Structure of PDB 8q5i Chain AK Binding Site BS01

Receptor Information

>8q5i Chain AK (length=86) Species: 5476 (Candida albicans)

GKGTPSLGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKMRSHNWAL
KAKRRRTTGTGRMAYLKHVTRRFKNGFQTGVAKAQT

Ligand information

>8q5i Chain 1 (length=3073)

ugaccucaaaucagguaggacuacccgcugaacuuaagcauaucaauaag
cggaggaaaagaaaccaacagggauugccucaguagcggcgagugaagcg
gcaaaagcucaaauuugaaaucuggcgucuuuggcguccgaguuguaauu
ugaagaagguaucuuugggcccggcucuugucuauguuccuuggaacagg
acgucacagagggugagaaucccgugcgaugagaugacccgggucugugu
aaaguuccuucgacgagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcuugagaucagacuugguaccgggcc
agcaucgguuuggagcggcaggauaauggcggaggaauguggcacggcuu
cugcuguguguuauagccucugacgauacugccagccuagaccgaggacu
gcgguuuuuaccuaggauguuggcauaaugaucuuaagucgcccgucuug
aaacacggaccaaggagucuaacgucuaugcgaguguuuggguguaaaac
ccguacgcguaaugaaagugaacgaaggugggggcccauuagggugcacc
aucgaccgauccugauguguucggauggauuugaguaagagcauagcugu
ugggacccgaaagauggugaacuaugccugaauagggugaagccagagga
aacucugguggaggcucguagcgguucugacgugcaaaucgaucgucgaa
uuuggguauaggggcgaaagacuaaucgaaccaucuaguagcugguuccu
gccgaaguuucccucaggauagcagaagcucguaucaguuuuaugaggua
aagcgaaugauuagaagucuugggcuuaacuuauucucaaacuuuaaaua
uguaagaaguccuuguugcuuaauugaacguggacaauugaaugaagagc
uuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaaccg
aacgugaaguuaaagugccggaaugcacgcucaucagacaccacaaaagg
uguuaguucaucuagacagccggccgaaugaacuagcccugaaaauggau
ggcgcucaagcgugcuacuuauacuucaccgugauugcuguuuugacgcu
uucacgaguaggcaggcguggaggucagugacgaagccuuugcuguaaag
cugggucgaacggccucuagugcagaucuuggugguaguagcaaauauuc
aaaugagaacuuugaagacugaaguggggaaagguuccaugucaacagca
guuggacauggguuagucgauccuaagagauggggaagcuccguuucaac
gugcuugauuuuucaggccaaccaucgaaagggaauccgguuaaaauucc
ggaacuuggauauggauucuucacggcaacguaacugaauguggagacgu
cggcgugagcccugggaggaguuaucuuuucuucuuaacagcuuaucacc
cuggaauugguuuauccggagauggggucuuauggcuggaagagcgcggu
aauuuugccgcguccggugcgcuuacgacgguccuugaaaauccacagga
aggaauaguuuucaugccaagucguacucauaaccgcagcaggucuccaa
gguuaacagccucuaguugauagaauaauguagauaagggaagucggcaa
aauagauccguaacuucgggauaaggauuggcucuaaggaucggaacgau
caacuuagaacugguacggacaaggggaaucugacugucuaauuaaaaca
uagcauugugauggucagaaagugauguugacacaaugugauuucugccc
agugcucugaaugucaaagugaagaaauucaaccaagcgcggguaaacgg
cgggaguaacuaugacucucuuaagguagccaaaugccucgucaucuaau
uagugacgcgcaugaauggauuaacgagauucccacugucccuaucuacu
aucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcgggga
aagaagacccuguugagcuugacucuaguuugacauugugaaaaguuuuu
acuuauucaaugaagcggagcuggaggucaaacuccacguucuagcauua
agcccucugggcgauccggguugaagacauugucagguggggaguuuggc
uggggcggcacaucuguuaaacgauaacgcagguguccuaagggggacuc
auggagaacagaaaucuccaguagaacaaaaggguaaaaguccccuugau
uuugauuuucagugugaauacaaaccaugaaaguguggccuaucgauccu
uuagucccucggaauuugaggcuagaggugccagaaaaguuaccacaggg
auaacuggcuuguggcagucaagcguucauagcgacauugcuuuuugauu
cuucgaugucggcucuuccuaucauaccgaagcagaauucgguaagcguu
ggauuguucacccacuaauagggaacgugagcuggguuuagaccgucgug
agacagguuaguuuuacccuacugaugaauguuaucgcaauaguaauuga
acuuaguacgagaggaaccguucauucagauaauugguuuuugcggcugu
cugaucaggcaacgccgcgaagcuaccaucugcuggauuauggcugaacg
ccucuaagucagaauccaugcuagaacgcgaugauuuuugcccugcacau
uuuagauggauacgaauaagacuuuuuagucgcuggaccauagcaggcug
gcaacggugcgcuuagcggaaaggcuuugugcgcuugccggcggauagca
augucaacaugcgcggggauaaauccuuugcauacgacuuagauguacaa
cggaguauuguaagcaguagaguagccuuguuguuacgaucugcugagau
uaagcucuuguugucugauuugu

