Structure of PDB 8fkp Chain SD Binding Site BS01

Receptor Information

>8fkp Chain SD (length=239) Species: 9606 (Homo sapiens)

EVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHK
EYRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVL
QLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGY
GKINKKRIALTDNALIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLW
PFKLSSPRGGMKKKTTHFVEGGDAGNREDQINRLIRRMN

Ligand information

>8fkp Chain L3 (length=1507)

gcgaccucagaucagacguggcgacccgcuggcauauuagucagcggagg
agaagaaacuaaccaggauucccucaguaacggcgagugaacagggaaga
gcccagcgccgaauccccgccccgggggcgcgggacauguggcguacgga
agacccgcuccccggcgccgcucguggggggcccaaguccuucugaucga
ggcccagcccguggacggugugaggccgguagcggcccccggcgcgccgg
gcccgggucuucccggagucggguugcuugggaaugcagcccaaagcggg
ugguccaucuaaggcuaaauaccggcacgagaccgauagucaacaaguac
cguaagggaaaguugaaaagaacuuugaagagagaguucaagagggcgug
aaaccguuaagaggacgggugggguccgcgcaguccgcccggaggauuca
acccggcggcggccgccgccgggcgcauuuccaccgcggcggugcgccgc
gaccggcuccgggacggcugggaaggcccggcggggaagguggcucgggc
ccgaguguuacagcccccccggcagcagcacucgccgaaucccggggccg
gcggcgacgucggcuacccacccgacccgucacggaccaaggagucuaac
acgugcgcgagucgggggcucgcacgaaagccgccguggcgcaagguggg
aucccgaggccaguccgccgagggcgcaccaccggccgcacgagcgcacg
uguuaggacccgaagcugguucccuccgaaguuucccucaggauagcugg
cgcucucgcaguuuuauccgggguaagaagccggcguggaaugcgagugc
cuagugggccacuuuuagaacuggcgcugcgggaugaaccgaacgccggg
uuaaggcgcccgaugccgacgcucggcgcuggagcgucgggcccauaccc
ggccgucgccggcagucgagaguggacggcgcggacgcuacgccgcgacg
aguaggagggccgcugcggugagccuugaagccuagggcgcgggcccggg
uggagccgccgcaggugcagaucuuggugguaguagcaauguuggaacaa
uguaggaccuacuauccagcgaaaccucagcacugaugaguuguugccau
gguaauccugcucaguacgagaggaaccgcagguucagacauuuggugua
ugugcuuggcugaggagccaauggggcgaagcuaccaucugugggcccgc
ccaggcggaacgauagcgccgcggagccucgguuggccucggauagccgg
uccccgggguccggugcggagugcccuucguccugggaaacggggcgcgg
ccggagaggcggccgcccccucgcccgucacgcaccgcacguucgugggg
aaccuggcgcuaaaccauucguagacgaccugcugggucgggguuucgua
cguagcagagcagcucccucgcugcgaucuauugaaagagcccucgacac
gguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fkp Principles of human pre-60S biogenesis
• Resolution: 2.85 Å
• Binding residue (original residue number in PDB): R22 F25 E27 K29 K31 K35 K36 H58 Y61 R62 Y65 R66 I69 R73 R76 R96 G97 I98 N99 P103 K107 L111 R113 Q116 I117 K124 A128 N131 M132 L147 N151 R157 K165 R166 R177 E188 K202 N206 K212 L213 S214 S215 P216 R217 G218 G219 M220 K223 R242
• Binding residue (residue number reindexed from 1): R13 F16 E18 K20 K22 K26 K27 H49 Y52 R53 Y56 R57 I60 R64 R67 R87 G88 I89 N90 P94 K98 L102 R104 Q107 I108 K115 A119 N122 M123 L138 N142 R148 K156 R157 R168 E179 K193 N197 K203 L204 S205 S206 P207 R208 G209 G210 M211 K214 R233

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0042802 identical protein binding

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• 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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fkp, PDBe:8fkp, PDBj:8fkp
• PDBsum: 8fkp
• PubMed: 37410842
• UniProt: P18124|RL7_HUMAN Large ribosomal subunit protein uL30 (Gene Name=RPL7)