Structure of PDB 9cai Chain CA Binding Site BS02

Receptor Information

>9cai Chain CA (length=249) Species: 6239 (Caenorhabditis elegans)

GRRIRIQRKGAGGIFKSHNKHRKGASKLRPLDYAERHGYIKGLVKDIIHD
PGRGAPLAIIAFRDPYKYKTVKTTVVAAEGMHTGQFIHCGAKAQIQIGNI
VPVGTLPEGTTICNVENKSGDRGVIARASGNYATVIAHNPDTKKTRIRLP
SGAKKVVQSVNRAMIGLVAGGGRTDKPLLKAGRSYHKYKAKRNSWPRVRG
VAMNPVEHPHGGGNHQHIGHPSTVRRDASAGKKVGLIAARRTGRIRGGK

Ligand information

>9cai Chain A5 (length=3022)

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

Structure summary

• PDB: 9cai High-Resolution Reconstruction of a C. elegans Ribosome Sheds Light on Evolutionary Dynamics and Tissue Specificity.
• Resolution: 2.59 Å
• Binding residue (original residue number in PDB): G2 R3 R4 R6 I7 Q8 R9 K10 G11 I15 K17 S18 H19 N20 K21 H22 R23 K24 G25 A26 D33 Y34 R37 H38 Y40 L44 H50 P52 R54 R64 Y67 K68 Y69 K70 T71 G85 Q86 F87 H89 Q95 Q97 G121 V125 I126 A127 R128 A129 S130 G131 N132 L150 P151 S152 K156 Q159 G173 R174 K177 L179 L180 K181 A182 G183 S185 Y186 H187 K188 K190 K192 R193 N194 S195 W196 P197 R198 V199 R200 G201 V202 A203 M204 N205 P206 V207 E208 H209 H211 G213 G214 N215 H216 Q217 H218 G220 H221 P222 S223 T224 V225 R226 R227 S230 A231 G232 K234 G236 L237 I238 A239 A240 R241 R242 T243 G244 R245 I246
• Binding residue (residue number reindexed from 1): G1 R2 R3 R5 I6 Q7 R8 K9 G10 I14 K16 S17 H18 N19 K20 H21 R22 K23 G24 A25 D32 Y33 R36 H37 Y39 L43 H49 P51 R53 R63 Y66 K67 Y68 K69 T70 G84 Q85 F86 H88 Q94 Q96 G120 V124 I125 A126 R127 A128 S129 G130 N131 L149 P150 S151 K155 Q158 G172 R173 K176 L178 L179 K180 A181 G182 S184 Y185 H186 K187 K189 K191 R192 N193 S194 W195 P196 R197 V198 R199 G200 V201 A202 M203 N204 P205 V206 E207 H208 H210 G212 G213 N214 H215 Q216 H217 G219 H220 P221 S222 T223 V224 R225 R226 S229 A230 G231 K233 G235 L236 I237 A238 A239 R240 R241 T242 G243 R244 I245

External links

• PDB: RCSB:9cai, PDBe:9cai, PDBj:9cai
• PDBsum: 9cai
• PubMed: 39209556
• UniProt: Q9XVF7|RL8_CAEEL Large ribosomal subunit protein uL2 (Gene Name=rpl-2)