Structure of PDB 8fl3 Chain LD Binding Site BS01

Receptor Information

>8fl3 Chain LD (length=154) Species: 9606 (Homo sapiens)

SMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLII
RKPVTVHSRARCRKNTLARRKGRHMGIGKRKGTANARMPEKVTWMRRMRI
LRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILMEHIHKLKADKAR
KKLL

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): S2 L4 R5 K8 R9 R16 G18 K19 K20 K21 W23 L24 S37 R38 Q39 Q40 R42 K43 K46 T56 H58 S59 R60 R62 R64 R71 K72 R74 H75 I78 G79 R81 K82 G83 T84 N86 A87 R88 K92 W95 M96 R100 R103 R104 R108 R110 K114 R117 H118 Y120 H121 Y124 L125 K128 N134 K135 R136 H143
• Binding residue (residue number reindexed from 1): S1 L3 R4 K7 R8 R15 G17 K18 K19 K20 W22 L23 S36 R37 Q38 Q39 R41 K42 K45 T55 H57 S58 R59 R61 R63 R70 K71 R73 H74 I77 G78 R80 K81 G82 T83 N85 A86 R87 K91 W94 M95 R99 R102 R103 R107 R109 K113 R116 H117 Y119 H120 Y123 L124 K127 N133 K134 R135 H142

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:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fl3, PDBe:8fl3, PDBj:8fl3
• PDBsum: 8fl3
• PubMed: 37410842
• UniProt: P84098|RL19_HUMAN Large ribosomal subunit protein eL19 (Gene Name=RPL19)