Structure of PDB 8pfr Chain QW Binding Site BS01

Receptor Information
>8pfr Chain QW (length=61) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKVEIDSFSGAKIYPGRGTLFVRGDSKIFRFQNSKSASLFKQRKNPRRIA
WTVLFRKHHKK
Ligand information
>8pfr Chain A (length=3038) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucuugaccuauucucaaacuuuaaauauguaaga
aguccuuguuacuuaauugaacguggacauuugaaugaagagcuuuuagu
gggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacguag
aguuaaggugccggaauacacgcucaucagacaccacaaaagguguuagu
ucaucuagacaggaaugaacuagcccugaaaauggauggcgcucaagcgu
guuaccuauacucuaccgucaggguugauaugaugcccugacgaguaggc
aggcguggaggucagugacgaagccuagaccguaaggucgggucgaacgg
ccucuagugcagaucuuggugguaguagcaaauauucaaaugagaacuuu
gaagacugaaguggggaaagguuccacgucaacagcaguuggacgugggu
uagucgauccuaagagauggggaagcuccguuucaaaggccugauuuuau
gcaggccaccaucgaaagggaauccgguuaagauuccggaaccuggauau
ggauucuucacgguaacguaacugaauguggagacgucggcgcgagcccu
gggaggaguuaucuuuucuucuuaacagcuuaucaccccggaauugguuu
auccggagauggggucuuauggcuggaagaggccagcaccuuugcuggcu
ccggugcgcuugugacggcccgugaaaauccacaggaaggaauaguuuuc
augccaggucguacugauaaccgcagcaggucuccaaggugaacagccuc
uaguugauagaauaauguagauaagggaagucggcaaaauagauccguaa
cuucgggauaaggauuggcucuaagggucggacgaucaacuuagaacugg
uacggacaaggggaaucugacugucuaauuaaaacauagcauugcgaugg
ucagaaagugauguugacgcaaugugauuucugcccagugcucugaaugu
caaagugaagaaauucaaccaagcgcggguaaacggcggaagguagccaa
augccucgucaucuaauuagugacgcgcaugaauggauuaacgagauucc
cacugucccuaucuacuaucuagcgaaaccacagccaagggaacgggcuu
ggcagaaucagcggggaaagaagacccuguugagcuugacucuaguuuga
cauugugaaguacuuauucaaugaagcggagcuggaccacguucuagcau
ucaaggucccauucggggcugauccggguugaagacauugucaggugggg
aguuuggcuggggcggcacaucuguuaaacgauaacgcagauguccuaag
gggggcucauggagaacagaaaucuccaguagaacaaaaggguaaaagcc
cccuugauuuugauuuucagugugaauacaaaccaugaaaguguggccua
ucgauccuuuagucccucggaauuugaggcuagaggugccagaaaaguua
ccacagggauaacuggcuuguggcagucaagcguucauagcgacauugcu
uuuugauucuucgaugucggcucuuccuaucauaccgaagcagaauucgg
uaagcguuggauuguucacccacuaauagggaacgugagcuggguuuaga
ccgucgugagacagguuaguuuuacccuacugaugaauguuaccgcaaua
guaauugaacuuaguacgagaggaacaguucauucggauaauugguuuuu
gcggcugucugaucaggcauugccgcgaagcuaccauccgcuggauuaug
gcugaacgccucuaagucagaauccaugcuagaacgcggugauuucuuug
cuccacacaauauagauggauacgaauaaggcguccuuguggcgucgcug
aaccauagcaggcuagcaacggugcacuuggcggaaaggccuugggugcu
ugcuggcgaauugcaaugucauuuugcguggggauaaaucauuuguauac
gacuuagauguacaacgggguauuguaagcaguagaguagccuuguuguu
acgaucugcugagauuaagccuuuguugucugauuugu
........................<<<<<<.....<......>......>
>>>>.>.........<<....>>..<<<<<......<<.....>>.....
>>>>>..[[[..<<.......<<.<<<<<<...>>>>>>.>>.......>
>....<<<<<<<.<<<<<<<<<<<<<<<<<<<<<....<<<<......>>
>>.(.......<<<......)>>>..>.>>>>>>>>..>>>>>>>>....
>>>>>>>>>>>........<<<<<<<........>>>>>>>.....((((
(..<<<<<<)))))..]]]...............................
...<<....>>...............<<<<....>>>>............
......................<<<<<.<<<<<......<<<<<<<.<<<
<<<<<<<<<<<<.....<<<<<<<<<......<<<<<......>>>>>..
.....>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>>
>.....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<<
<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>...
