Structure of PDB 5myj Chain B7 Binding Site BS01

Receptor Information

>5myj Chain B7 (length=64) Species: 416870 (Lactococcus cremoris subsp. cremoris MG1363)

PKQKTHRASAKRFKRTGNGGLKRFRAYTSHRFHGKSVKQRRQLRKASMVS
KGDFKRIRRMVATM

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): P2 K3 Q4 K5 T6 R8 A9 T17 N19 R24 R26 A27 Y28 S30 H31 R32 F33 H34 G35 K36 K39 Q40 R41 R42 R45 M49 D54 R57 R60 M65
• Binding residue (residue number reindexed from 1): P1 K2 Q3 K4 T5 R7 A8 T16 N18 R23 R25 A26 Y27 S29 H30 R31 F32 H33 G34 K35 K38 Q39 R40 R41 R44 M48 D53 R56 R59 M64

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: A2RMR2|RL35_LACLM Large ribosomal subunit protein bL35 (Gene Name=rpmI)