Structure of PDB 9bdn Chain AL12 Binding Site BS01

Receptor Information
>9bdn Chain AL12 (length=153) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRI
TVKLTIQNRQAQIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDE
IVNIARQMRHRSLARELSGTIKEILGTAQSVGCNVDGRHPHDIIDDINSG
AVE
Ligand information
>9bdn Chain A28S (length=3557) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgcgggggcccaaguccuucuga
ucgaggcccagcccguggacggugugaggccgguagcggcccccggcgcg
ccgggcccgggucuucccggagucggguugcuugggaaugcagcccaaag
cgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauaguc
aacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaa
gagggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgc
ccggaggauucaacccggcggcgcgguccggccgugccggcggggcggau
ccccgcucucggcgggggaccgccccccggccggcgaccggccgccgccg
ggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacggcugg
gaaggccccggcggggaagguggcccgggggccccggguguuacagcccc
gccccggcagcagcagcucgccgaaucccggggccgagggagcgagaccc
gugcgccgcgcucuccccccggggggccgggccaccccucccacggcgcg
accgcuggggcggacuguccagugcgccccgggcgggucgcgccgucggg
cccggggggccacgcguccagcgcacggggucggcggcgaugucggcuac
ccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcga
gucgggggcuacgaaagccgccguggcgcaaugaaggugaaggccggccg
gccgaggugggaucccgaggccuuccaguccgccgagggcgcaccaccgg
cccgucucgcccgccgcgccggggagguggagcacgagcgcacguguuag
gacccgaaagauggugaacuaugccugggcagggcgaagccagaggaaac
ucugguggagguccguagcgguccugacgugcgaaucggucguccgaccu
ggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucccucc
aaaguuucccucaggauagcuggcgcucuccgcaguuuuauccgguaaag
cgaaugauuagaggucuuggggccgaaacgaucucaaccuauucucaaac
uuuaaauggguaagaagcccggcucgcugguguggagccgggcguggaau
gcgagugccuagugggccacuuuugguaagcagaacuggcgcugcgggau
gaaccgaacgccggguuaaggcgcccgaugccgacgcucaucagacccca
gaaaagguguugguugauauagacagcaggaugguggccauggaagucgg
aauccgcuaaggaguguguaacaacucaccugccgaaucaacuagcccug
aaaauggauggcgcuggagcgucgggcccauacccggccgucgcuggcag
ucggcagagcgagaaagagagggacgcuacgccgcgacgaguaggagggc
cgcugcggugagccuugaagccuagggcgcgggcccggguggagccgccg
caggugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaa
ggccgaaguggagaaggguuccaugugaacagcaguugaacaugggucag
ucgguccugagagaugggcgagcgccguuccgaagggacgggcgauggcc
uccguugcccucagccgaucgaaagggagucggguucagauccccgaauc
cggaguggcggagaugggcgccgcgaggcguccagugcgguaacgcgacc
gaucccggagaagccggcgggagccccggggagaguucucuuuucuuugu
gaagggcagggcgcccuggaauggguucgccccgagagaggggcccgugc
cuuggaaagcgucgcgguuccggcggcguccggugagcucucgcuggccc
uugaaaauccgggggagaggguguaaaucucgcgccgggccguacccaua
uccgcagcaggucuccaaggugaacagccucuggcauguuggaacaaugu
agguaagggaagucggcaagccggauccguaacuucgggauaaggauugg
cucuaagggcucagccgacuuagaacuggugcggaccaggggaauccgac
uguuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugacgcg
augugauuucugcccagugcucugaaugucaaagugaagaaauucaauga
agcgcggguaaacggcgggaguaacuaugacucucuuaagguagccaaau
