Structure of PDB 5apn Chain V Binding Site BS01

Receptor Information

>5apn Chain V (length=136) Species: 559292 (Saccharomyces cerevisiae S288C)

SGNGAQGTKFRISLGLPVGAIMNCADNSGARNLYIIAVKGSGSRLNRLPA
ASLGDMVMATVKKGKPELRKKVMPAIVVRQAKSWRRRDGVFLYFEDNAGV
IANPKGEMKGSAITGPVGKECADLWPRVASNSGVVV

Ligand information

>5apn Chain 5 (length=3112)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacgggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguugaccuauucucaaacuuuaaauauguaagaaguccuuguu
acuuaauugaacguggacauuugaaugaagagcuuuuagugggccauuuu
ugguaagcagaacuggcgaugcgggaugaaccgaacguagaguuaaggug
ccggaauacacgcucaucagacaccacaaaagguguuaguucaucuagac
agccggacgguggccauggaagucggaauccgcuaaggaguguguaacaa
cucaccggccgaaugaacuagcccugaaaauggauggcgcucaagcgugu
uaccuauacucuaccgucaggguugauaugaugcccugacgaguaggcag
gcguggaggucagugacgaagccuagaccguaaggucgggucgaacggcc
ucuagugcagaucuuggugguaguagcaaauauucaaaugagaacuuuga
agacugaaguggggaaagguuccacgucaacagcaguuggacguggguua
gucgauccuaagagauggggaagcuccguuucaaaggccugauuuuaugc
aggccaccaucgaaagggaauccgguuaagauuccggaaccuggauaugg
auucuucacgguaacguaacugaauguggagacgucggcgcgagcccugg
gaggaguuaucuuuucuucuuaacagcuuaucaccccggaauugguuuau
ccggagauggggucuuauggcuggaagaggccagcaccuuugcuggcucc
ggugcgcuugugacggcccgugaaaauccacaggaaggaauaguuuucau
gccaggucguacugauaaccgcagcaggucuccaaggugaacagccucua
guugauagaauaauguagauaagggaagucggcaaaauagauccguaacu
ucgggauaaggauuggcucuaagggucgguuuuuuuuuuaaaaaaaaaaa
cgaucaacuuagaacugguacggacaaggggaaucugacugucuaauuaa
aacauagcauugcgauggucagaaagugauguugacgcaaugugauuucu
gcccagugcucugaaugucaaagugaagaaauucaaccaagcgcggguaa
acggcgcuuaagguagccaaaugccucgucaucuaauuagugacgcgcau
gaauggauuaacgagauucccacugucccuaucuacuaucuagcgaaacc
acagccaagggaacgggcuuggcagaaucagcggggaaagaagacccugu
ugagcuugacucuaguuugacauugugaauuacuuauucaaugaagcgga
gcuggaauucauuuuccacguucuagcauucaaggucccauucggggcug
auccggguugaagacauugucagguggggaguuuggcuggggcggcacau
cuguuaaacgauaacgcagauguccuaaggggggcucauggagaacagaa
aucuccaguagaacaaaaggguaaaagcccccuugauuuugauuuucagu
gugaauacaaaccaugaaaguguggccuaucgauccuuuagucccucgga
auuugaggcuagaggugccagaaaaguuaccacagggauaacuggcuugu
ggcagucaagcguucauagcgacauugcuuuuugauucuucgaugucggc
ucuuccuaucauaccgaagcagaauucgguaagcguuggauuguucaccc
acuaauagggaacgugagcuggguuuagaccgucgugagacagguuaguu
uuacccuacugaugaauguuaccgcaauaguaauugaacuuaguacgaga
ggaacaguucauucggauaauugguuuuugcggcugucugaucaggcauu
gccgcgaagcuaccauccgcuggauuauggcugaacgccucuaagucaga
auccaugcuagaacgcggugauugcuccacacaauauagauggauacgaa
uaaggcguccuuguggcgucgcugaaccauagcaggcuagcaacggugca
cuuggcggaaaggccuugggugcuugcuggcgaauugcaaugucauuuug
cguggggauaaaucauuuguauacgacuuagauguacaacgggguauugu
aagcaguagaguagccuuguuguuacgaucugcugagauuaagccuuugu
ugucugauuugu

