Structure of PDB 9cai Chain CD Binding Site BS02

Receptor Information
>9cai Chain CD (length=289) Species: 6239 (Caenorhabditis elegans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKVIKNKAYFKRYQVKLRRRREGKTDYYARKRLTVQDKNKYNTPKYRLIV
RITNKDVVAQLAYSKIEGDVVVASAYSHELPRYGLKVGLTNYAAAYATGL
LLARRHLKTIGLDSTYKGHEELTGEDYNVEEEGDRAPFKAVLDIGLARTT
TGSKIFAVMKGVADGGINVPHSESRFFGFDQESKEYNAEAHRDRILGKHV
ADYMTYLKEEDEDRYKRQFSKFLAAGLNADNLVATYQKVHSAIRADASPA
AKKAAKPSKRHTAKRLTYDERKQRVADKKALLLQLKEQQ
Ligand information
>9cai Chain A5 (length=3022) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cucaaccugaacucagucgugauuacccgcugaacuuaagcauaucauuu
agcggaggaaaagaaacuaaaaaggauucccuuaguaacggcgagugaaa
cgggaagagcccagcgccgaaucgaucagucuuuggcugcuucgaaaugu
ggcguauagguguaaguuuccagcagugucguauguccgaaguccuuacg
auugaggccauaaaccagagagggugcgagccccguucuggauagcggca
cuguugguucgcuugcuccuuggagucggguugcuugaaagugcagccua
aagugggugauaaacuucaucuaaggcuaaauaucgacucgauugcgaua
gcgaacaaguaccgugagggaaaguugcaaaggacuuugaagagagaguu
caagagaacgugaaaucgcuggaguggaaccggagacaguugauuacgcc
gacggcguuggcugcucguucuagcccgacaguguugcgucuugcuggcg
guaguggguucguggcggcuagcguacgucggugugaaagucgacgacgu
uuccgacccgucuugaaacacggauugcggagugcuugucuacugcgagu
caaaggguguuaaaaccuugcggcgaaaugaaaguaaaggucagucucga
auuggccgacgugggaucugugugugcagcgcaccacggcccugugcgug
ucacuugugacugugcagagguugagcaguuggcaaacgacccgaaagau
ggugaacuaugccugagcaggaugaagccagaggaaacucugguggaagu
ccguaucgguucugacgugcaaaucgaucgauagacuuggguauaggggc
gaaagacuaaucgaaccaucuaguagcugguuccuuccgaaguuucccuc
aggauagcuggaucucaggcaguuauauucgguaaagcuaaugauuagag
gaaccuauucucaaacuuucaauggauaugaaguugcaguuucuuuagug
aacugucaacgugaaugcgagguccaagugggccauuuuugguaagcaga
acuggcgcugugggaugaaccaaacguggaguuaaggugccuaacuucuc
gcucaugagaccccauaaaagguguugguugauauugacagcaaucaacu
agcccugaaaauggauggcgcuuaagcgagagaccuauacuccgccguug
cgacaaggucguaacgaguaggaaggucguggcgguugcguugaaggcug
agcguaggcucggcuggagcuuccgucagugcagaucguaaugguaguag
caaauauucaaguucgauccuugaagacugaaguggagaaggguuccacg
ugaacaguaguuggaugugggucagucgauccuaagguacuggcgaacgc
cuuguaucaucgguggcgguccccgcuugucgaaagggaauaggguuaau
auucccuaacugagaugcaaagauugugugcacaagcgcgguaacgcauu
cgaacuugguuagucgcucaaagaccgagcuagaguuuucuucucuaguu
aaggaacggacucccuggaauugguucagccagagauggggacguuguuu
ccgaaaagcaccgcguggugucucgugcucuuugaacggcccuuaaaaca
ccaagggaggcuauuaauuugcacucaaucguaccgauauccgcauuagg
ucuccaaggugaacagccucuagucgauagaauaauguagguaagggaag
ucggcaaacuagauccguaacuucgggaaaaggauuggcuccagugguua
ccguacuggaaccgguacggacucagggaauccgacugucuaauuaaaac
agaggugacagaugguccuugcggacguugacugucacugauuucugccc
agugcucugaauguuaaaucguaguaauucgaguaagcgcggguaaacgg