gccucgucaucuaauuagugacgcgcaugaauggaugaacgagauuccca
cugucccuaccuacuauccagcgaaaccacagccaagggaacgggcuugg
cggaaucagcggggaaagaagacccuguugagcuugacucuagucuggca
cggugaagagacaugagagguguagaauaagugggaggccggccgccggu
gaaauaccacuacucugaucguuuuuucacugacccggugaggcgggggg
gcgagggcucucgcuucuggcgccaagcgcccggcgccgggcgcgacccg
cuccggggacagugccagguggggaguuugacuggggcgguacaccuguc
aaacgguaacgcagguguccuaaggcgagcucagggaggacagaaaccuc
ccguggagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaa
uacagaccgugaaagcggggccucacgauccuucugaccuuuuggguuuu
aagcaggaggugucagaaaaguuaccacagggauaacuggcuuguggcgg
ccaagcguucauagcgacgucgcuuuuugauccuucgaugucggcucuuc
cuaucauugugaagcagaauucaccaagcguuggauuguucacccacuaa
uagggaacgugagcuggguuuagaccgucgugagacagguuaguuuuacc
cuacugaugauguguuguugccaugguaauccugcucaguacgagaggaa
ccgcagguucagacauuugguguaugugcuuggcugaggagccaaugggg
cgaagcuaccaucugugggauuaugacugaacgccucuaagucagaaucc
cgcccaggcggaacgauagccggagccucgguuggccucggauagccggu
cccccggggguccggugcggagagcccuucgucccgggaaacggggcggc
cggaaagggggccgcccucucgcccgucacgcaccgcacguucgugggga
accuggcgcuaaaccauucguagacgaccugcuucugggucgggguuucg
uacguagcagagcaggcugcgaucuauugaaagucagcccucgacacaag
gguuugu
.........................<<<<<<.....<......>......
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..>>>.>..<<<<<<<<<....<<<<<<<.<<<<<<<<....<<<<....
..>>>>.....((......<<<.....))>>>...>.>>>>>>>....>>
>>>>>...>>>>>>>>>.......<<<<<<<........>>>>>>>....
.<<<<<..((((((>>>>>..>>>..........................
........<<....>>...............<<<<....>>>>.......
...........................<<<<<<<<..<<<.<....<<<<
<<<<.<<<.....<<<<<<<<<<....<<<<<<<.<<<<<.<<<<<<<.<
<<<<<<.....>>>>>.>>>>>>>>>>>>>>>>>>...>>>.>>>>>>>>
>>......>>>.>>>.>>>>>...<<<<<<<<<<<<<<<<<<.<<<<...
<<..<<<..<<<<<<<......<<<<<<<...>>>>>>>.......>>>>
>>>..>>>.........>>>>>>...>>>>>>>>>>.....<<.......
>>.........<...<<<<...>>>>...<.<...<<<.<<<<<<<<<<<
<<<<<<<<<<<<.<<<<..>>>>.>>>>>>.>>>>.>>>>>>>>>>.>>>
...>>>.>.>..........>........>>>.>>>>>....>>>>...>
>>>>>>>..<<<<........>>>><<<<<<....<<<<<<<<<<<<<..
<<<...<<<<.....>>>>.....>>>...<<....>>...<<<<<..>>
>>>..<<<<<...<<<..<<<.......[[.>>>..>>>....>>>>>.<
<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>>>>>>>>>>>>>
..<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>
>>>>>>.....>>>...<<<..<<.<<........>>>>.>>>....>>>
>>>>>>...<<.......>>......>>>>>>...>..>.>>..<<<<<<
....<.<<<....>>>.><<.<<<<<<<...<<<.<<<<<<<<<...<<<
....<<<....<<<..<<<<.............>>>>>>>....>>>..>
>.>...>>>>>>>...<<<<<<<<<.........>>>>>>>>>....>>>
>>>>>>>>>..>>..<<<<.<<<<<.....>>>>>.>>>>....<<<...
...>>>...<<<<<<<...<<<(((.......<<<<<.....<<......
....<<<.<<<<<<<<<........<<<<<....................
...............<<......>>...>>>>>....>>>>>>>>>>>>.
.........))).>>...>>>>>..>>>...>>>>>>><<<<<<.<<<..
