Structure of PDB 5myj Chain B6 Binding Site BS01

Receptor Information
>5myj Chain B6 (length=44) Species: 416870 (Lactococcus cremoris subsp. cremoris MG1363) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKRTYQPHKKSRKTTHGFRSRMATKNGRRVLAARRRKGRASLTV
Ligand information
>5myj Chain BA (length=2897) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
caaaguuaauaagggcgcacgguggaugccuuggcacuaagagccgauga
aggacgugacuaacgacgauauucuagggggagcaguaaguacgcauuga
ucccuaggucuccgaauggggaaacccagcuguuacuagcaguuauucau
gagugaauacauagcucauguaaagguaacgcagagaacugaaacaucua
aguaccugcaggaagagaaaguaaaaacgauuucguaaguagcggcgagc
gaacgcgaagaagggcaaaccaagaagcuugcuucuugggguuguaggac
ugcaacguggacuuaagcauuauagucgaauaaccugggaagguuaauca
aagaggguaauaaucccguagacaaaauagcgcuuauaccuagcaguauc
cugaguagggcuggacacgcgaaauccaguuugaauccgggaggaccauc
ucccaacccuaaauacuccuuagugaccgauagugaaccaguaccgugag
ggaaaggugaaaagaaccccgagaggggagugaaauagcaccugaaaccg
ugugccuacaagaaguucgagcccguuaaugggugagagcgugccuuuug
uagaaugaaccggcgaguuacguuaugaugcgagguuaaguugaagagac
ggagccguagggaaaccgagucugaauagggcgacuuaguaucaugaugu
agacccgaaaccuagugaccuauccaugagcagggugaaggugugguaag
acgcacuggaggcccgaaccaggacacguugaaaaguguuuggaugacuu
guggauagcggagaaauuccaaacgaacugggagauagcugguucucucc
gaaauagcuuuagggcuagcgucgaaauguaaguguauuggagguagagc
acuguuugggugagggguccgucuaggauuaccaaucucagauaaacucc
gaaugcuaauacacauguucggcagucagacugcgagugcuaagauccgu
agucgaaagggaaacagcccagaccaacagcuaaggucccaaaauauaug
uuaaguggaaaaggaugugggguugcacagacaacuaggauguuagcuca
gaagcagcuaucauucaaagagugcguaauagcucacuagucgagugacc
cugcgccgaaaauguaccggggcuaaacauauuaccgaagcuuuggauug
auauuuuaucaaugguaggagagcguucuuaaccgcaaugaagguauacc
gugaggagugcuggagcguuaagaagugagaaugccgguaugaguagcgc
aagauaagugagaaucuuauccaccguaagacuaagguuuccaggggaag
gcucguccgcccuggguuagucgggaccuaaggcgaggccgaaaggcgua
gucgauggacaacugguugauauuccaguacuagauaugaucgugaugga
gggacgcaguaggcuaagagaugccaguuaauggauccuggucuaagcag
ugaggugugagaugugucaaaugcauuucucucuaacauugagcugugau
ggggaagcaacuacgguugcgaacucucugaugucacacugccaagaaaa
gcuucuagcguaaagucauaucuacccguaccgcaaaccgacacagguag
ucgaggcgaguagccucaggugaucgagagaacucucguuaaggaacucg
gcaaaauagccccguaacuucgggagaaggggugcugguguaaaagccag
ccgcagugaauaggcccaagcaacuguuuaucaaaaacacagcucucugc
uaaaccgcaaggugauguauagggggugacgccugcccggugcuggaagg
uuaagaggagugcuuagacguaagucgaagguaugaauugaagccccagu
aaacggcggccguaacuauaacgguccuaagguagcgaaauuccuugucg
gguaaguuccgacccgcacgaaaggcguaaugauuugggcacugucucaa
cgagagacucggugaaauuuuaguaccugugaagaugcagguuacccgcg
acaggacggaaagaccccauggagcuuuacuguaguuugauauugaguac
cuguaagucauguacaggauagguaggagccauugaaauagggacgcuag
uuucuauugaggcguuguugggauacuacccuugacuuaugguuacucua
acccgcuggcauaaucggccagggagacagugucugacggacaguuugac
uggggcggucgccuccuaaagaguaacggaggcgcucaaagguuggcuca
gauugguuggaaaucaaucguagaguguaaagguaaaagccagcuugacu
gcgagagcuacaacucgagcagguaggaaacuaggacuuagugauccggu
gguaccgcauggaagggccaucgcucaacggauaaaagcuacccugggga
uaacaggcuuaucucccccaagaguucacaucgacggggagguuuggcac
cucgaugucggcucgucgcauccuggggcuguagucggucccaaggguug
ggcuguucgcccauuaaagcggcacgcgagcuggguucagaacgucguga
gacaguucggucccuauccgucgcgggcguagguaauuugagaggaucug
uccuuaguacgagaggaccgggauggacuuaccgcugguguaccaguugu
uccgccaggagcacggcuggauagcuauguagggaagggauaagcgcuga
aagcaucuaagugcgaagcccaccucaagaugagauuacccauucguaag
aauuaagagcccagagagaugaucugguagauaggcuggaaguggaagag
uugcgagacuuggagcggaccaguacuaaucgcucgaggacuuuacc
.<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<.....