cgggaguaacuaugacucucuuaagguagccaaaugccucgucauuuaau
uguugacgcgcaugaauggauuaacgagauuccuacugucccuaacuacu
uucuagcgaaaccacagccaagggaacgggcuuggcaaaaauagcgggga
aagaagacccuguugagcuugacucuaguuugacauugugaagagucaga
cucuuuacuuauucgguuaaaagagaauuucgaagcauuaagcggagcca
uuauggcaccgugacucuccucgaagacagugucaagcggggaguuugac
uggggcgguacaucuaucaaaucguaacguagguguccuaaggcgagcuc
agagaggacggaaaccucucguagagcaaaagggcaaaagcuugcuugau
cuugacuuucaguacgaguacagaccgcgaaagcguggccuaucgauccu
uuuaauccugauuguuucagguaagaggugucagaaaaguuaccacaggg
auaacuggcuuguggcagccaagcguccauagcgacguugcuuuuugauc
cuucgaugucggcucuuccuaucauugcgaagcagaauucgccaagcguu
ggauuguucacccacuaauagggaacgugagcuggguuuagaccgucgug
agacagguuaguuuuacccuacuguugacuuguuauugcgaaaguaaucc
ugcuuaguacgagaggaacagcggguucaaacauuugguucauagacuug
aucgacagaucaauggucugaagcuaccauuugagagauuauaacugaac
gccucuaaguuagaaucucgccuugucaaggcgaaaauuuugcuucccgg
ugucgggaggcaucucuaucucguggcaacacgagagcuuaugcccuaug
uauggccuuggcgucguagugauucugcgacgcuugccaacgccagauca
cucugguucaaugucggggcgcuaaaucacuugcauacgacuuggugguc
aagguguuguauucaguagagcaguccuuuuauacugcgaucuguugaga
cuauccuuugauugauuuuugu
.........................<<<<<<.....<......>......
>>>>>.>.........<<....>>..<<<<<......<<.....>>....
.>>>>>..<<<..<<<<<<..<<<<.<<<<<...>>>>>..>>>>....>
>>>>>..<<<.<<<<<<..<<<<<<<<<<<<<.<<<<<.....<<<<...
...>>>>..............<<<.......>>>.....>>>>>>>>>>>
>>>>>>>...>>>>>>.>>>.......<<<<<<<........>>>>>>>.
....<<<<<..((((..>>>>>..>>>.......................
...........<<....>>...............<<<<....>>>>....
..............................<<<<<<<.<<<<<..<<<<<
<<<<<<<<<<<<<<<<<<..<<.<<<<<.<<<<...<...>..>>>>.>>
>..>>.>>..>>.>>>>>>>>>>>>.>>>>>>>>>.....>>>>>...>>
>>>>>..<<<<........>>>><<<<<<...<<.<<<<<.<<<<<..<<
<...<<<<......>>>>...>>>...<<....>>...<<<<<<<.....
>>>>>>>..<<<<<...<<<<<..>>>>>....>>>>><<<<<<<<<<.<
<<<<..>>>>>>>>>>>>.>>>...>>>>>.>>>>>.>>.<<.<..<<<<
<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>.....>
>>..<<<<..<<.<<........>>>>.>>>>...>>>>>>>>>...<<.
......>>......>>>>>>...>..>.>>..<<<<<<....<.<<<...
.>>>.><<<<<<<<<<..<<<.<<<<<<<<<...<<<....<<<....<<
<..>>>....>>>..>.>>...>>>>>>>...<<<<<<<<<.<......>
>>>>>.>>>>...>>>>>>>>>>>>>.>>..<<<<.<<<<<.....>>>>
>.>>>>....<<<......>>>...<<<<<<<..<<<<(((.....<<<<
<<......<..........<<<.<<<<<<<<<<..........>>>>>>>
>>>>>>..........))).>....>>>>>>.>>>>..>>>>>>><<<<<
<<<<...>>>>>>>>>....>>>>>>...<<<<<<..<<......<<<<<
<<<....>>>>>>>>...>>..>>>>>>........>>>>>><<.....<
<.....<<<<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<
....<<.....>>..>>>>>....((<<<<<<...<<<...<<<....>>
>.........<<<.<<...>>.>>>...>>>....>>...<<<<<.....
