Structure of PDB 9bdl Chain AL17 Binding Site BS01

Receptor Information
>9bdl Chain AL17 (length=153) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDV
TLKKQCVPFRRYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESN
AELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILT
EKE
Ligand information
>9bdl 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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PDB9bdl Structural mechanism of angiogenin activation by the ribosome.
Resolution2.8 Å
Binding residue
(original residue number in PDB)
R3 Y4 S17 R18 S20 R23 H25 K27 N28 R30 Q34 K37 K54 K55 R62 Y63 G65 G66 G68 R69 A71 Q72 K74 Q75 T79 Q80 R82 W83 P84 K85 K86 N97 S100 N101 Q118 V119 R127 T129 Y130 R131 A132 H133 G134 R135 I136 N137 P138 Y139 M140 S141
Binding residue
(residue number reindexed from 1)
R2 Y3 S16 R17 S19 R22 H24 K26 N27 R29 Q33 K36 K53 K54 R61 Y62 G64 G65 G67 R68 A70 Q71 K73 Q74 T78 Q79 R81 W82 P83 K84 K85 N96 S99 N100 Q117 V118 R126 T128 Y129 R130 A131 H132 G133 R134 I135 N136 P137 Y138 M139 S140
External links
PDB RCSB:9bdl, PDBe:9bdl, PDBj:9bdl
PDBsum9bdl
PubMed38718836
UniProtG1SCJ6|RL17_RABIT Large ribosomal subunit protein uL22 (Gene Name=RPL17)

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