Structure of PDB 8fkq Chain SC Binding Site BS01

Receptor Information

>8fkq Chain SC (length=211) Species: 9606 (Homo sapiens)

PHCSRNPVLVRGIGRYSRSAMYSRKAMYKLATVTKPVGGDKNGGTRVVKL
RKMPRYYPTEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRG
KRVVFLKQLASGLLLVTGPLVLNRVPLRRTHQKFVIATSTKIDISNVKIP
KHLTDAYFKKKKYEITEQRKIDQKAVDSQILPKIKAIPQLQGYLRSVFAL
TNGIYPHKLVF

Ligand information

>8fkq Chain L3 (length=1565)

gcgaccucagaucagacguggcgacccgcuggcauauuagucagcggagg
agaagaaacuaaccaggauucccucaguaacggcgagugaacagggaaga
gcccagcgccgaauccccgccccgggggcgcgggacauguggcguacgga
agacccgcuccccggcgccgcucguggggggcccaaguccuucugaucga
ggcccagcccguggacggugugaggccgguagcggcccccggcgcgccgg
gcccgggucuucccggagucggguugcuugggaaugcagcccaaagcggg
ugguccaucuaaggcuaaauaccggcacgagaccgauagucaacaaguac
cguaagggaaaguugaaaagaacuuugaagagagaguucaagagggcgug
aaaccguuaagaggaacgggugggguccgcgcaguccgcccggaggauuc
aacccggcggcggccgccgccgggcgcauuuccaccgcggcggugcgccg
cgaccggcuccgggacggcugggaaggcccggcggggaagguggcucggg
cccgaguguuacagcccccccggcagcagcacucgccgaaucccggggcc
gagggagcgccgcgcucuccggccgggccaggccacgcgagcgcacgggg
ucggcggcgacgucggcuacccacccgacccgucuacacggaccaaggag
ucuaacacgugcgcgagucgggggcucgcacgaaagccgccguggcgcaa
ggugggaucccgaggccgccgagggcgcaccaccggccgcacgagcgcac
guguuaggacccgaaagauggugaaaccaucuaguagcugguucccuccg
aaguuucccucaggauagcuggcgcucucgcaguuuuauccgguggguaa
gaagccggcguggaaugcgagugccuagugggccacuuuuagaacuggcg
cugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucgg
cgcuggagcgucgggcccauacccggccgucgccggcagucacgcuacgc
cgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgcgg
gcccggguggagccgccgcaggugcagaucuuggugguaguagcaauguu
ggaacaauguaggaccuacuauccagcgaaaccucagcacugaugauguu
guugccaugguaauccugcucaguacgagaggaaccgcagguucagacau
uugguguaugugcuuggcugaggagccaauggggcgaagcuaccaucugu
gggcccgcccaggcggaacgauagcgccgcggagccucgguuggccucgg
auagccgguccccgggguccggugcggagugcccuucguccugggaaacg
gggcgcggccggagaggcggccgcccccucgcccgucacgcaccgcacgu
ucguggggaaccuggcgcuaaaccauucguagacgaccugcugggucggg
guuucguacguagcagagcagcucccucgcugcgaucuauugaaagagcc
cucgacacgguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fkq Principles of human pre-60 S biogenesis.
• Resolution: 2.76 Å
• Binding residue (original residue number in PDB): H43 S45 R46 R52 S58 R59 S60 Y63 S64 K66 A67 Y69 K70 G97 D99 N101 R105 V107 L109 R110 K111 P113 R114 R123 K124 L125 L126 H128 K130 P132 F133 S134 H136 K139 T154 R156 H157 R158 L172 L179 L181 R183 P185 R187 R188 H190 K192 F217 K219 Y240 I242 R246 K247 K262 Q266 R272 S273 V274 N279
• Binding residue (residue number reindexed from 1): H2 S4 R5 R11 S17 R18 S19 Y22 S23 K25 A26 Y28 K29 G38 D40 N42 R46 V48 L50 R51 K52 P54 R55 R64 K65 L66 L67 H69 K71 P73 F74 S75 H77 K80 T95 R97 H98 R99 L113 L120 L122 R124 P126 R128 R129 H131 K133 F158 K160 Y163 I165 R169 K170 K185 Q189 R195 S196 V197 N202

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