.<<<<<<.....((.>>>....<<<<<<<<..<<.))......>>.....
>>>>>>>>..>>>....<<<....>>><<<<<<.....>>>>>>.<<<<<
<<<<.........>>>>>>>.>>.>>...<<<<<......<<....>>..
.....>>>>.>.........<......>..<<<<<<.....<<.....>>
....>>>>>>..(((....<<<<<<........>>>>>>......<<<<<
<............<<<<<.<<...<<<....<<<<......>>>>.((..
....<<<.....))>>>...>>>.....>>.>>>>>........>>..>>
>>.....<<<<<<<<.........>>>>>>>>......<<<<<..<<<<>
>>>>..)))......]].>>>>>>>.]]...............<<....>
>....]].........<<<<....>>>>..................>>>>
>>>>>>>.......<<<<..<<<<......>>>>..>>>>...<.<....
....>.>.<<<<<<....<<<<<<<<<<<<<..<<<...<<<.....>>>
...>>>...<<....>>..<<<<.....>>>>......>>>>>>>>>>>>
>..<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<<<......
..>>>>>.....>>>...<<<.<<<<<........>>>>>>>>....>>>
>>>>>>...<<<.....>>>......>>>>>>......>.>>..<<<<<<
....<<<<<....>>>>><<<<<<<<......<<<<<<<<<.....<<<.
..<<.<<<<<...<<..<<......>>....>>...>>>>>.>>..>>.>
.....>>>>>>>>>...>>>>>>.>>..<<<<<<<.<<......>>.>>>
>>>>....<<<......>>>...<<<<.<<<...<<<(((.....<<<<<
<...........<<...<<<<<<<<........<<<.<.<....<<....
.......>>....>.........<<......>>...>.>>>....>>>>>
>>>..>>...........))).....>>>>>>.>>>...>>>>>>><<<<
<<.....>>>>>>....>>>>>>..<<<<..<.<<<......<<<<<.<<
....>>.>>>>>...>>>.>.>>>>........>>>>>><<.....<...
..<<<<<<.......>>>>>><<<<....<<<<..<<<..<<<<<<...<
<.....>>.>>>>>>....((<<<<.<<.<.<<<...<<<....>>>...
>>>..>>>....<<<<........>>>>.))<<<<<...........<<<
<....<<<<...<...<<<<<...........{.............<<<<
<.<<....<.<...<<<.....>>>..>.>........>>..>>>>>...
..<...<<<<<....>>>>>...>>>>>>....>....>>>>........
.>>>>..............>>>>>>>>>.>>>.....<<......>>.>>
>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<<.......
........<<<<<...............>>>>><<<<<........>>>>
>............<<<<<<<<<..<<<.........>>>..<<<<<<<..
...<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<
<...<<...<<<<<..<<......>>..>>.>>>...>>...>>>>>>>>
..>>>>><<<<<<.......>>>>>>........<...........<<<<
<<.....>>>>>>.....>....>>>>>..>>.>>>>>>>.....>>.>>
>>>>>>.>>>>.>...>>......<<<<<........>>>>>..<<<<<<
<<.(((.[[......<<<<.[[<<<<..<<<<<.<<<.<<<<<.<<<<<<
<......<<<...........<<.<<..<<<......<<<<...<....>
...>>>>...>>>............>>.>>..>>>.....>>.>>>>>..
..<<.<<<<<.......>>>>>>>.....>>>>>.>>>..>>>>>..<<<
<.....>>>><<<<<<...........>>>>>>..<<...<<<<<<<...
<<<<<<.......>>>>>>.....<<.[.(((>>....>>>>>>>...<<
<<..<<<......>>>..>>>>.<<<....>>>.>>)))]......<<<<
<<<.((..>>>>..))>>>>>>>.............>>>>..]]>>>>..
.....<<<<...<<<<<<...<<.......>>...>>>>>>....>>>.>
.......<.<<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>.<<
<<<.....>>>>>.....>>>>>..>...>>>..>....<<<<<<<....
>>>.>>>>....]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<
<<<<...............>>>>>>>.<<<<<...<<<<...<<<<<<<<
<<<.}..>>>>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<..
.........>>>>>....>>>.>>>>.......>>>>>>>..<<<....>
>>....<<<<<<<<<.......>>>>>....<<<<<<<<..<<....<<<
<<....>>>>>...>>...>>>>>.>>>...>>>>....>>>>>...
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5myj A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy.
Resolution5.6 Å
Binding residue
(original residue number in PDB)
M1 R3 T4 Y5 Q6 P7 H8 K9 K10 S11 R12 K13 H16 G17 F18 R19 R21 K25 N26 R28 R29 V30 R34 R35 R36 K37 R39 A40
Binding residue
(residue number reindexed from 1)
M1 R3 T4 Y5 Q6 P7 H8 K9 K10 S11 R12 K13 H16 G17 F18 R19 R21 K25 N26 R28 R29 V30 R34 R35 R36 K37 R39 A40
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:5myj, PDBe:5myj, PDBj:5myj
PDBsum5myj
PubMed28959045
UniProtA2RHL6|RL34_LACLM Large ribosomal subunit protein bL34 (Gene Name=rpmH)

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