Structure of PDB 8fkz Chain SC Binding Site BS01

Receptor Information

>8fkz Chain SC (length=214) Species: 9606 (Homo sapiens)

PHCSRNPVLVRGIGRYSRSAMYSRKAMYKRLATVTKPVGGDKNGGTRVVK
LRKMPRYYPTEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHR
GKRVVFLKQLASGLLLVTGPLVLNRVPLRRTHQKFVIATSTKIDISNVKI
PKHLTDAYFKKKKEKYEITEQRKIDQKAVDSQILPKIKAIPQLQGYLRSV
FALTNGIYPHKLVF

Ligand information

>8fkz Chain L3 (length=2833)

gcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguca
gcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaaca
gggaagagcccagcgccgaauccccgccccggggcgcgggacauguggcg
uacggaagacccgcuccccggcgccgcgggggcccaaguccuucugaucg
aggcccagcccguggacggugugaggccgguagcggcccccggcgcgccg
ggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcgg
gugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaac
aaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaagag
ggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgcccg
gaggauucaacccggcggcggccggccgugucggcggcccggcggaucug
ggaccgucccccgaccggcgaccggccgccgccgggcgcauuuccaccgc
ggcggugcgccgcgaccggcuccgggacggcugggaaggcccggcgggga
agguggcucgggcccgaguguuacagcccccccggcagcagcacucgccg
aaucccggggccgagggagucgccgcgcucuccccccggggggccgggcc
accccucccacggcgcgcgccgucgggcccggggggccacgcgcgcgucc
cccgaagagggggacggcggagcgagcgcacggggucggcggcgacgucg
gcuacccacccgacccgucaaacacggaccaaggagucuaacacgugcgc
gagucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggcc
gcggccgaggugggaucccgaggccgccgagggcgcaccaccggcccguc
ucgcccgccgcgccggggagguggagcacgagcgcacguguuaggacccg
aaagauggugaacuaugccugggcagggcgaagccagaggaaacucuggu
ggagguccguagcguccgaccuggguauaccaucuaguagcugguucccu
ccgaaguuucccucaggauagcuggcgcucuccgcaguuuuauccggggg
uaagaagcccggcucgcuggcguggagccgggcguggaaugcgagugccu
agugggccacuuuugguaagcagaacuggcgcugcgggaugaaccgaacg
ccggguuaaggcgcccgaugccgacgcucaucagaccagaaaagguguug
guugauauagacagcaggacgguggccauggaagucggaauccgcuaagg
aguguguaacaacucaccugccgaaucaacuagcccugaaaauggauggc
gcuggagcgucgggcccauacccggccgucgccggcagugacgcuacgcc
gcgacgaguaggagggccgcugcggugagccuugaagccuagggcgcggg
cccggguggagccgccgcaggugcagaucuuggugguaguagcaaauauu
caaacgagaacuuugaaggccgaaguggagaaggguuccaugugaacagc
aguugaacaugggucagucgguccugagagaugggcgagcgccguuccga
agggacgggcgauggccuccggcccucgaucgaaagggagucggguucag
auccccgaauccggaguggcggagaugggcgccgcgaggcguccagugcg
guaacgcgaccgaucccggagaagccggcgggagccccggggagaguucu
cuuuucuuugugaagggcagggcgcccuggaauggguucgccccgagaga
ggggcccgugccuuggaaagcgucgcgguuccggcggcguccggugagcu
cucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgccggg
ccguacccauauccgcagcaggucuccaaggugaacagccucuggcaugu
uggaacaauguagguaaggggcucuaagggcugggucggucgggcugggg
cgcgaagcggggucccguggaucgccccagccggccggcgccuagcagcc
gacuuagaacugcaucgcgaaggcccgggguguugacgcgauguuguccc
uaccuacuauccagcgaaaccacagccaagggaacgggcuuggcggaauc
agacccggugaggcggggggcuucuggcgccaagcgcccggccgcgcgcc
ggccgggcgcgacccgcuccggggcuucugaccuuuuggguuuuaagcag
gagggcuuguggcggccaagcgagcgacgucgcuuuuugcggcucuuccu
aucauugugaagcagaauucaccaagcguuggauuguucacccacuaaua
gggaacgugagcuggcuacugaugauguguuguugccaugguaauccugc
ucaguacgagaggaaccgcagguucagacauuugguguaugugcuuggcu
gaggagccaauggggcgaagcuaccaucugugggauuaugacugaacgcc
ucuaagucagaaucccgcccaggcggaacgauagcgccgcggagccucgg
uuggccucggauagccgguccccgggguccggugcggagugcccuucguc
cugggaaacggggcgcggccggagaggcggccgcccccucgcccgucacg
caccgcacguucguggggaaccuggcgcuaaaccauucguagacgaccug
cuucugggucgggguuucguacguagcagagcagcucccucgcugcgauc
uauugaaagucagcccucgacacaaggguuugu

