
cguaccggucaggguaauaccgggguaagccuguagggagucgauaggua
aauccgucuggcauccugagaggugaugcauagccgcgaauucggugauc
cuaugcugccgagaaaagccucuagcgacacggcccguaccccaaaccaa
cacagguggucagguagagaauacuaaggcguacgagugaacuaugguua
aggaacucggcaaaaugcccccguaacuucgggagaagggggacccacau
ggcguguaagcgugaguggguggcacaaaccagugagaagcgacuguuua
cuaaaaacacagguccgugcgaagucgcaagacgauguauacggacugac
gccugcccggugcuggaagguuaagaggacccguuaacugugaagcggag
aauuuaagccccaguaaacggcggugguaacuauaaccauccuaagguag
cgaaauuccuugucggguaaguuccgaccugcacgaauggcguaacgacu
ucucaacugucucaaccauagacucggcgaaauugcacuacgaguaaaga
ugcucguuacgcgcggcaggacgaaaagaccccgggaccuucacuacaac
uugguauuggugcucgagggccucuaaccucggaccguaauccgguucag
ggacagugccugguggguaguuuaacuggggcgguugccuccuaaaaugu
aacggaggcgcccaaagguucccucaaccuggacggcaaucagguguuga
guguaagugcacaagggagcuugacugcgagacggacaugucgagcaggg
acgaaagucgggacuagugauccggcaccucugaguggaaggggugucgc
ucaacggauaaaagguaccccggggauaacaggcugaucuuccccaagag
uccauaucgacgggaugguuuggcaccucgaugucggcucgucgcauccu
ggggcuggagcaggucccaaggguugggcuguucgcccauuaaagcggca
cgcgagcuggguuuagaacgucgugagacaguucggucucuauccgccgc
gcgcgucagaagcuugaggaaaccugucccuaguacgagaggaccgggac
ggacgaaccucugguauaccaguugucccaccaggggcacggcuggauag
ccacguucggacaggauaaccgcugaaagcaucuaagcgggaaaccucuu
ccaagaccaggcuucucacccucuaggagggauaaggccccccgcagacc
acgggauugauagaccagaccuggaagccuaguaauaggugcagggaacu
ggcacuaacggccga

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xym Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers.
• Resolution: 3.08 Å
• Binding residue (original residue number in PDB): A2 K3 R6 T7 F8 Q9 P10 N11 N12 R13 R14 R15 A16 R17 H19 G20 F21 R22 R24 R28 A29 I33 N36 R37 R38 K40 G41 R42 R43
• Binding residue (residue number reindexed from 1): A1 K2 R5 T6 F7 Q8 P9 N10 N11 R12 R13 R14 A15 R16 H18 G19 F20 R21 R23 R27 A28 I32 N35 R36 R37 K39 G40 R41 R42

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5xym, PDBe:5xym, PDBj:5xym
• PDBsum: 5xym
• PubMed: 28875450
• UniProt: A0R7K0|RL34_MYCS2 Large ribosomal subunit protein bL34 (Gene Name=rpmH)