Structure of PDB 9cai Chain CO Binding Site BS01

Receptor Information

>9cai Chain CO (length=201) Species: 6239 (Caenorhabditis elegans)

GLSNRAIIIDGKNHLLGRLASIVAKKLLQGDKVVVLRAEEIVISGNFHRS
KLKYMSFLRKRCNINPARGAFHYRAPGKIFWRTVRGMLPHKTNRGNEALK
NLRAYEGVPAKYQKTKSLHAPSASRFRLQPRRKFCVVGRLSHEVGWQFQD
VVAKLEAKRKVKGAAYFEQKKKMDKLAVQAKKNAAPKIAQYQKIIEALGY
N

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): R6 K13 G18 R19 S22 K26 L29 R38 S45 H49 R50 L53 K54 S57 R60 K61 R62 C63 N64 N66 P67 R69 A71 F72 H73 Y74 R75 R83 T84 R86 G87 M88 H91 K92 R95 N97 K101 R104 G108 V109 Q114 K115 T116 K117 F127 R128 L129 Q130 R133 E144 V145 G146 Q148 L156 E157 K163 A165 Y167 F168 K171 K172
• Binding residue (residue number reindexed from 1): R5 K12 G17 R18 S21 K25 L28 R37 S44 H48 R49 L52 K53 S56 R59 K60 R61 C62 N63 N65 P66 R68 A70 F71 H72 Y73 R74 R82 T83 R85 G86 M87 H90 K91 R94 N96 K100 R103 G107 V108 Q113 K114 T115 K116 F126 R127 L128 Q129 R132 E143 V144 G145 Q147 L155 E156 K162 A164 Y166 F167 K170 K171

External links

• PDB: RCSB:9cai, PDBe:9cai, PDBj:9cai
• PDBsum: 9cai
• PubMed: 39209556
• UniProt: Q27389|RL13A_CAEEL Large ribosomal subunit protein uL13 (Gene Name=rpl-16)