Structure of PDB 8oj5 Chain LL Binding Site BS01

Receptor Information

>8oj5 Chain LL (length=194) Species: 9606 (Homo sapiens)

APSRNGMVLKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPA
SGPIRPIVRCPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPR
RRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDSSAEELKLATQLT
GPVMPVRNVYKKEKARVITEEEKNFKAFASLRMARANARLFGIR

Ligand information

>8oj5 Chain 5 (length=3474)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcggggggcccaaguccuucugau
cgaggcccagcccguggacggugugaggccgguagcggcccccggcgcgc
cgggcccgggucuucccggagucggguugcuugggaaugcagcccaaagc
gggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauaguca
acaaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaag
agggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgcc
cggaggauucaacccggcggcggguccggccgugccggcgaccggccgcc
gccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacgg
cugggaaggcccggcggggaagguggcucgggggcccccgaguguuacag
cccccccggcagcagcacucgccgaaucccggggccgagggagcgagacc
cgucgccgcgcucuccccccggggggccgggccaccccucccacggcgcg
accgcucggggcggacuguccccagugcgccccgggcgggucgcgccguc
gggcccggggggccacgcgcgcgucccccgggggacggcggagcgagcgc
acggggucggcggcgacgucggcuacccacccgacccgucuugaaacacg
gaccaaggagucuaacacgugcgcgagucgggggcucgcacgaaagccgc
cguggcgcaaugaaggugaaggccggcgccggccgaggugggaucccgag
gccucuccaguccgccgagggcgcaccaccggcccgucucgcgggaggug
gagcacgagcgcacguguuaggacccgaaagauggugaacuaugccuggg
cagggcgaagccagaggaaacucugguggagguccguagcgguccugacg
ugcaaaucggucguccgaccuggguauaggggcgaaagacuaaucgaacc
aucuaguagcugguucccuccgaaguuucccucaggauagcuggcgcucu
cgcagacccgacgcaguuuuauccgguaaagcgaaugauuagaggucuug
gggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagcc
cggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcca
cuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguuaa
ggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugaua
uagacagcgccgaaucaacuagcccugaaaauggauggcgcuggagcguc
gggcccauacccggccgucgccggcagucgagaguggacgggagccccgc
ggacgcuacgccgcgacgaguaggagggccgcugcggugagccuugaagc
cuagggcgcgggcccggguggagccgccgcaggugcagaucuugguggua
guagcaaauauucaaacgagaacuuugaaggccgaaguggagaaggguuc
caugugaacagcaguugaacaugggucagucgguccugagagaugggcga
gcgccguuccgaagggacgggcgcccucggccgaucgaaagggagucggg
uucagauccccgaauccggagcggagaugggcgccgcgaggcguccagug
cgguaacgcgaccgaucccggagaagccggcgggagccccggggagaguu
cucuuuucuuugugaagggcagggcgcccuggaauggguucgccccgaga
gaggggcccgugccuuggaaagcgucgcgguuccggcggcguccggugag
cucucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgccg
ggccguacccauauccgcagcaggucuccaaggugaacagccucuggcau
guuggaacaauguagguaagggaagucggcaagccggauccguaacuucg
ggauaaggauuggcucuaagggcugguagcagccgacuuagaacuggugc
ggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggccc
gcggcggguguugacgcgaugugauuucugcccagugcucugaaugucaa
agugaagaaauucaaugaagcgcggguaaacggcgggaguacucucuuaa
gguagccaaaugccucgucaucuaauuagugacgcgcaugaauggaugaa
cgagauucccacugucccuaccuacuauccagcgaaaccacagccaaggg
aacgggcuuggcggaaucagcggggaaagaagacccuguugagcuugacu
cuagucuggcacggugaagagacaugagagguguagaauaagugggaggc
ccgccggugaaauaccacuacucugauguuuuuucacugacccggugagg
cgggggggcgaucucgcuucuggcgccaagcgcccggccgcggccgggcg
cgacccgcuccggggacagugccagguggggaguuugacuggggcgguac
accugucaaacgguaacgcagguguccuaaggcgagcucagggaggacag
aaaccucccguggagcagaagggcaaaagcucgcuugaucuugauuuuca
guacgaauacagaccgugaaagcggggccucacgauccuucugaccuuuu
ggguuuuaagcaggaggugucagaaaaguuaccacagggauaacuggcuu
guggcggccaagcguucauagcgacgucgcuuuuugauccuucgaugucg
gcucuuccuaucauugugaagcagaauucaccaagcguuggauuguucac
ccacuaauagggaacgugagcuggguuuagaccgucgugagacagguuag
uuuuacccuacugaugauguguuguugccaugguaauccugcucaguacg
agaggaaccgcagguucagacauuugguguaugugcuuggcugaggagcc
aauggggcgaagcuaccaucugugggauuaugacugaacgccucuaaguc
agaaucccgcccaggcggaacgauacggcagcgccgcggagccucgguug
gccucggauagccgguccccgggguccggugcggagugcccuucguccug
ggaaacggggcgcggcuggaaaggcggccgcccccucgcccgucacgcac
cgcacguucguggggaaccuggcgcuaaaccauucguagacgaccugcuu
cugggucgggguuucguacguagcagagcagcgcugcgaucuauugaaag
ucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8oj5 UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): A2 R5 M8 L10 K11 H13 F14 H15 K16 W18 Q19 W25 Q28 P29 R31 K32 I33 R35 R36 K37 R39 Q40 K42 R56 R60 C61 P62 T63 V64 Y66 H67 K69 R71 R74 L78 R92 D99 P100 R101 R102 R103 S106 R129 R158 N159 R183 R186
• Binding residue (residue number reindexed from 1): A1 R4 M7 L9 K10 H12 F13 H14 K15 W17 Q18 W24 Q27 P28 R30 K31 I32 R34 R35 K36 R38 Q39 K41 R55 R59 C60 P61 T62 V63 Y65 H66 K68 R70 R73 L77 R91 D98 P99 R100 R101 R102 S105 R128 R157 N158 R182 R185

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0001824 blastocyst development
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0060348 bone development

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8oj5, PDBe:8oj5, PDBj:8oj5
• PDBsum: 8oj5
• PubMed: 38383785
• UniProt: P26373|RL13_HUMAN Large ribosomal subunit protein eL13 (Gene Name=RPL13)