Structure of PDB 8inf Chain p Binding Site BS01

Receptor Information

>8inf Chain p (length=225) Species: 9606 (Homo sapiens)

NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMAR
MARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFV
KLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNA
LIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKK
TTHFVEGGDAGNREDQINRLIRRMN

Ligand information

>8inf Chain 2 (length=3654)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcg
agucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccg
gcgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcaaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccgaaguuucccucaggauagcuggcgcucucgcagacc
cgacgcccgccacgcaguuuuauccgguaaagccuuuaaauggguaagaa
gcccggcucgcuggcguggagccgggcguggaaugcgagugccuaguggg
ccacuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccgggu
uaaggcgcccgaugccgacgcucaucagaccccagaaaagguguugguug
auauagacagcaggacgguggccauggaagucggaauccgcuaaggagug
uguaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcug
gagcgucgggcccauacccggccgucgccggcagucgagaguggacggga
gcggcggcccggagccccgcggacgcuacgccgcgacgaguaggagggcc
gcugcggugagccuugaagccuagggcgcgggcccggguggagccgccgc
aggugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaag
gccgaaguggagaaggguuccaugugaacagcaguugaacaugggucagu
cgguccugagagaugggcgagcgccguuccgaagggacgggcgauggccu
gcccuccgaucgaaagggagucggguucagauccccgaauccggaguggc
ggagaugggcgccgcgaggcguccagugcgguaacgcgaccgaucccgga
gaagccggcgggagccccggggagaguucucuuuucuuugugaagggcag
ggcgcccuggaauggguucgccccgagagaggggcccgugccuuggaaag
cgucgcgguuccggcggcguccggugagcucucgcuggcccuugaaaauc
cgggggagaggguguaaaucucgcgccgggccguacccauauccgcagca
ggucuccaaggugaacagccucuggcauguuggaacaauguagguaaggg
aagucggcaagccggauccguaacuucgggauaaggauuggcucuaaggg
cugggucggucgcggccggcgccuagcagccgacuuagaacuggugcgga
ccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcg
gcggguguugacgcgaugugauuucugcccagugcucugaaugucaaagu
gaagaaauucaaugaagcgcggguaaacggcgggaguacucucuuaagaa
cgagauucccacugucccuaccuacuauccagcgaaaccacagccaaggg
aacgggcuuggcggaaucagcggggaaagaagacccuguugagcuugacu
cuagucuggcacggugaagagacaugagagguguagaauaagugggaggc
ccccggcgcccccccgguguccccgcgaggggcccggggcgggguccgcc
ggcccugcgggccgccggugaaauaccacuacucugaucguuuuuucacu
gacccggugaggcgggggggcgagccccgaggggcucucgcuucuggcgc
caagcgcccggccgcgcgccggccgggcgcgacccgcuccggggacagug
ccagguggggaguuugacuggggcgguacaccugucaaacgguaacgcag
guguccuaaggcgagcucagggaggacagaaaccucccguggagcagaag
ggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccgugaaa
gcggggccucacgauccuucugaccuuuuggguuuuaagcaggagguguc
agaaaaguuaccacagggauauuguggcggccaagcguucauagcgacgu
cgcuuuuugcuucgaugucggcucuuccuaucauugugaagcagaauuca
ccaagcguuggauuguucacccacuaauagggaacgugagcuggguuuag
accgucgugagacagguuaguuuuacccuacugaugauguguuguugcca
ugguaauccugcucaguacgagaggaaccgcagguucagacauuuggugu
augugcuuggcugaggagccaauggggcgaagcuaccaucugugggauua
ugacugaacgccucuaagucagaaucccgcccaggcggaacgauacggca
gcgccgcggagccucgguuggccucggauagccggucccccgccgggguc
cggugcggagugcccuucguccugggaaacggggcgcggccggagaggcg
gccgcccccucgcccgucacgcaccgcacguucguggggaaccuggcgcu
aaaccauucguagacgaccugcuucugggucgggguuucguacguagcag
agcagcucccucgcugcgaucuauugaaagucagcccucgacacaagggu
uugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8inf Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): N24 F25 A26 E27 L28 K29 I30 K31 R32 R34 K35 K36 F37 Q39 R43 R46 R47 K48 Y51 E52 H58 K59 Y61 R62 Y65 R66 I69 R70 R73 M74 R76 G97 I98 N99 P103 K104 K107 L111 R113 Q116 I117 K124 K127 A128 N131 K165 R166 A176 R177 G180 K181 E188 R200 K202 K212 L213 S214 S215 P216 R217 G218 G219 M220 K222 K223 R242
• Binding residue (residue number reindexed from 1): N1 F2 A3 E4 L5 K6 I7 K8 R9 R11 K12 K13 F14 Q16 R20 R23 R24 K25 Y28 E29 H35 K36 Y38 R39 Y42 R43 I46 R47 R50 M51 R53 G74 I75 N76 P80 K81 K84 L88 R90 Q93 I94 K101 K104 A105 N108 K142 R143 A153 R154 G157 K158 E165 R177 K179 K189 L190 S191 S192 P193 R194 G195 G196 M197 K199 K200 R219

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:8inf, PDBe:8inf, PDBj:8inf
• PDBsum: 8inf
• PubMed: 37491604
• UniProt: P18124|RL7_HUMAN Large ribosomal subunit protein uL30 (Gene Name=RPL7)