Structure of PDB 8ipd Chain F Binding Site BS01

Receptor Information

>8ipd Chain F (length=109) Species: 9606 (Homo sapiens)

VQRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPG
RLRGVRAVRPKVLMRLSKTKKHVSRAYGGSMCAKCVRDRIKRAFLIEEQK
IVVKVLKAQ

Ligand information

>8ipd Chain 2 (length=3485)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaacacggaccaaggagucuaacacgugcgcga
gucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccgg
cgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgagg
gcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacgag
cgcacguguuaggacccgaaagauggugaacuaugccugggcagggcgaa
gccagaggaaacucugguggagguccguagcgguccugacgugcaaaucg
gucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguag
cugguucccuccgaaguuucccucaggauagcuggcgcucucgcagaccc
gacgcccgccacgcaguuuuauccgguauggguaagaagcccggcucgcu
ggcguggagccgggcguggaaugcgagugccuagugggccacuuuuggua
agcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcccga
ugccgacgcucaucagacccagaaaagguguugguugauauagacagcag
gacgguggccauggaagucggaauccgcuaaggaguguguaacaacucac
cugccgaaucaacuagcccugaaaauggauggcgcuggagcgucgggccc
auacccggccgucgccggcagucgagaguggacgggagcggcggcccgga
gccccgcggacgcuacgccgcgacgaguaggagggccgcugcggugagcc
uugaagccuagggcgcgggcccggguggagccgccgcaggugcagaucuu
ggugguaguagcaaauauucaaacgagaacuuugaaggccgaaguggaga
aggguuccaugugaacagcaguugaacaugggucagucgguccugagaga
ugggcgagcgccguuccgaagggacgggcgauggccuccguugcccucgg
ccgaucgaaagggagucggguucagauccccgaauccggaguggcggaga
ugggcgccgcgaggcguccagugcgguaacgcgaccgaucccggagaagc
cggcgggagccccggggagaguucucuuuucuuugugaagggcagggcgc
ccuggaauggguucgccccgagagaggggcccgugccuuggaaagcgucg
cgguuccggcggcguccggugagcucucgcuggcccuugaaaauccgggg
gagaggguguaaaucucgcgccgggccguacccauauccgcagcaggucu
ccaaggugaacagccucuggcauguuggaacaauguagguaagggaaguc
ggcaagccggauccguaacuucgggauaaggauuggcucuaagggcuggg
ucggucgcggccggcgccuagcagccgacuuagaacuggugcggaccagg
ggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcggg
uguugacgcgaugugauuucugcccagugcucugaaugucaaagugaaga
aauucaaugaagcgcggguaaacggcgguuaagaacgagauucccacugu
cccuaccuacuauccagcgaaaccacagccaagggaacgggcuuggcgga
aucagcggggaaagaagacccuguugagcuugacucuagucuggcacggu
gaaguuuuuucacugacccggugaggcgggggggcgagccccgaggggcu
cucgcuucuggcgccaagcgcccggccgcgcgccggccgggcgcgacccg
cuccggggacagugccagguggggaguuuccugucgcagguguccuaagg
cgagcucagggaggacagaaaccucccguggagcagaagggcaaaagcuc
gcuugaucuugauuuuuacgaauacagaccgugaaagcggggccgauccu
ucugaccuuuuggguuuuaagcaggagguaaguuaccacagggauaggcu
uguggcggccaagcguucauagcgacgucgcuuuuugauccuucgauguc
ggcucuuccuaucauugugaagcagaauucaccaagcguuggauuguuca
cccacuaauagggaacgugagcuggguuuagaccgucgugagacagguua
guuuuacccuacugaugauguguuguugccaugguaauccugcucaguac
gagaggaaccgcagguucagacauuugguguaugugcuuggcugaggagc
caauggggcgaagcuaccaucugugggauuaugacugaacgccucuaagu
cagaaucccgcccaggcggaacgauacggcagcgccgcggagccucgguu
ggccucggauagccggucccccgccgggguccggugcggagugcccuucg
uccugggaaacggggcgcggccggagaggcggccgcccccucgcccguca
cgcaccgcacguucguggggaaccuggcgcuaaaccauucguagacgacc
ugcuucugggucgggguuucguacguagcagagcagcucccucgcugcga
ucuauugaaagucagcccucgacacaaggguuugu

