Structure of PDB 8ipd Chain V Binding Site BS01

Receptor Information

>8ipd Chain V (length=201) Species: 9606 (Homo sapiens)

EVQVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKL
KYLAFLRKRMNTNPSRGPYHFRAPSRIFWRTVRGMLPHKTKRGQAALDRL
KVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLGRLAHEVGWKYQAV
TATLEEKRKEKAKIHYRKKKQLMRLRKQAEKNVEKKIDKYTEVLKTHGLL
V

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): Q5 G17 R18 L28 R37 S44 Y48 R49 R59 K60 R61 M62 N63 N65 R68 P70 Y71 H72 F73 R74 T83 M87 P89 H90 K91 K93 R94 D106 I108 P110 D113 K114 K115 K116 R117 R128 L129 K130 R133 E144 V145 K148 Y149 L156 K163 H167 Y168 R169 K171 K172 M175 R176 K188 V203
• Binding residue (residue number reindexed from 1): Q3 G15 R16 L26 R35 S42 Y46 R47 R57 K58 R59 M60 N61 N63 R66 P68 Y69 H70 F71 R72 T81 M85 P87 H88 K89 K91 R92 D104 I106 P108 D111 K112 K113 K114 R115 R126 L127 K128 R131 E142 V143 K146 Y147 L154 K161 H165 Y166 R167 K169 K170 M173 R174 K186 V201

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0017148 negative regulation of translation
• GO:0032496 response to lipopolysaccharide
• GO:0042592 homeostatic process
• GO:0048246 macrophage chemotaxis
• GO:0060425 lung morphogenesis
• GO:0071346 cellular response to type II interferon
• GO:1901194 negative regulation of formation of translation preinitiation complex

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0015934 large ribosomal subunit
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0097452 GAIT complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ipd, PDBe:8ipd, PDBj:8ipd
• PDBsum: 8ipd
• PubMed: 37491604
• UniProt: P40429|RL13A_HUMAN Large ribosomal subunit protein uL13 (Gene Name=RPL13A)