Structure of PDB 8fks Chain L7 Binding Site BS01

Receptor Information

>8fks Chain L7 (length=184) Species: 9606 (Homo sapiens)

QVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKY
LAFFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMV
VPAALKVVRLKPTRKFAYLGRLAHEVGWKYQAVTATLEEKRKEKAKIHYR
KKKQLMRLRKQAEKNVEKKIDKYTEVLKTHGLLV

Ligand information

>8fks Chain L3 (length=1824)

gcgaccucagaucagacguggcgacccgcugaaagcauauuagucagcgg
aggagaagaaacuaaccaggauucccucaguaacggcgagugaacaggga
agagcccagcgccgaauccccgccccgggggcgcgggacauguggcguac
ggaagacccgcuccccggcgccgcucguggggggcccaaguccuucugau
cgaggcccagcccguggacggugugaggccgguagcggcccccggcgcgc
cgggcccgggucuucccggagucggguugcuugggaaugcagcccaaagc
gggugguccaucuaaggcuaaauaccggcacgagaccgauagucaacaag
uaccguaagggaaaguugaaaagaacuuugaagagagaguucaagagggc
gugaaaccguuaagaggacgggugggguccgcgcaguccgcccggaggau
ucaacccggcggcggccgccgccgggcgcauuuccaccgcggcggugcgc
cgcgaccggcuccgggacggcugggaaggcccggcggggaagguggcucg
ggcccgaguguuacagcccccccggcagcagcacucgccgaaucccgggg
ccgagggagcgccgcgcucuccggccgggccaggccacgcgagcgcacgg
ggucggcggcgacgucggcuacccacccgacccgucuacacggaccaagg
agucuaacacgugcgcgagucgggggcucgcacgaaagccgccguggcgc
aaggugggaucccgaggcgccgagggcgcaccaccggcccgucucgcccg
gggagguggagcacgagcgcacguguuaggacccgaaagauggugaacca
ucuaguagcugguucccuccgaaguuucccucaggauagcuggcgcucuc
cgcaguuuuauccgggguaagaagcccggcucgagccgggcguggaaugc
gagugccuagugggccacuuuugguaagcagaacuggcgcugcgggauga
accgaacgccggguuaaggcgcccgaugccgacgcucacccagaaaaggu
guugguugauauagacagcaggacgguggccauggaagucggaauccgcu
aaggaguguguaacaacucaccugccgaaucaacuagcccugaaaaugga
uggcgcuggagcgucgggcccauacccggccgucgccggcagucacgcua
cgccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcg
cgggcccggguggagccgccgcaggugcagaucuuggugguaguagcaau
guuggaacaauguaggaccuacuauccagcgaaaccagccaagcuuggcu
cagcggggcuggcuuguggcggccaagcgcgacgucgcuuuuugauugug
aagcagaauucaccaacccuacugaugguuguugccaugguaauccugcu
caguacgagaggaaccgcagguucagacauuugguguaugugcuuggcug
aggagccaauggggcgaagcuaccaucugugggauuaugacugaacgccu
cuaagucagaaucccgcccaggcggaacgauagcgccgcggagccucggu
uggccucggauagccgguccccgggguccggugcggagugcccuucgucc
ugggaaacggggcgcggccggagaggcggccgcccccucgcccgucacgc
accgcacguucguggggaaccuggcgcuaaaccauucguagacgaccugc
ugggucgggguuucguacguagcagagcagcucccucgcugcgaucuauu
gaaagagcccucgacacgguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fks Principles of human pre-60 S biogenesis.
• Resolution: 2.88 Å
• Binding residue (original residue number in PDB): R12 G17 R18 K25 L28 R37 S44 R82 M87 P89 R94 I108 K114 K115 K116 R117 M118 R128 L129 K130 R133 L156 K161 A164 H167 Y168 R169 K172 M175 K179 K188
• Binding residue (residue number reindexed from 1): R8 G13 R14 K21 L24 R33 S40 R63 M68 P70 R75 I89 K95 K96 K97 R98 M99 R109 L110 K111 R114 L137 K142 A145 H148 Y149 R150 K153 M156 K160 K169

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0017148 negative regulation of translation
• GO:0032496 response to lipopolysaccharide
• GO:0042592 homeostatic process
• GO:0048246 macrophage chemotaxis
• GO:0060425 lung morphogenesis
• GO:0071346 cellular response to type II interferon
• GO:1901194 negative regulation of formation of translation preinitiation complex

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0015934 large ribosomal subunit
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0097452 GAIT complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fks, PDBe:8fks, PDBj:8fks
• PDBsum: 8fks
• PubMed: 37410842
• UniProt: P40429|RL13A_HUMAN Large ribosomal subunit protein uL13 (Gene Name=RPL13A)