Structure of PDB 8fl9 Chain LV Binding Site BS01

Receptor Information

>8fl9 Chain LV (length=104) Species: 9606 (Homo sapiens)

VNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQ
TKPIFRKKAKTTKKIVLRLECVEPNCRSKRMLAIKRCKHFELGGDKKRKG
QVIQ

Ligand information

>8fl9 Chain L3 (length=3361)

gcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguca
gcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaaca
gggaagagcccagcgccgaauccccgccccggggcgcgggacauguggcg
uacggaagacccgcuccccggcgccgcgggggcccaaguccuucugaucg
aggcccagcccguggacggugugaggccgguagcggcccccggcgcgccg
ggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcgg
gugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaac
aaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaagag
ggcgugaaaccguuaagaggaacgggugggguccgcgcaguccgcccgga
ggauucaacccggcggcggccggccgugucggcggcccggcggaucuggg
accgucccccgaccggcgaccggccgccgccgggcgcauuuccaccgcgg
cggugcgccgcgaccggcuccgggacggcugggaaggcccggcggggaag
guggcucgggcccgaguguuacagcccccccggcagcagcacucgccgaa
ucccggggccgagggaggucgccgcgcucuccccccggggggccgggcca
ccccucccacggcgcgaccgcucggggcggacuguccccagugcgccccg
ggcgggucgcgccgucgggcccggggggccacgcgcgcgucccccgaaga
gggggacggcggagcgagcgcacggggucggcggcgacgucggcuaccca
cccgacccgucuuacacggaccaaggagucuaacacgugcgcgagucggg
ggcucgcacgaaagccgccguggcgcaaugaaggugaaggccgcggccga
ggugggaucccgaggccucuccaguccgccgagggcgcaccaccggcccg
ucucgcccgccgcgccggggagguggagcacgagcgcacguguuaggacc
cgaaagauggugaacuaugccugggcagggcgaagccagaggaaacucug
guggagguccguagcgguccugacgugcaaaucggucguccgaccugggu
auaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaag
uuucccucaggauagcuggcgcucuccgcaguuuuauccgguaaagcuuu
aaauggguaagaagcccggcucgcuggcguggagccgggcguggaaugcg
agugccuagugggccacuuuugcagaacuggcgcugcgggaugaaccgaa
cgccggguuaaggcgcccgaugccgacgcucaucagaccccaaaaggugu
ugguugauauagacagcaggacgguggccauggaagucggaauccgcuaa
ggaguguguaacaacucaccugccgaaucaacuagcccugaaaauggaug
gcgcuggagcgucgggcccauacccggccgucgccggcagucgagagugg
acgggagcggcgcgcggacgcuacgccgcgacgaguaggagggccgcugc
ggugagccuugaagccuagggcgcgggcccggguggagccgccgcaggug
cagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggccga
aguggagaaggguuccaugugaacagcaguugaacaugggucagucgguc
cugagagaugggcgagcgccguuccgaagggacgggcgagcccugaucga
aagggagucggguucagauccccgaauccggaguggcggagaugggcgcc
gcgaggcguccagugcgguaacgcgaccgaucccggagaagccggcggga
gccccggggagaguucucuuuucuuugugaagggcagggcgcccuggaau
ggguucgccccgagagaggggcccgugccuuggaaagcgucgcgguuccg
gcggcguccggugagcucucgcuggcccuugaaaauccgggggagagggu
guaaaucucgcgccgggccguacccauauccgcagcaggucuccaaggug
aacagccucuggcauguuggaacaauguagguaagggaagucggcaagcc
ggauccguaacuucgggauaaggauuggcucuaagggcugggucggucgc
ggccggcgccuagcagccgacuuagaacuggugcggaccaggggaauccg
acuguuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugacg
cgaugugauuucugcccagugcucugaaugucaaagugaagaaauucaau
gaagcgcggguaaacggcaagugaacgagauucccacugucccuaccuac
uauccagcgaaaccacagccaagggcgggcuuggcggaaucagcggggaa
agaagacccuguugagcuugacucuagucuggcacggugaaguuuuuuca
cugacccggugaggcggggggcuucuggcgccaagcgcccggccgcgcgc
cggccgggcgcgacccgcuccggggacagugccagguggggaguuugacu
guacaccugucaaacgguaacgcagguguccuaaggcgagcucagggagg
acagaaaccucccguggagcagaagggcaaaagcucgcuugaucuugauu
uucaguacgaauacagaccgugaaagcggggccucacgauccuucugacc
uuuuggguuuuaagcaggaggugucagaaaaguuaccacagggaucuugu
ggcggccaagcgagcgacgucgcuuuuuggaugucggcucuuccuaucau
ugugaagcagaauucaccaagcguuggauuguucacccacuaauagggaa
cgugagcuggguuuagaccgucgugagacagguuaguuuuacccuacuga
ugauguguuguugccaugguaauccugcucaguacgagaggaaccgcagg
uucagacauuugguguaugugcuuggcugaggagccaauggggcgaagcu
accaucugugggauuaugacugaacgccucuaagucagaaucccgcccag
gcggaacgauagcgccgcggagccucgguuggccucggauagccgguccc
cgggguccggugcggagugcccuucguccugggaaacggggcgcggccgg
agaggcggccgcccccucgcccgucacgcaccgcacguucguggggaacc
uggcgcuaaaccauucguagacgaccugcuucugggucgggguuucguac
guagcagagcagcucccucgcugcgaucuauugaaagucagcccucgaca
caaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fl9 Principles of human pre-60 S biogenesis.
• Resolution: 2.75 Å
• Binding residue (original residue number in PDB): V2 N3 P5 R9 T10 F11 K13 K17 H18 Y26 K28 G29 D31 S32 Y34 A35 Q36 G37 R39 R40 K44 G47 Y48 G50 Q51 T52 K53 P54 I55 F56 K58 K59 A60 K61 T63 K64 K65 K80 R81 M82 K86 C88 K89 K97 K98 K100
• Binding residue (residue number reindexed from 1): V1 N2 P4 R8 T9 F10 K12 K16 H17 Y25 K27 G28 D30 S31 Y33 A34 Q35 G36 R38 R39 K43 G46 Y47 G49 Q50 T51 K52 P53 I54 F55 K57 K58 A59 K60 T62 K63 K64 K79 R80 M81 K85 C87 K88 K96 K97 K99

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005886 plasma membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fl9, PDBe:8fl9, PDBj:8fl9
• PDBsum: 8fl9
• PubMed: 37410842
• UniProt: P83881|RL36A_HUMAN Large ribosomal subunit protein eL42 (Gene Name=RPL36A)