Structure of PDB 8q5i Chain n Binding Site BS01

Receptor Information

>8q5i Chain n (length=155) Species: 5476 (Candida albicans)

QVAPKWYQSEDVPAPKQTRKTARPQKLRASLVPGTVLILLAGRFRGKRVV
YLKNLEDNTLLVSGPFKVNGVPLRRVNARYVIATSTKVNVSGVDVSKFNV
EYFAREKEIKAERVADQKSVDAALLSEIKKTPLLKQYLAASFSLKNGDRP
HLLKF

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): W8 Y9 A16 P17 K18 Q19 T20 R21 K22 T23 R25 Q27 A43 G44 R45 F46 D59 T61 F68 K69 G72 P74 R76 R77 N79 R81 Y82 R107 E108 K128 I130 Q157 S162 K166 N167
• Binding residue (residue number reindexed from 1): W6 Y7 A14 P15 K16 Q17 T18 R19 K20 T21 R23 Q25 A41 G42 R43 F44 D57 T59 F66 K67 G70 P72 R74 R75 N77 R79 Y80 R105 E106 K107 I109 Q136 S141 K145 N146

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• 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: Q9P834