........................<<<<<<.....<<....>>......>
>>>>.>.........<<....>>..<<<<<<.....<<.....>>....>
>>>>>..[[[..<<<<<...<<<<<<<<<..>>>>>.>>>>.....>>>>
>..<<<<<<<<<<...<<<<<<<<.<<<<<<<<<<....<<<<......>
>>>.....((......<<<.....))>>>...>.>>>>>>>.>>>>>>>>
>>..>>>>>>>>>>.......<<<<<<<........>>>>>>>.....((
(((..<<<<<<)))))..]]].............................
.....<<....>>...............<<<......>>>..........
........................<<<<<<<<..<<<.<<...<<<<<<<
<.<<<.....<<<<<<<<<<<<<<<<<<.<<<<<.<<...<<<<<.<<<.
>>>>>>>>>>>>>>>>>>>...>>>>>>>>>>>>>>......>>>.>>>.
>>>>>...<<<<<<<<<<<<<<<<<<<<<<<...<<..<<<.<<.<<<<.
.....<<<<<<..>>>>>>.......>>>>>>.>>>........>>>>>>
..>>>>>>>>>>>...........<<<<<<.<<<<<..>>>>>.<<<<<<
.<<<<.<<<<<<<<<..>>>>>>.>>>...>>>>>>>>.>>..<<<<<<<
<<.......>>>>>>>.>>....>>>>>>.....>>>.>>>>>...>>>>
>...>>>>>>>>..<<<<.....>>>><<<<<<....<<<<<<<<<<<<<
..<<<...<<<<........>>>>.....>>>...<<....>>...<<<<
..>>>>..<<<<<...<<<..<<<.>>>..>>>....>>>>>.<<<<<<<
<<.<<<<......>>>>>>>>>>>.>>....>>>>>>>>>>>>>..<<.<
...<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>
.....>>>...<..>....>>>>>>>>>>>>>>>......>.>>..<<<<
<<......<<<....>>>..<<.<<<<<<<...<<<.<<<<<<<<..>>>
>>>...<<<<<<<<<.<......>>>>>>>>>>....>>>>>>>>>>>>.
.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>...<
<<<<<<...<<<(((.......<<<<<.....<<........<<<.<<<<
<<<<<<.......<<<<<.<<<...<<.........>>...>>>......
...<<......>>...>>>>>...>>>>>>>>>>>>>..........)))
.>>...>>>>>..>>>...>>>>>>><<<<<<.<<<...........>>>
>>>>>>....>>>>>>.<.<<<<<<<<.<<......<<<<.<<<<....>
>>>>>>>...>>>>>>>>>>..>.....>>>>>><<.....<<.....<<
<<<<.......>>>>>>.<<<.....<<<<<.<<...<<<<<<...<<..
...>>.>>>>>>....((<<<<<<...<<....<<<....>>>.......
......<<<<...........>>>>....>>....>>>..<<<<<.....
...>>>>>))<<<<....<<<<<..<<<<<<<<....>>>>>>>>..<<<
....>>>...<..<<<<<<<...<<<<<<<<<<<<.<<<<<<<<<<..{{
{..>>>>>>....<<<<<.<<<<.<<<<.....<<<.....>>>.....>
>>>>>>>..>>>>>.....<<<<<<<.......>>>>>>>>>>>...>>>
>>>>>>>>>.........>>>>>>>..>..........>>.>>>.>>>>.
>>>..>>.....<<......>>>>>>>.<<<<.....>>>>..>>>....
<<<<.....<<<<<<<.<<.<.<<<<<<<<<<<.<<<<<<<<.<<<<<<<
<<....<<<<<..>>>>>....>>>>>>>>>>>>>>>>>......>>>>>
..>>>>>>.>.<<<<<<<....<<<<.>>>>......>>>>>>>...>>.
>>>>>>>..>>>>>>....>>....<<<<<........>>>>>....[[[
[[.<<<<<.....<<<<................<<<<<<<<<<.......
>>>>>>>>>>..>>>>..>>>>>.((((((..(((..>>>>>>.))))))
))).......<<<<<<...<<..>>...>>>>>>.....<<<<.<<<<<<
..<.<.<<<<<......>>>>>...>.>.<<<.........>>>.....>
>>>>..>...>>>>....]]]]].....<<<<<<.<..<<<..<.<<<<<
.................>>>>>.><<<<....<<<<....<<.<<<<<<.
}}}..>>>>..>>.>>...>>>>...>>>><<<<<...<<<<<.......
....>>>>>...>>>>>.>>>...>.>>>>>>.<<<<<<.<<..<<<<..
..<<<........<<<<<.<<<<>>>>.>>>>>.......>>>...<<<.
.<<<<....<<<<.<<<<<<<......>>>>>>>>>>>...>>>>..>>>
..............>>>>..>>>>>>>>.<<<<<.<.............>
....<<.<<<<<<<.<<.....<<<<....<<<<<......>>>>>...>
>>>....>>....>>>.>>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fkz Principles of human pre-60 S biogenesis.
• Resolution: 3.04 Å
• Binding residue (original residue number in PDB): H43 C44 S45 R46 R52 S58 R59 S60 M62 Y63 R65 K66 A67 Y69 K70 R71 P95 V96 V107 L109 K111 P113 R114 Y115 V121 R123 K124 L125 L126 S127 H128 K130 P132 F133 S134 H136 T154 R156 H157 R158 L172 L179 L181 R183 P185 R187 R188 H190 K192 F217 K219 Y240 I242 K247 Q266 Q268 R272 V274 N279
• Binding residue (residue number reindexed from 1): H2 C3 S4 R5 R11 S17 R18 S19 M21 Y22 R24 K25 A26 Y28 K29 R30 P37 V38 V49 L51 K53 P55 R56 Y57 V63 R65 K66 L67 L68 S69 H70 K72 P74 F75 S76 H78 T96 R98 H99 R100 L114 L121 L123 R125 P127 R129 R130 H132 K134 F159 K161 Y166 I168 K173 Q192 Q194 R198 V200 N205

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006355 regulation of DNA-templated transcription
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005791 rough endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0014069 postsynaptic density
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0036464 cytoplasmic ribonucleoprotein granule
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fkz, PDBe:8fkz, PDBj:8fkz
• PDBsum: 8fkz
• PubMed: 37410842
• UniProt: Q02878|RL6_HUMAN Large ribosomal subunit protein eL6 (Gene Name=RPL6)