Structure of PDB 8fla Chain LD Binding Site BS01

Receptor Information

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

SMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLII
RKPVTVHSRARCRKNTLARRKGRHMGIGKRKGTANARMPEKVTWMRRMRI
LRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILMEHIHKLKADKAR
KKLL

Ligand information

>8fla Chain L3 (length=3420)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccggggcgcgggacauguggc
guacggaagacccgcuccccggcgccgcgggggcccaaguccuucugauc
gaggcccagcccguggacggugugaggccgguagcggcccccggcgcgcc
gggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcg
ggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaa
caaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaaga
gggcgugaaaccguuaagaggaacgggugggguccgcgcaguccgcccgg
aggauucaacccggcggcggccggccgugucggcggcccggcggaucugg
gaccgucccccgaccggcgaccggccgccgccgggcgcauuuccaccgcg
gcggugcgccgcgaccggcuccgggacggcugggaaggcccggcggggaa
gguggcucgggcccgaguguuacagcccccccggcagcagcacucgccga
aucccggggccgagggaggucgccgcgcucuccccccggggggccgggcc
accccucccacggcgcgaccgcucggggcggacuguccccagugcgcccc
gggcgggucgcgccgucgggcccggggggccacgcgcgcgucccccgaag
agggggacggcggagcgagcgcacggggucggcggcgacgucggcuaccc
acccgacccgucuugaaacacggaccaaggagucuaacacgugcgcgagu
cgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccgcgg
ccgaggugggaucccgaggccucuccaguccgccgagggcgcaccaccgg
cccgucucgcccgccgcgccggggagguggagcacgagcgcacguguuag
gacccgaaagauggugaacuaugccugggcagggcgaagccagaggaaac
ucugguggagguccguagcgguccugacgugcaaaucggucguccgaccu
ggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucccucc
gaaguuucccucaggauagcuggcgcucuccgcaguuuuauccgguaaag
uuuaaauggguaagaagcccggcucgcuggcguggagccgggcguggaau
gcgagugccuagugggccacuuuugguaagcagaacuggcgcugcgggau
gaaccgaacgccggguuaaggcgcccgaugccgacgcucaucagaccccg
aaaagguguugguugauauagacagcaggacgguggccauggaagucgga
auccgcuaaggaguguguaacaacucaccugccgaaucaacuagcccuga
aaauggauggcgcuggagcgucgggcccauacccggccgucgccggcagu
cgagaguggacgggagcggcgcgcggacgcuacgccgcgacgaguaggag
ggccgcugcggugagccuugaagccuagggcgcgggcccggguggagccg
ccgcaggugcagaucuuggugguaguagcaaauauucaaacgagaacuuu
gaaggccgaaguggagaaggguuccaugugaacagcaguugaacaugggu
cagucgguccugagagaugggcgagcgccguuccgaagggacgggcgaug
gccuccggcccugaucgaaagggagucggguucagauccccgaauccgga
guggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgauc
ccggagaagccggcgggagccccggggagaguucucuuuucuuugugaag
ggcagggcgcccuggaauggguucgccccgagagaggggcccgugccuug
gaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuuga
aaauccgggggagaggguguaaaucucgcgccgggccguacccauauccg
cagcaggucuccaaggugaacagccucuggcauguuggaacaauguaggu
aagggaagucggcaagccggauccguaacuucgggauaaggauuggcucu
aagggcugggucggucgggcuggggcgcgaagcggggucccguggaucgc
cccagccggccggcgccuagcagccgacuuagaacuggugcggaccaggg
gaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcgggu
guugacgcgaugugauuucugcccagugcucugaaugucaaagugaagaa
auucaaugaagcgcggguaaacggcaagugaacgagauucccacuguccc
uaccuacuauccagcgaaaccacagccaagggaacgggcuuggcggaauc
agcggggaaagaagacccuguugagcuugacucuagucuggcacggugaa
guuuuuucacugacccggugaggcggggggcuucuggcgccaagcgcccg
gccgcgcgccggccgggcgcgacccgcuccggggacagugccaggugggg
aguuugacuguacaccugucaaacgguaacgcagguguccuaaggcgagc
ucagggaggacagaaaccucccguggagcagaagggcaaaagcucgcuug
aucuugauuuucaguacgaauacagaccgugaaagcggggccucacgauc
cuucugaccuuuuggguuuuaagcaggaggugucagaaaaguuaccacag
ggaucuuguggcggccaagcgagcgacgucgcuuuuuggaugucggcucu
uccuaucauugugaagcagaauucaccaagcguuggauuguucacccacu
aauagggaacgugagcuggguuuagaccgucgugagacagguuaguuuua
cccuacugaugauguguuguugccaugguaauccugcucaguacgagagg
aaccgcagguucagacauuugguguaugugcuuggcugaggagccaaugg
ggcgaagcuaccaucugugggauuaugacugaacgccucuaagucagaau
cccgcccaggcggaacgauagcgccgcggagccucgguuggccucggaua
gccgguccccgggguccggugcggagugcccuucguccugggaaacgggg
cgcggccggagaggcggccgcccccucgcccgucacgcaccgcacguucg
uggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucggg
guuucguacguagcagagcagcucccucgcugcgaucuauugaaagucag
cccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fla Principles of human pre-60 S biogenesis.
• Resolution: 2.63 Å
• Binding residue (original residue number in PDB): M3 L4 R5 K8 G18 K19 K20 K21 W23 L24 P26 S37 R38 Q39 Q40 R42 K43 K46 T56 V57 H58 S59 R60 R62 C63 R64 R71 R74 H75 G77 I78 G79 R81 K82 G83 T84 N86 A87 R88 P90 K92 W95 M96 R100 R103 R104 R108 R110 K114 R117 H118 Y120 H121 Y124 L125 K128 N134 K135 H143
• Binding residue (residue number reindexed from 1): M2 L3 R4 K7 G17 K18 K19 K20 W22 L23 P25 S36 R37 Q38 Q39 R41 K42 K45 T55 V56 H57 S58 R59 R61 C62 R63 R70 R73 H74 G76 I77 G78 R80 K81 G82 T83 N85 A86 R87 P89 K91 W94 M95 R99 R102 R103 R107 R109 K113 R116 H117 Y119 H120 Y123 L124 K127 N133 K134 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:8fla, PDBe:8fla, PDBj:8fla
• PDBsum: 8fla
• PubMed: 37410842
• UniProt: P84098|RL19_HUMAN Large ribosomal subunit protein eL19 (Gene Name=RPL19)