...>>>>>))<<<<.<<<<<<..<<<<<..>>>>><<<<<....>>>...
<.((<<<<<<..<<<<.<<<<<<<.<<<<<<<<<<...[[..>>>>>><.
..<<<<<<...<<<<<<....<<<<...>>>>....>>>>>>...>>>>.
>>....><<<<<<..>>>>>>>>>>...>>>>>>>.>>>>.........>
>>>>>...>>>......>>>>>>>>>>>>>>..>>.....<<......>>
>>>>>.<<<<.....>>>>..>>>>..<<<<<....<<<<.<<.<<....
.....<.....<<<<<....<<..>>.....>>>>><<.<<<<<<<<<.>
>>..>>>>>>.>>............<<<<<<<<<..<<<.........>>
>..<<<<<<<....<<<<....>>>>......>>>>>>>...<<..<<<.
.<<<<<<.....<<....<<<.<....>.>>>....>>..>>>>..>>>>
><<<<<<.......>>>>>>........<...........<<<<.<....
.>.>>>>.....>.....>>....>>.>>>>>>>..>..>>.>>.>>>>.
>>>>>>>....>>....<<<<<........>>>>>....<<<<<..<<<.
<<......<<<<.<<<<<<..<<<<<.<<<<<<<<<.<<<<<<<<<<.>>
>>>>>>>>...<<<<<.....<<<<............))..<<<<.<<<<
<.>>>>>.>>>>..>>>>..>>>>>....>>>>>>>>>..>>>>>...<<
<.....>>>..<<<<<<...........>>>>>>..<<...<<<<<<<..
.<<<<<<.......>>>>>>.....<<...(((>>....>>>>>>>...<
<<.<<<<<.......>>>>.>>>>.<<<....>>>.>>))).......<<
<<<<..<<<<...))))>>>>>>>>>>..........>>>>..>>>>>>.
......<<.<...<<<<<<...<<.......>>...>>>>>>....>.>.
>.......<<<<<.<<<<<<..<.<.<<<<<......>>>>>...>.>.<
<<.........>>>.....>>>>>..>...>>>.>>....<<<<<<<...
.>>>.>>>>....>>..>>>.>>>>>.....<<<.<<<<..<<<..<.<<
<<<<...............>>>>>>.><<<<....<<<<....<<<<<<<
<<<]]..>>>>>..>>>>>...>>>>...>>>>.<<<<...<<<<<....
.......>>>>>...>>>>..>>>......>>>>.>>>...<<.<<<<<<
<<<.<<..<<<.......<<<<<<<....>>>>>>>......>>>....<
..<<<<...<<<<<<<<<<.....>>>>>>>>>>.>>>>...>.......
.......>>.>>>>>>>>>.>>.<<<...<.............>.<<<<<
<<<<.<<<.....<<<....<<<<<........>>>>>...>>>....>>
>...>>>.>>>>>>...>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB9cai High-Resolution Reconstruction of a C. elegans Ribosome Sheds Light on Evolutionary Dynamics and Tissue Specificity.
Resolution2.59 Å
Binding residue
(original residue number in PDB)
V4 K8 A11 R15 Y16 Q17 K19 R23 T28 R35 L36 K43 Y44 K48 R138 A139 P140 F141 L145 I147 L149 R151 T152 F159 H174 S175 R178
Binding residue
(residue number reindexed from 1)
V1 K5 A8 R12 Y13 Q14 K16 R20 T25 R32 L33 K40 Y41 K45 R135 A136 P137 F138 L142 I144 L146 R148 T149 F156 H171 S172 R175
External links
PDB RCSB:9cai, PDBe:9cai, PDBj:9cai
PDBsum9cai
PubMed39209556
UniProtP49405|RL5_CAEEL Large ribosomal subunit protein uL18 (Gene Name=rpl-5)

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