Structure of PDB 8fkx Chain LT Binding Site BS01

Receptor Information

>8fkx Chain LT (length=109) Species: 9606 (Homo sapiens)

SGRLWSKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVY
KAKNNTVTPGGKPNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRI
RVMLYPSRI

Ligand information

>8fkx Chain L3 (length=2250)

gcgaccucagaucagacguggcgacccgcugaaagcauauuagucagcgg
aggagaagaaacuaaccaggauucccucaguaacggcgagugaacaggga
agagcccagcgccgaauccccgccccgggggcgcgggacauguggcguac
ggaagacccgcuccccggcgccgcucguggggggcccaaguccuucugau
cgaggcccagcccguggacggugugaggccgguagcggcccccggcgcgc
cgggcccgggucuucccggagucggguugcuugggaaugcagcccaaagc
gggugguccaucuaaggcuaaauaccggcacgagaccgauagucaacaag
uaccguaagggaaaguugaaaagaacuuugaagagagaguucaagagggc
gugaaaccguuaagaggaacgggugggguccgcgcaguccgcccggagga
uucaacccggcggcggccgccgccgggcgcauuuccaccgcggcggugcg
ccgcgaccggcuccgggacggcugggaaggcccggcggggaagguggcuc
gggcccgaguguuacagcccccccggcagcagcacucgccgaaucccggg
gccgagggagcgccgcgcucuccggccgggccaggccacggagcgcacgg
ggucggcggcgacgucggcuacccacccgacccgucuugaaacacggacc
aaggagucuaacacgugcgcgagucgggggcucgcacgaaagccgccgug
gcgcaaggugggaucccgaggcccgccgagggcgcaccaccggcccgucu
cgcccggggagguggagcacgagcgcacguguuaggacccgaaagauggu
gaacuaugccgguauaggggcgaaagacuaaccaucuaguagcugguucc
cuccgaaguuucccggauagcuggcgcucuccgcaguuuuauccgguggg
uaagaagcccggcucgagccgggcguggaaugcgagugccuagugggcca
cuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguuaa
ggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugaua
uagacagcaggacgguggccauggaagucggaauccgcuaaggagugugu
aacaacucaccugccgaaucaacuagcccugaaaauggauggcgcuggag
cgucgggcccauacccggccgucgccggcagucacgcuacgccgcgacga
guaggagggccgcugcggugagccuugaagccuagggcgcgggcccgggu
ggagccgccgcaggugcagaucuuggugguaguagcauucaaacgagaac
uuugaaggccgaggggcgauggccuccggcccucgcggagagugaaucuc
gcuggcaauguagguaagggaagucgggaauccgauucccacugucccua
ccuacuauccagcgaaaccacagccaagggaacgggcuuggcggaaucag
cggggagaagacccuguugagcuugacucuagucuggcacggugaagaga
caugagagguguagaauaagugggaggcggccgccggugaaauaccacua
cucugaucguuuuuuccagugccagguggggaguuauccuucugaccuuu
uggguuuuaagcaggaggugucagaaaaguuaccacagggauaacuggcu
uguggcggccaagcgcgacgucgcuuuuugaugaugucggcucuuccuau
cauugugaagcagaauucaccaagcguuggauuguucacccacuaauagg
gaacgugagcuggggaccgucgugagacagguuagucccuacugaugguu
guugccaugguaauccugcucaguacgagaggaaccgcagguucagacau
uugguggugcuuggcugaggagccaauggggcgaagcuaccaucuguggg
auuaugacugaacgccucuaagucagaaucccgcccaggcggaacgauaa
gcgccgcggagccucgguuggccucggauagccgguccccgggguccggu
gcggagugcccuucguccugggaaacggggcgcggccggagaggcggccg
cccccucgcccgucacgcaccgcacguucguggggaaccuggcgcuaaac
cauucguagacgaccugcuucugggucgggguuucguacguagcagagca
gcucccucgcugcgaucuauugaaagucagcccucgacacaaggguuugu

