Structure of PDB 8pfr Chain QT Binding Site BS01

Receptor Information

>8pfr Chain QT (length=159) Species: 4932 (Saccharomyces cerevisiae)

GKSHGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKG
MPHKFYQGKTGVVYNVTKSSVGVIINKMVGNRYLEKRLNLRVEHIKHSKC
RQEFLERVKANAAKRAEAKAQGVAVQLKRQPAQPRESRIVSTEGNVPQTL
APVPYETFI

Ligand information

>8pfr Chain A (length=3038)

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

Structure summary

• PDB: 8pfr Real-space refinement in PHENIX for cryo-EM and crystallography.
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): G2 K3 S4 H5 G6 Y7 R8 S9 R10 R12 Y13 M14 Q16 R17 F19 H22 G23 K35 G46 S47 Q49 G51 H54 Y57 Q58 G59 K60 T61 T68 K69 S70 S71 K78 V80 N82 R83 K87 R88 L89 N90 R92 K100 C101 E104 F105 R108 V109 K110 N112 R116 Q127 K129 R130
• Binding residue (residue number reindexed from 1): G1 K2 S3 H4 G5 Y6 R7 S8 R9 R11 Y12 M13 Q15 R16 F18 H21 G22 K34 G45 S46 Q48 G50 H53 Y56 Q57 G58 K59 T60 T67 K68 S69 S70 K77 V79 N81 R82 K86 R87 L88 N89 R91 K99 C100 E103 F104 R107 V108 K109 N111 R115 Q126 K128 R129

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8pfr, PDBe:8pfr, PDBj:8pfr
• PDBsum: 8pfr
• UniProt: Q02753|RL21A_YEAST Large ribosomal subunit protein eL21A (Gene Name=RPL21A)