Structure of PDB 8ipx Chain B Binding Site BS01

Receptor Information

>8ipx Chain B (length=402) Species: 9606 (Homo sapiens)

SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKA
GMTHIVREVDRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRT
FKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDEDGKKQLEKDFS
SMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERL
EQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKV
ACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSL
LVQTKRRALEKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEE
GA

Ligand information

>8ipx Chain 2 (length=3475)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucaaacacggaccaaggagucuaacacgugcgcgagu
cgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccggcg
cgcucgccggccgaggugggaucccgaggccucuccaguccgccgagggc
gcaccaccggcccgucucgcccgccgcgccggggagguggagcacgagcg
cacguguuaggacccgaaagauggugaacuaugccugggcagggcgaagc
cagaggaaacucugguggagguccguagcgguccugacgugcaaaucggu
cguccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcu
gguucccuccgaaguuucccucaggauagcuggcgcucucgcagacccga
cgcccgccacgcaguuuuauccgguauggguaagaagcccggcucgcugg
cguggagccgggcguggaaugcgagugccuagugggccacuuuugguaag
cagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaug
ccgacgcucaucagacccagaaaagguguugguugauauagacagcagga
cgguggccauggaagucggaauccgcuaaggaguguguaacaacucaccu
gccgaaucaacuagcccugaaaauggauggcgcuggagcgucgggcccau
acccggccgucgccggcagucgagaguggacgggagcggcggcccggagc
cccgcggacgcuacgccgcgacgaguaggagggccgcugcggugagccuu
gaagccuagggcgcgggcccggguggagccgccgcaggugcagaucuugg
ugguaguagcaaauauucaaacgagaacuuugaaggccgaaguggagaag
gguuccaugugaacagcaguugaacaugggucagucgguccugagagaug
ggcgagcgccguuccgaagggacgggcgauggccugcccuccgaucgaaa
gggagucggguucagauccccgaauccggaguggcggagaugggcgccgc
gaggcguccagugcgguaacgcgaccgaucccggagaagccggcgggagc
cccggggagaguucucuuuucuuugugaagggcagggcgcccuggaaugg
guucgccccgagagaggggcccgugccuuggaaagcgucgcgguuccggc
ggcguccggugagcucucgcuggcccuugaaaauccgggggagagggugu
aaaucucgcgccgggccguacccauauccgcagcaggucuccaaggugaa
cagccucuggcauguuggaacaauguagguaagggaagucggcaagccgg
auccguaacuucgggauaaggauuggcucuaagggcugggucggucgcgg
ccggcgccuagcagccgacuuagaacuggugcggaccaggggaauccgac
uguuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugacgcg
augugauuucugcccagugcucugaaugucaaagugaagaaauucaauga
agcgcggguaaacggcgguuaagaacgagauucccacugucccuaccuac
uauccagcgaaaccacagccaagggaacgggcuuggcggaaucagcgggg
aaagaagacccuguugagcuugacucuagucuggcacggugaaguuuuuu
cacugacccggugaggcgggggggcgagccccgaggggcucucgcuucug
gcgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccggggac
agugccagguggggaguuuccugucgcagguguccuaaggcgagcucagg
gaggacagaaaccucccguggagcagaagggcaaaagcucgcuugaucuu
gauuuuuacgaauacagaccgugaaagcggggccgauccuucugaccuuu
uggguuuuaagcaggagguaaguuaccacagggauaggcuuguggcggcc
aagcguucauagcgacgucgcuuuuugauccuucgaugucggcucuuccu
aucauugugaagcagaauucaccaagcguuggauuguucacccacuaaua
gggaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccu
acugaugauguguuguugccaugguaauccugcucaguacgagaggaacc
gcagguucagacauuugguguaugugcuuggcugaggagccaauggggcg
aagcuaccaucugugggauuaugacugaacgccucuaagucagaaucccg
cccaggcggaacgauacggcagcgccgcggagccucgguuggccucggau
agccggucccccgccgggguccggugcggagugcccuucguccugggaaa
cggggcgcggccggagaggcggccgcccccucgcccgucacgcaccgcac
guucguggggaaccuggcgcuaaaccauucguagacgaccugcuucuggg
ucgggguuucguacguagcagagcagcucccucgcugcgaucuauugaaa
gucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ipx Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 4.3 Å
• Binding residue (original residue number in PDB): S2 H3 R4 S7 P9 R10 H11 G12 S13 F16 L17 P18 R19 K20 R21 H25 R26 K28 K30 S31 M53 T54 H55 R62 S65 A75 Y92 T95 P96 R97 L99 R100 T101 F102 T104 R116 R117 Y119 K120 H123 K127 K128 F130 K132 Y133 Y156 R161 R174 Q175 K176 K177 E182 K224 G225 Y228 G230 K238 K239 R242 K243 G247 R249 K250 A252 C253 A256 W257 H258 A260 R261 V262 S265 R268 A269 Q271 H276 R277 T278 E279 I280 L317 G318 H322 G324 K334 C336 V337 T340 K341 K342 R343 R357 S372 K373 F374 H376 K385 M389 L392 K393 R396
• Binding residue (residue number reindexed from 1): S1 H2 R3 S6 P8 R9 H10 G11 S12 F15 L16 P17 R18 K19 R20 H24 R25 K27 K29 S30 M52 T53 H54 R61 S64 A74 Y91 T94 P95 R96 L98 R99 T100 F101 T103 R115 R116 Y118 K119 H122 K126 K127 F129 K131 Y132 Y155 R160 R173 Q174 K175 K176 E181 K223 G224 Y227 G229 K237 K238 R241 K242 G246 R248 K249 A251 C252 A255 W256 H257 A259 R260 V261 S264 R267 A268 Q270 H275 R276 T277 E278 I279 L316 G317 H321 G323 K333 C335 V336 T339 K340 K341 R342 R356 S371 K372 F373 H375 K384 M388 L391 K392 R395

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:8ipx, PDBe:8ipx, PDBj:8ipx
• PDBsum: 8ipx
• PubMed: 37491604
• UniProt: P39023|RL3_HUMAN Large ribosomal subunit protein uL3 (Gene Name=RPL3)