Structure of PDB 8fkp Chain LN Binding Site BS01

Receptor Information

>8fkp Chain LN (length=377) Species: 9606 (Homo sapiens)

PRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVDRPGSKV
NKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRR
FYKNWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQ
MRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMI
DVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVACIGAWHPAGQKGYHH
RTEINKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGFVHYGEV
TNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALEKIDLKFIDTTSKFGH
GRFQTMEEKKAFMGPLKKDRIAKEEGA

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): R19 K20 R21 R24 R26 K28 K30 S31 K50 M53 T54 H55 G64 S65 A75 Y92 R97 L99 T101 T104 R116 R117 F118 Y119 K120 H123 S125 K126 K128 A129 F130 K132 Y133 R161 R174 Q175 K176 K177 E182 T223 K224 G225 G227 Y228 K229 R234 K238 R242 R246 R249 Q271 H276 T278 E279 I280 N281 K282 G318 H322 Y323 K334 G335 C336 V337 K341 K342 R343 R357 R358 S372 F374 K385 M389 L392 K393
• Binding residue (residue number reindexed from 1): R2 K3 R4 R7 R9 K11 K13 S14 K33 M36 T37 H38 G47 S48 A58 Y75 R80 L82 T84 T87 R99 R100 F101 Y102 K103 H106 S108 K109 K111 A112 F113 K115 Y116 R144 R157 Q158 K159 K160 E165 T206 K207 G208 G210 Y211 K212 R217 K221 R225 R229 R232 Q245 H250 T252 E253 I254 N255 K256 G292 H296 Y297 K308 G309 C310 V311 K315 K316 R317 R331 R332 S346 F348 K359 M363 L366 K367

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0071353 cellular response to interleukin-4

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fkp, PDBe:8fkp, PDBj:8fkp
• PDBsum: 8fkp
• PubMed: 37410842
• UniProt: P39023|RL3_HUMAN Large ribosomal subunit protein uL3 (Gene Name=RPL3)