..................]]..........>>>>>>>>>....>>>>>>.
<.<<<<<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>>>
>>>..>.....>>>>>><<.....<<.....<<<<<<.......>>>>>>
.<<<.....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....(
(<<<<<<...<<....<<<....>>>..........<<.<<<<<<<<<..
.>>>>>>>>>>>......>>....>>>..<<<<<........>>>>>))<
<<<....<<<<<..<<<<<<<<....>>>>>>>>..<<<....>>>...<
..<<<<<<<...<<<<<<<<<<<<.<<<<<<<<<<..[[[..>>>>>>..
..<<<<<.<<<<.<<<<.....<<<.....>>>.....>>>>>>>>..>>
>>>.....<<<<<<<.......>>>>>>>>>>>...>>>>>>>>>>>>..
.......>>>>>>>..>..........>>.>>>.>>>>.>>>..>>....
.<<......>>>>>>>.<<<<.....>>>>..>>>....<<<<.....<<
<<<<<.<<.........<.....<<<<<.....<..>......>>>>><<
.<<<<<<<<<<.>>>>..>>>>>>.>>............<<<<<<<<<..
<<<.........>>>..<<<<<<<....<<<<.....>>>>......>>>
>>>>...<<..<<<..<<<<<<....<<<.....<<<<....>>>>....
.>>>.>>>>..>>>>><<<<<<.......>>>>>>........<......
.....<<<<<.......>>>>>.....>.....>>....>>.>>>>>>>.
.>..>>.>>>>>>>..>>>>>>....>>....<<<<<........>>>>>
....<<<<<..<<<.<<......<<<<.<<<<<<..<<<<<.<<<<<<<<
<.<<<<<<<<<<<<.<<<<...........<......<<..>>.......
.........>..>>>>.>>.>>>>>>>>>>...<<<<<.....<<<<..<
<.........>>..............<<<<<<<<..>>>>>>>>..>>>>
..>>>>>....>>>>>>>>>..>>>>>...<<<.....>>>..<<<<<<.
..........>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>
>>.....<<.[.(((>>....>>>>>>>...<<<..<<<<.......>>>
>..>>>.<<<....>>>.>>)))].....<<<<<<<..<<<..)))))).
>>>>>>>>>>.........>>>>..>>>>>>.......<<.<.<.<<<<<
<...<<.......>>...>>>>>>...>>.>.>.......<<<<<.<<<<
<<..<.<.<<<<<......>>>>>...>.>.<<<.........>>>....
.>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>....>>..>
>>.>>>>>.....<<<<<<.<..<<<....<<<<<...............
..>>>>>..<<<<....<<<<....<<.<<<<<<.]]]..>>>>..>>.>
>...>>>>...>>>><<<<<...<<<<<...........>>>>>...>>>
>>.>>>...>.>>>>>>.<<<<<..<<<<....<<<........<<<<<.
.<<<<.>>>>.>>>>>.......>>>...<<<..<<<<.......<<<<<
<........>>>>>.>......>>>>..>>>..............>>>>.
.>.>>>>...<<<<<....................<<.<<<<<<<.<<..
...<<<<.<..<<<<.>>>>..>>>>>....>>....>>>>.>>>.>>..
>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB9bdn Structural mechanism of angiogenin activation by the ribosome.
Resolution3.1 Å
Binding residue
(original residue number in PDB)
R16 T25 R57 T59 S76 A77 S78 K94 I98 K99 K130 E131 G134 T135 Q137 S138 R146 H147
Binding residue
(residue number reindexed from 1)
R8 T17 R49 T51 S68 A69 S70 K86 I90 K91 K122 E123 G126 T127 Q129 S130 R138 H139
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0070180 large ribosomal subunit rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

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Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:9bdn, PDBe:9bdn, PDBj:9bdn
PDBsum9bdn
PubMed38718836
UniProtG1SMR7|RL12_RABIT Large ribosomal subunit protein uL11 (Gene Name=RPL12)

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