Structure of PDB 8fl3 Chain LK Binding Site BS01

Receptor Information

>8fl3 Chain LK (length=117) Species: 9606 (Homo sapiens)

PSRLRKTRKLRGHVSHGHGRIGKHVGMKHYHLKRNQSFCPTVNLDKLWTL
VSEQTRVNAAKNKTGAAPIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSR
RAEEKIKSVGGACVLVA

Ligand information

>8fl3 Chain L3 (length=3494)

gcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguca
gcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaaca
gggaagagcccagcgccgaauccccgccccggggcgcgggacauguggcg
uacggaagacccgcuccccggcgccgcgggggcccaaguccuucugaucg
aggcccagcccguggacggugugaggccgguagcggcccccggcgcgccg
ggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcgg
gugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaac
aaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaagag
ggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgcccg
gaggauucaacccggcggcggccggccgugucggcggcccggcggaucug
ggaccgucccccgaccggcgaccggccgccgccgggcgcauuuccaccgc
ggcggugcgccgcgaccggcuccgggacggcugggaaggcccggcgggga
agguggcucgggcccgaguguuacagcccccccggcagcagcacucgccg
aaucccggggccgagggagucgccgcgcucuccccccggggggccgggcc
accccucccacggcgcgcgccgucgggcccggggggccacgcgcgcgucc
cccgaagagggggacggcggagcgagcgcacggggucggcggcgacgucg
gcuacccacccgacccgucuugaaacacggaccaaggagucuaacacgug
cgcgagucgggggcucgcacgaaagccgccguggcgcaaugaaggugaag
gccgcggccgaggugggaucccgaggcccgccgagggcgcaccaccggcc
cgucucgcccgccgcgccggggagguggagcacgagcgcacguguuagga
cccgaaagauggugaacuaugccugggcagggcgaagccagaggaaacuc
ugguggagguccguagcgguccugacgugcaaaucggucguccgaccugg
guauaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccga
aguuucccucaggauagcuggcgcucuccgcaguuuuauccgguaaagcg
aaugauuagaggucuuggggccggaucucaaccuauucucggguaagaag
cccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggc
cacuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguu
aaggcgcccgaugccgacgcucaucagaccccagaaaagguguugguuga
uauagacagcaggacgguggccauggaagucggaauccgcuaaggagugu
guaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugg
agcgucgggcccauacccggccgucgccggcagugacgcuacgccgcgac
gaguaggagggccgcugcggugagccuugaagccuagggcgcgggcccgg
guggagccgccgcaggugcagaucuuggugguaguagcaaauauucaaac
gagaacuuugaaggccgaaguggagaaggguuccaugugaacagcaguug
aacaugggucagucgguccugagagaugggcgagcgccguuccgaaggga
cgggcgauggccuccggcccucgaucgaaagggagucggguucagauccc
cgaauccggaguggcggagaugggcgccgcgaggcguccagugcgguaac
gcgaccgaucccggagaagccggcgggagccccggggagaguucucuuuu
cuuugugaagggcagggcgcccuggaauggguucgccccgagagaggggc
ccgugccuuggaaagcgucgcgguuccggcggcguccggugagcucucgc
uggcccuugaaaauccgggggagaggguguaaaucucgcgccgggccgua
cccauauccgcagcaggucuccaaggugaacagccucuggcauguuggaa
caauguagguaagggaagucggcaagccggauccguaacuucgggauaag
gauuggcucuaagggcugggucggucgggcuggggcgcgaagcggggucc
cguggaucgccccagccggccggcgccuagcagccgacuuagaacuggug
cggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcc
cgggguguugacgcgaugugauuucugcccagugcucugaaugucaaagu
gaagaaauucaaugaagcgcggguaaacggcgggaguaacuaugacucuc
uuaagguagccaaaugccucgucaugugacgcgcaugaauggaugaacga
gauucccacugucccuaccuacuauccagcgaaaccacagccaagggaac
gggcuuggcggaaucagcggggaaagaagacccuguugagcuugacucua
gucuggcacggugaagagacaugagagguguagaauaagugggaggcggc
cgccggugaaauaccacuacucugaucguuuuuucacugacccggugagg
cggggggcuucuggcgccaagcgcccggccgcgcgccggccgggcgcgac
ccgcuccggggacagugccagguggggaguuugguacaccugucaaacgg
uaacgcagguguccuaaggcgagcucagggaggacagaaaccucccgugg
agcagaagggcaaaagcucgcuugaucuugauuuuguacgaauacagacc
gugaaagcggggccucacccuucugaccuuuuggguuuuaagcaggagga
aguuaccacagggauaacuggcuuguggcggccaagcgagcgacgucgcu
uuuugauccuucgaugucggcucuuccuaucauugugaagcagaauucac
caagcguuggauuguucacccacuaauagggaacgugagcuggguuuaga
ccgucgugagacagguuaguuuuacccuacugaugauguguuguugccau
gguaauccugcucaguacgagaggaaccgcagguucagacauuuggugua
ugugcuuggcugaggagccaauggggcgaagcuaccaucugugggauuau
gacugaacgccucuaagucagaaucccgcccaggcggaacgauagcgccg
cggagccucgguuggccucggauagccgguccccgggguccggugcggag
ugcccuucguccugggaaacggggcgcggccggagaggcggccgcccccu
cgcccgucacgcaccgcacguucguggggaaccuggcgcuaaaccauucg
uagacgaccugcuucugggucgggguuucguacguagcagagcagcuccc
ucgcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fl3 Principles of human pre-60 S biogenesis.
• Resolution: 2.53 Å
• Binding residue (original residue number in PDB): P2 S3 R4 R6 K7 T8 R9 K10 R12 G13 H14 V15 H17 G18 H19 G20 I22 G57 M58 K59 H60 Y61 H62 L63 K64 R65 Q67 T72 N74 S83 Q85 T86 D102 R105 K110 L112 G113 K114 S130 R131 R132
• Binding residue (residue number reindexed from 1): P1 S2 R3 R5 K6 T7 R8 K9 R11 G12 H13 V14 H16 G17 H18 G19 I21 G26 M27 K28 H29 Y30 H31 L32 K33 R34 Q36 T41 N43 S52 Q54 T55 D71 R74 K79 L81 G82 K83 S99 R100 R101

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:0005654 nucleoplasm
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fl3, PDBe:8fl3, PDBj:8fl3
• PDBsum: 8fl3
• PubMed: 37410842
• UniProt: P46776|RL27A_HUMAN Large ribosomal subunit protein uL15 (Gene Name=RPL27A)