Structure of PDB 9bdl Chain AL15 Binding Site BS01

Receptor Information

>9bdl Chain AL15 (length=203) Species: 9986 (Oryctolagus cuniculus)

GAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRL
GYKAKQGYVIYRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSV
AEERAGRHCGALRVLNSYWVGEDSTYKFFEVILIDPFHKAIRRNPDTQWI
TKPVHKHREMRGLTSAGRKSRGLGKGHKFHHTIGGSRRAAWRRRNTLQLH
RYR

Ligand information

>9bdl Chain A28S (length=3557)

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

Structure summary

• PDB: 9bdl Structural mechanism of angiogenin activation by the ribosome.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): G2 Y4 K5 Q8 R12 K14 Q15 R24 R31 S34 A35 P40 R41 R44 K47 R49 R50 L51 K54 A55 K56 Q57 R65 R67 R68 G69 G70 R71 R73 P74 P76 K77 Y81 G82 K83 P84 V85 H86 H87 N90 Q91 K93 F94 A95 R96 S97 E104 R105 R108 A112 W120 S125 Y127 F138 K140 R144 W150 H156 K157 H158 M161 R162 L164 S166 R169 K170 S171 R172 K176 G177 H178 K179 H181 H182 G185 G186 S187 R189 W192 R193 R194 R195 Q199 H201 R202 R204
• Binding residue (residue number reindexed from 1): G1 Y3 K4 Q7 R11 K13 Q14 R23 R30 S33 A34 P39 R40 R43 K46 R48 R49 L50 K53 A54 K55 Q56 R64 R66 R67 G68 G69 R70 R72 P73 P75 K76 Y80 G81 K82 P83 V84 H85 H86 N89 Q90 K92 F93 A94 R95 S96 E103 R104 R107 A111 W119 S124 Y126 F137 K139 R143 W149 H155 K156 H157 M160 R161 L163 S165 R168 K169 S170 R171 K175 G176 H177 K178 H180 H181 G184 G185 S186 R188 W191 R192 R193 R194 Q198 H200 R201 R203

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0044391 ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:9bdl, PDBe:9bdl, PDBj:9bdl
• PDBsum: 9bdl
• PubMed: 38718836
• UniProt: G1T0C1|RL15_RABIT Large ribosomal subunit protein eL15 (Gene Name=RPL15)