Structure of PDB 5myj Chain BZ Binding Site BS01

Receptor Information

>5myj Chain BZ (length=75) Species: 416870 (Lactococcus cremoris subsp. cremoris MG1363)

STSNGRDSQAKRLGAKASDGELVSGGSILFRQRGTHIHPGTNVGRGGDDT
LFAKIEGTVKFEMKRGKKHVSVYPV

Ligand information

>5myj Chain BA (length=2897)

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

Structure summary

• PDB: 5myj A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy.
• Resolution: 5.6 Å
• Binding residue (original residue number in PDB): S17 T18 N20 R22 D23 S24 Q25 K27 R28 L29 K32 S34 D35 E37 S40 G41 G42 S43 I44 R47 R49 G50 T51 H52 G63 D64 D65 F68 K70 F77 K84
• Binding residue (residue number reindexed from 1): S1 T2 N4 R6 D7 S8 Q9 K11 R12 L13 K16 S18 D19 E21 S24 G25 G26 S27 I28 R31 R33 G34 T35 H36 G47 D48 D49 F52 K54 F61 K68

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:5myj, PDBe:5myj, PDBj:5myj
• PDBsum: 5myj
• PubMed: 28959045
• UniProt: A2RLA2|RL27_LACLM Large ribosomal subunit protein bL27 (Gene Name=rpmA)