.........................<<<<<<<....<......>.....>
>>>>>.>.........<<....>>..<<<<<<.....<<.....>>....
>>>>>>..[[[..<<<<<...<<<<<<<<<<.....>>>>>>.>>>>...
..>>>>>..<<<<<<<<<<...<<<<<<<<........<<<<<<<<....
<<<<......>>>>.....((......<<<.....))>>>...>.>>>>>
>>...>>>>>>>>..>>>>>>>>>>.......<<<<<<<........>>>
>>>>.....(((((..<<<<<<)))))..]]]..................
................<<....>>...............<<<<....>>>
>..................................<<<<<<<<..<<<.<
<...<<<<<<<<.<<<.....<<<<<<<<<<<..<<<<<<<.......<<
....<<<<.<<<..<<<<..>>>>>>>>>>>>>......>>>>...>>>>
>>>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<<<<<<<<<<<<
<<<<<...<<..<<<..<.<<<<......<<<<<<<<..>>>>>>>>...
....>>>>.>.>>>........>>>>>>..>>>>>>>>>>>.........
...........<<<<<<.<<<<<<<............>>>>>>>.<<<<<
<.<<<<.<<<<<<<<<<.<<<<<..<<<<....<<......>>....>>>
>..>>>>.>.>>>>>>>.>>>...>>>>..>>>>.>>..<<<<<<<<<..
.....>>>>>>>.>>....>>>>>>.....>>>.>>>>>...>>>>>...
>>>>>>>>..<<<<.......>>>><<<<<<....<<<<<<<<<<<<<..
<<<...<<<<........>>>>.....>>>...<<....>>...<<<<<<
<......>>>>>>>..<<<<<...<<<..<<<..(((...(((>>>..>>
>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>
>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<....
<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<........>>>
>.>>>....>>>>>>>>>...<<.......>>......>>>>>>...>..
>.>>..<<<<<<....<.<........>.><<.<<<<<<<..........
............<<<.<<<<<<<<<...>>>>>>>...<<<<<<<<<...
......>>>>>>>>>....>>>>>>>>>>>>..>>..<<<<.<<<<<...
..>>>>>.>>>>....<<<......>>>...<<<<<<<...<<<(((...
....<<<<<.....<<.........<<<.<<<<<<<<<<.......<<<<
<.<<<...<<.........>>...>>>.........<<......>>...>
>>>>...>>>>>>>>>>>>>..........))).>>...>>>>>..>>>.
..>>>>>>><<<<<<.<<<..........)))...)))............
................>>>>>>>>>....>>>>>>.<.<<<<<<<<.<<.
.....<<<<.<<<<....>>>>>>>>...>>>>>>>>>>..>.....>>>
>>><<.....<<.....<<<<<<.......>>>>>>.<<<.....<<<<<
.<<...<<<<<....<<.....>>..>>>>>....((<<<<<<...<<..
..<<<....>>>..........<<.<<<<...<<...>>...>>>>>>..
....>>....>>>..<<<<<........>>>>>))<<<<....<<<<<..
.<<<<.<<....>>.>>>>...<<<....>>>...<..<<<<<<<...<<
<<<<<<<<<<<<<<<<<<<<<..[[[..>>>>>>....<<<<<.<<<<.<
<<<.....<<<.....>>>.....>>>>>>>>..>>>>>.....<<<<<<
<.......>>>>>>>>>>>.>.>>>>>>>>>>>>.........>>>>>>>
..>..........>>.>>>.>>>>.>>>..>>.....<<......>>>>>
>>.<<<<.....>>>>..>>>....<<<<.....<<<<<<<.<<......
.........<<<<<....<....>.....>>>>><<.<<<<<<<<<<<..
<............>.......>>>>>..>>>>>>.>>............<
<<<<<<<<..<<<.........>>>..<<<<<<<....<<<<.....>>>
>......>>>>>>>.......<<<..<<<<<<....<<<.....<<<<..
..>>>>.....>>>.>>>>..>>>>>.........>>.>>>>>>>.....
>>.>>>>>>>..>>>>>>....>>....<<<<<........>>>>>....
(((((..[[[........(((((.[[((((..<<<<..<<<<<<<<<.<<
<<<<...>>>>>>...<<<<<.....<<<<.....<<............>
>................<.<<<<<<<<.......>>>>>>>>.>..>>>>
..>>>>>....>>>>>>>>>...>>>>...<<......>>..........
<<<<<...<<<<<<.......>>>>>>...........((......>>>>
>.....<<<..<<<<....>>>>..>>>.<<<....>>>...)).....(
(((...(((..>>>>>>.))).))))....))))..]]))))).......
...<<<<<<.................>>>>>>.................<
<<<.<<<<<<..<.<.<<<<<......>>>>>...>.>.<<<........
.>>>.....>>>>>..>...>>>>......<<<<<<<....>>>.>>>>.
.......]]].))))).....<<<<<<.<..<<<..<.<<<<<.......
..........>>>>>.><<<<....<<<<....<<.<<<<<<.]]]..>>
>>..>>.>>...>>>>...>>>><<<<<...<<<<<...........>>>
>>...>>>>>.>>>...>.>>>>>>.....<<<<<<..<<..<<<<....
<<<........<<<<<.<<<<....>>>>.>>>>>.......>>>...<<
<..<<<<....<<<<.<<<<<<<......>>>>>>>>>>>...>>>>..>
>>..............>>>>..>>.>>>>>><<<<<.<............
.>....<<.<<<<<<<.<<.....<<<<.<..<<<<<......>>>>>..
>>>>>....>>....>>>>.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ipd Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): V2 R4 L5 T6 Y7 R10 L11 S12 Y13 N14 T15 R21 R24 T25 P26 N28 R29 Y32 Y34 K36 K37 K40 R52 R54 G55 R60 P61 K62 L64 M65 R66 S68 K69 T70 K72 V74 S75 R76 Y78 G79 S81 R90 R93 A94 I97 Q100 K101
• Binding residue (residue number reindexed from 1): V1 R3 L4 T5 Y6 R9 L10 S11 Y12 N13 T14 R20 R23 T24 P25 N27 R28 Y31 Y33 K35 K36 K39 R51 R53 G54 R59 P60 K61 L63 M64 R65 S67 K68 T69 K71 V73 S74 R75 Y77 G78 S80 R89 R92 A93 I96 Q99 K100

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ipd, PDBe:8ipd, PDBj:8ipd
• PDBsum: 8ipd
• PubMed: 37491604
• UniProt: P49207|RL34_HUMAN Large ribosomal subunit protein eL34 (Gene Name=RPL34)