........................<<<<<<...............>>>>>
.>.........<<....>>..<<<<<<.....<<.....>>....>>>>>
>..<<<..<<<<<...<<<<<<<<<<.>>>>>>.>>>>.....>>>>>..
<<<<<<<<<<...<<<<<<<<.<<.....<<<<<<<<....<<<<.....
.>>>>.....((......<<<.....))>>>...>.>>>>>>>.>>>>>>
>>>>..>>>>>>>>>>.......<<<<<<<........>>>>>>>.....
<<<<<<.>>>>>>..>>>................................
..<<....>>...............<<<<....>>>>.............
...................<<<<<<<<..<<<.<<...<<<<<<<<.<<<
.....<<<<<<<<<<..>>>>>>>>>>......>>>.>>>.>>>>>...<
<<<<<<.<<<<<<<<<<<<<<<...<<..<<<.<<.<<<<......<<<<
<<..>>>>>>.......>>>>>>.>>>........>>>>>>..>>>>>>>
>>>>..........<<<<<<.<..>.<<<<<<.>>>>.>>>>>>>>....
..>>.>>>>>...>>>>>...>>>>>>>>..<<<<........>>>><<<
<<<....<<<<<<<<<<<<<..<<<...<<<<........>>>>.....>
>>....<<<<<...<<<..<<<..>>>..>>>....>>>>>.<<<<<<<<
<.<<..>>>>>>>>>.>>....>>>>>>>>>>>>>..<<.<...<<<<<<
...<<<<<<..>>>>>><<.<....>.>>.>>>>>>......>.>>..<<
<<<<......<<<.>>>..<<.<<<<<<<...<<<.<<<<<<<<...>>>
>>>...<<<<<<<<..>>>>>>>>....>>>>>>>>>>>>..>>..<<<<
.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<...
<<<(((.......<<<<<.....<<..........<<<.<<<<<<<<<<.
....<.<<<<<.<<....<<.........>>....>>.........<<..
....>>...>>>>>.>.>>>>>>>>>>>>>..........))).>>...>
>>>>..>>>...>>>>>>><<<<<<.<<<...........>>>>>>>>>.
...>>>>>>.<.<<<<<<<<.<<......<<<<.<<<<....>>>>>>>>
...>>>>>>>>>>..>.....>>>>>><<.....<<.<<<<<<.......
>>>>>>.<<<<..<<<<...........>>>>..<<<<<.......>>.>
>>>>>>...<<<<<<.<<<<<<<<..<<<<<<.>>>>>>.>>>.>>>>>>
>>>>>......>>....>>...<<<<<<........>>>>>>....<<<<
.<<<<......<<<<<<.<<<<<<.<<<<<.<<<<<<<<<...<<<<<<<
<<<.<<<<..........<<<<<..<<<.>>>............>>>>>.
>>>>.>>.>>>>>>>>..>>>>>>>>>..>>>>>...<<<<<<<..<<<.
........>>>>>>>>>>........>>>>>.>.>>>>>>..........
...<<<<<<...<..>...>>>>>>.......((...<<<<<<<<<<<..
<.<.<<<<<......>>>>>...>.>.<<<.....))..>>>.....>>>
>>....>>>>>>..<<<<<<<....>>>.>>>>...>>>>.>>>>..<<<
<<<.<..<<<..<.<<<<<.................>>>>>.><<<<...
.<<<<.<<.<<<<<<<....>>>>>..>>.>>...>>>>...>>>><<<<
<...<<<<<...........>>>>>...>>>>>.>>>...>.>>>>>>.<
<<<<<<.<<..<<<<....<<<........<<<<<.<<<<>>>>.>>>>>
.......>>>...<<<..<<<<....<<<<.<<<<<<<......>>>>>>
>>>>>...>>>>..>>>..............>>>>..>>>>>>>>><<<<
<.<.............>....<<.<<<<<<<.<<.....<<<<....<<<
<<......>>>>>...>>>>....>>....>>>>.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fkx Principles of human pre-60 S biogenesis.
• Resolution: 2.59 Å
• Binding residue (original residue number in PDB): S2 G3 R4 W6 K8 K15 R16 L18 R19 Q21 R22 E23 Y34 R36 G44 Y51 K52 K54 N55 N56 T57 V58 P60 T67 R68 V69 W71 K73 T75 R76 H78 G79 N80 S81 R85 K87 R89 S90 N91 P93 A94 R100 R102
• Binding residue (residue number reindexed from 1): S1 G2 R3 W5 K7 K14 R15 L17 R18 Q20 R21 E22 Y33 R35 G43 Y50 K51 K53 N54 N55 T56 V57 P59 T66 R67 V68 W70 K72 T74 R75 H77 G78 N79 S80 R84 K86 R88 S89 N90 P92 A93 R99 R101

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fkx, PDBe:8fkx, PDBj:8fkx
• PDBsum: 8fkx
• PubMed: 37410842
• UniProt: P18077|RL35A_HUMAN Large ribosomal subunit protein eL33 (Gene Name=RPL35A)