Structure of PDB 9bdp Chain AL25 Binding Site BS01

Receptor Information
>9bdp Chain AL25 (length=118) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDHYAIIKFPLTTESAMK
KIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYV
RLAPDYDALDVANKIGII
Ligand information
>9bdp 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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PDB9bdp Structural mechanism of angiogenin activation by the ribosome.
Resolution3.7 Å
Binding residue
(original residue number in PDB)
P44 T45 R47 R48 P49 K50 T51 R53 R56 Q57 P58 K59 Y60 R62 T83 S85 K89 N105 K106 H107 K123 N125 T126 I128 R129 P130 K134 K135 Y137 R139
Binding residue
(residue number reindexed from 1)
P6 T7 R9 R10 P11 K12 T13 R15 R18 Q19 P20 K21 Y22 R24 T45 S47 K51 N67 K68 H69 K85 N87 T88 I90 R91 P92 K96 K97 Y99 R101
External links
PDB RCSB:9bdp, PDBe:9bdp, PDBj:9bdp
PDBsum9bdp
PubMed38718836
UniProtG1SE76|RL23A_RABIT Large ribosomal subunit protein uL23 (Gene Name=RPL23A)

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