.......................<<<<<<.....<......>......>>
>>>.>.........<<....>>..<<<<<......<<.....>>.....>
>>>>..[[[...........<<.<<<<<<...>>>>>>.>>.........
....<<<<<...<<<<<<<<<<<<.<<<<<<<.....<<<<......>>>
>.(.......<<<......)>>>....>>>>>>>....>>>>>>>>....
>>>>..>>>>>........<<<<<<<........>>>>>>>.....((((
(..<<<<<<)))))..]]]...............................
...<<....>>...............<<<<....>>>>............
......................<<<<<<<<<<<<.....<<..>>..<<<
<<<<.<<<<<<<<.<<<<<<<....<<.<<<<<<<......<<<<<<...
...>>>>>>.......>>>>>>.>.>>.>>>>>.>>>>>>>>>>......
..<<<....>>>.....>>>>>>>....>>>>>>>>>>>>..<<<<....
....>>>><<<<<<....<<<<<<.<<<<<<..<<<..<<<<<.....>>
>>>..>>>...<<....>>.......<<<<<..<<<<....>>>>...>>
>>>.<<<<<<<<...<<....>>...>>>.>>>.>>....>>>>>>.>>>
>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<..
..>>>>>>>.....>>>...<<<..<<.<<........>>>>.>>>....
>>>>>>>>>...<<.......>>......>>>>>>...>..>.>>..<<<
<<<....<.<<<....>>>.><<<<<<<<<<...<<<.<<<<<<<.....
<<<....<<<....<<<<...<<..>>.>>>>....>>>..>.>>.....
>>>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>>>>.>>>>
>>>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>
...<<<<<<<..<<<<(((.....<<<<<<.....<<..........<<<
.<<<<<<<<<<.......<<..>>...>>>>>>>>>>>>>..........
))).>>...>>>>>>.>>>>..>>>>>>><<<<<..<<.........>>.
.>>>>>....>>>>>><.<<<<<<<<.<<......<<<<..<<<....>>
>.>>>>...>>>>>>>>>>..>.....>>>>>><<.....<<.....<<<
<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<<...<<...
..>>.>>>>>>....((<<<<<<...<<....<<<....>>>........
..<<<<<<....>>>>>>......>>....>>...<<<<<........>>
>>>))<<<<.<<<<<<<.....<<<....>>>.......<<<<<<...<<
<<.<<<<<<<.<<<<<<<<<<..{{{..>>>>>><...<<<<<....<<<
<<<....<<<.....>>>....>>>>>>.....>>>>>....><<<<<<<
......>>>>>>>>>>>...>>>>>>>.>>>>.........>>>>>>...
.......>>>..>>>>>>>>>>>>..>>.....<<......>>>>>>>.<
<<<.....>>>>..>>>>..<<<<.....<<<<<<<.<<.........<.
....<<<<<...............>>>>><<.<<<<<<<<<<<...>>>>
>..>>>>>>.>>............<<<<<<<<<..<<<.........>>>
..<<<<<<<....<<<<.....>>>>......>>>>>>>...<<..<<<.
.<<<<<<....<<<.....<<<<....>>>>.....>>>.>>>>..>>>>
><<<<...........>>>>........<...........<<<<<.....
..>>>>>.....>.....>>....>>.>>>>>>>..>..>>.>>>>>>>.
.>>>>>>....>>....<<<<<........>>>>>....[[[[[..{{{.
{{......[[[[.{{[[[[..<<<<<.<<<<<<<<..<<<<<<<.>>>>>
>>...<<<<<.....<<<<..<<<<<......>>>>>.............
.<<<<...>>>>..>>>>..>>>>>.....>>>>>>>>..>>>>>...<<
<.....>>>..<<<<<<...........>>>>>>..<<...<<<<<<<..
.<<<<<<.......>>>>>>.....<<...(((>>....>>>>>>>...<
<<.<<<<<.......>>>>.>>>>.<<<....>>>.>>))).......((
((((..((((.>>>>>>))))))))))..........]]]]..}}]]]].
......<<.<.<.<<<<<<...<<.......>>...>>>>>>...>>.>.
>.......<<<<<.<<<<<<..<.<<<<<<<......>>>>>>>...>.<
<<.........>>>.....>>>>>..>...>>>.>>....<<<<<<<...
.>>>.>>>>....}}..}}}.]]]]]....<<<<<<<<..<<<<...<<<
<<.................>>>>>..<<<<<...<<<<....<<<<<<<<
<<}}}.>>>>>..>>>>>...>>>>..>>>>>.<<<<...<<<<<.....
......>>>>>...>>>>.>>>>....>>>>>>>>.....<<<<<<.<<<
..<....<<..........<<<<....>>>>......>>.......<<<<
<<...<<<<<<<..<<<......>>>..>>>>>>>.>>>>>>........
......>.>>>.>>>>>>..<<<<<<<.............>>....<<<<
<<<<<.<<<....<<<<.<..<<<<<......>>>>>..>>>>>...>>>
....>>>>.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8q5i Structural characterization of cephaeline binding to the eukaryotic ribosome using Cryo-Electron Microscopy
• Resolution: 2.45 Å
• Binding residue (original residue number in PDB): G2 K3 G4 T5 P6 S7 L8 G9 K10 R11 H12 N13 K14 S15 H16 R24 R25 S26 H28 Q30 K31 S35 K43 M44 R45 H47 N48 W49 K52 R55 R56 T58 T71
• Binding residue (residue number reindexed from 1): G1 K2 G3 T4 P5 S6 L7 G8 K9 R10 H11 N12 K13 S14 H15 R23 R24 S25 H27 Q29 K30 S34 K42 M43 R44 H46 N47 W48 K51 R54 R55 T57 T70

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:8q5i, PDBe:8q5i, PDBj:8q5i
• PDBsum: 8q5i
• UniProt: A0A1D8PF45|RL37B_CANAL Large ribosomal subunit protein eL37 (Gene Name=RPL37B)