Structure of PDB 9bdp Chain ALNW Binding Site BS01

Receptor Information
>9bdp Chain ALNW (length=124) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAHLQWMVVRNCSSFLIKRNKQTYSTEPNNLKARNSFRYNGLIHRKTVGV
EPAADGKGVVVVMKRRSGQRKPATSYVRTTINKNARATLSSIRHMIRKNK
YHPDLRMAAIRRASAILRSQKPVM
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)
W7 R11 K19 R20 K22 T24 K33 R35 N36 S37 F38 R39 Y40 R66 R67 Q70 R71 T81 I82 K84 N85 R87 R94 H95 R98 K99 N100 K101 D105 R107 M108 R112
Binding residue
(residue number reindexed from 1)
W6 R10 K18 R19 K21 T23 K32 R34 N35 S36 F37 R38 Y39 R65 R66 Q69 R70 T80 I81 K83 N84 R86 R93 H94 R97 K98 N99 K100 D104 R106 M107 R111
Gene Ontology
Cellular Component
GO:0005737 cytoplasm
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Cellular Component
External links
PDB RCSB:9bdp, PDBe:9bdp, PDBj:9bdp
PDBsum9bdp
PubMed38718836
UniProtG1U7L1|RL28_RABIT Large ribosomal subunit protein eL28 (Gene Name=RPL28)

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