Structure of PDB 8pfr Chain QP Binding Site BS01

Receptor Information

>8pfr Chain QP (length=185) Species: 4932 (Saccharomyces cerevisiae)

GIDHTSKQHKRSGHRTAPKSDNVYLKLLVKLYTFLARRTDAPFNKVVLKA
LFLSKINRPPVSVSRIARALKQEGAANKTVVVVGTVTDDARIFEFPKTTV
AALRFTAGARAKIVKAGGECITLDQLAVRAPKGQNTLILRGPRNSREAVR
HFGMGPHKGKAPRILSTGRKFERARGRRRSKGFKV

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 I3 H5 S7 K8 Q9 H10 K11 R12 S13 H15 R16 K20 S21 F35 R38 P43 F44 S55 K56 I57 S63 S65 R66 R69 Q73 K79 T86 T88 D89 D90 R92 T107 A108 N136 T137 I139 R141 P143 R144 N145 R147 E148 R151 F153 H158 A162 R164 S167 R170 K171 F172 R176 R179 S181 K182 G183 F184 K185
• Binding residue (residue number reindexed from 1): G1 I2 H4 S6 K7 Q8 H9 K10 R11 S12 H14 R15 K19 S20 F34 R37 P42 F43 S54 K55 I56 S62 S64 R65 R68 Q72 K78 T85 T87 D88 D89 R91 T106 A107 N135 T136 I138 R140 P142 R143 N144 R146 E147 R150 F152 H157 A161 R163 S166 R169 K170 F171 R175 R178 S180 K181 G182 F183 K184

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• 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:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8pfr, PDBe:8pfr, PDBj:8pfr
• PDBsum: 8pfr
• UniProt: P0CX49|RL18A_YEAST Large ribosomal subunit protein eL18A (Gene Name=RPL18A)