<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<<
<<<...<<....>>...>>>.>>>.>>....>>>>>>.>>>>>>..<<.<
..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>
.....>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>>>
...<<.......>>......>>>>>>...>..>.>>..<<<<<<....<.
<<<....>>>.><<<<<<<<<<...<<<.<<<<<<<.....<<<....<<
<....<<<<...<<....>>.>>>>....>>>..>.>>.....>>>>>..
.<<<<.<<<<.<......>>>>>.>>>>.....>>>>>.>>>>>>>>.>>
..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<
<<<..<<<<(((.....<<<<<<......<..........<<<.<<<<<<
<<<<..........>>>>>>>>>>>>>..........))).>....>>>>
>>.>>>>..>>>>>>><<<<<<<<<.........>>>>>>>>>....>>>
>>><.<<<<<<<..<<......<<<<.<<<<....>>>>>>>>...>>.>
>>>>>>..>.....>>>>>><<<....<<.....<<<<<<.......>>>
>>><<<<.....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>..
..((<<<<<<...<<....<<<....>>>........<<..<<<.....>
.>>..>>....>>....>>...<<<<<........>>>>>))<<<<.<<<
<<<<.....<<<....>>>...<...<<<<<<...<<<<.<<<<<<<.<<
<<<<<<<<..{{{..>>>>>><...<<<<<....<<<<<<....<<<...
..>>>....>>>>>>.....>>>>>....><<<<<<<......>>>>>>>
>>>>...>>>>>>>.>>>>.........>>>>>>...>......>>>..>
>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<.....>>>>.
.>>>>..<<<<.....<<<<<<<.<<...............<<<<<....
<<..>>.....>>>>><<.<<<<<<<<<<....>>>>..>>>>>>.>>..
..........<<<<<<<<<..<<<.........>>>..<<<<<<<....<
<<<.....>>>>......>>>>>>>.<.<<..<<<..<<<<<<.<...<<
....<<<<<....>>>>.>...>>.>>>>>..>>>>>........<....
.......<<<<<.......>>>>>.....>.....>>.>..>>.>>>>>>
>.....>>.>>>>>>>..>>>>>>...>>>....<<<<<........>>>
>>....[[[[[..{{{.{{......[[[[.{{[[[[..<<<<<.<<<<<<
<<..<<<...>>>...<<<<<.....<<<<..<<<.>>>...........
....<<<<<<....>>>>>>..>>>>..>>>>>.....>>>>>>>>..>>
>>>...<<<.....>>>..<<<<<<...........>>>>>>..<<...<
<<<<<<...<<<<<<.......>>>>>>.....<<...(((>>....>>>
>>>>...<<<.<<<<<.......>>>>.>>>>.<<<....>>>.>>))).
......((((((..((((.>>>>>>))))))))))..........]]]].
.}}]]]].......<<.<.<.<<<<<<...<<.......>>...>>>>>>
...>>.>.>.......<<<<<.<<<<<<..<.<<<<<<<......>>>>>
>>...>.<<<.........>>>.....>>>>>..>...>>>.>>....<<
<<<<<....>>>.>>>>....}}..}}}.]]]]]....<<<<<<<<..<<
<<...<<<<<<...............>>>>>>..<<<<<...<<<<....
<<<<<<<<<<}}}.>>>>>..>>>>>...>>>>..>>>>>.<<<<...<<
<<<...........>>>>>...>>>>.>>>>....>>>>>>>>.......
<<<<<..<<<.<<....<<..........<<<<<<.....>>>>>>....
..>>.......<<<<<<...<<<<<.<..<<<......>>>..>.>>>>>
.>>>>>>.............>>.>>>..>>>>>..<<<<<.<........
.....>.....<<<<<<<<<.<<<....<<<<....<<<<<......>>>
>>...>>>>...>>>....>>>>.>>>>>..>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8pfr Real-space refinement in PHENIX for cryo-EM and crystallography.
Resolution2.15 Å
Binding residue
(original residue number in PDB)
G16 G18 S34 K35 S38 Q42 K44 R48 I49 A50 W51 R56 K61
Binding residue
(residue number reindexed from 1)
G16 G18 S34 K35 S38 Q42 K44 R48 I49 A50 W51 R56 K61
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0003735 structural constituent of ribosome
Biological Process
GO:0002181 cytoplasmic translation
GO:0006413 translational initiation
GO:0006414 translational elongation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8pfr, PDBe:8pfr, PDBj:8pfr
PDBsum8pfr
PubMed
UniProtP04449|RL24A_YEAST Large ribosomal subunit protein eL24A (Gene Name=RPL24A)

[Back to BioLiP]