........................<<<<<<.....<......>......>
>>>>.>...<.....<<....>>..<<<<<......<<.....>>.....
>>>>>..<<<...<.......<<.<<<<<<...>>>>>>.>>.......>
.....<<<<<<.<<<<<<<<<<<<<<<<<<<<<<....<<<<......>>
>>.(.......<<<......)>>>..>.>>>>>>>>..>>>>>>>>....
>>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<<<
<..((((((>>>>>..>>>....>..........................
...<<....>>...............<<<<....>>>>............
......................<<<<<.<<<<<......<<<<<<<.<<<
<<<<<<<<<<<<.....<<<<<<<<<......<<<<<<....>>>>>>..
.....>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>>
>.....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<<
<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>...
<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<<
<<<...<<....>>...>>>.>>>.>>....>>>>>>.>>>>>>..<<.<
...<<<<<<.....<<<<<<<<<...<<....<<<<<<<....>>>>>>>
.....>>....<<<<.<<.<<........>>>>>>>>....>>>>>>>>>
...<<.......>>......>>>>>>......>.>>..<<<<<<....<.
<<<....>>>.><<<<<<<<<<....<<.<<<<<<<.....<<<....<<
<....<<<<..>>>>....>>>..>.>>.....>>>>>...<<<<.<<<<
.<......>>>>>.>>>>.....>>>>..>>>>>>>>.>>..<<<<.<<<
<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<..<<<<(
((.....<<<<<<.....<<..........<<<.<<<<<<<<<<......
.<<<<<.<<<...<<.........>>...>>>.........<<......>
>...>>>>>...>>>>>>>>>>>>>..........))).>>...>>>>>>
.>>>>..>>>>>>><<<<<<<<<.........>>>>>>>>>....>>>>>
><.<<<<<<<..<<......<<<<.<<<<....>>>>>>>>...>>.>>>
>>>>..>.....>>>>>><<.....<<.....<<<<<<.......>>>>>
><<<<.....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....
((<<<<<<...<<....<<<....>>>........<<<<<<<.....>.>
>>>>>....>>....>>...<<<<<........>>>>>))<<<<.<<<<<
<<.....<<<....>>>.......<<<<<<...<<<<.<<<<<<<.<<<<
<<<<<<..[[[..>>>>>><...<<<<<....<<<<<<....<<<.....
>>>....>>>>>>.....>>>>>....><<<<<<<......>>>>>>>>>
>>...>>>>>>>.>>>>.........>>>>>>..........>>>..>>>
>>>>>>>>>..>>.....<<......>>>>>>>.<<<<.....>>>>..>
>>>..<<<<.....<<<<<<<.<<.........<.....<<<<<......
.........>>>>><<.<<<<<<<<<<<.<<<<<<<<<..>>>>>>>>>.
>>>>>..>>>>>>.>>............<<<<<<<<<..<<<........
.>>>..<<<<<<<....<<<<.....>>>>......>>>>>>>....<<.
<<<..<<<<<<.<..<<<.....<<<<....>>>>.....>>>>>>>>..
>>>>>..........<...........<<<<<.......>>>>>.....>
.....>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>....>>
....<<<<<........>>>>>....<<<<<..<<<.<<......<<<<.
..<<<<..<<<<<.<<<<<<<<..<<<<.>>>>...<<<<<.....<<<<
..<<<<<......>>>>>...............<<<<<......>>>>>.
.>>>>..>>>>>.....>>>>>>>>..>>>>>...<<<.....>>>..<<
<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<......
.>>>>>>.....<<...(((>>....>>>>>>>...<<<.<<<<<.....
..>>>>.>>>>.<<<....>>>.>>)))......<<<<<<<..<<<<.))
))))>>>>>>>>>>>.........>>>>....>>>>.......<<.<.<.
<<<<<<...<<.......>>...>>>>>>...>>..>>.......<<<<<
.<<<<<<..<.<<<<<<<......>>>>>>>...>.<<<.........>>
>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>....
>>..>>>.>>>>>....<<<<<<<<..<<<<.<.<<<<<<..........
.....>>>>>>.><<<<<...<<<<....<<<<<<<<<<]]].>>>>>..
>>>>>...>>>>..>>>>>.<<<<...<<<<<...........>>>>>..
.>>>>.>>>>....>>>>>>>>..<<<<<<.<<<.<<....<<.......
...<<<<<<.....>>>>>>......>>.......<<<<<<...<<<<<.
<..<<<......>>>..>.>>>>>.>>>>>>.............>>.>>>
.>>>>>>..<<<<<.<.............>.....<<<<<<<<<.<<<..
..<<<<....<<<<<......>>>>>...>>>>...>>>....>>>>.>>
>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5apn Insertion of the Biogenesis Factor Rei1 Probes the Ribosomal Tunnel during 60S Maturation.
• Resolution: 3.91 Å
• Binding residue (original residue number in PDB): N4 T9 K10 F11 R12 S14 G16 P18 A21 I22 I37 S42 G43 S44 R45 L46 N47 R48 L49 T61 K83 R86 F92 N98
• Binding residue (residue number reindexed from 1): N3 T8 K9 F10 R11 S13 G15 P17 A20 I21 I36 S41 G42 S43 R44 L45 N46 R47 L48 T60 K82 R85 F91 N97

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 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:5apn, PDBe:5apn, PDBj:5apn
• PDBsum: 5apn
• PubMed: 26709046
• UniProt: P0CX41|RL23A_YEAST Large ribosomal subunit protein uL14A (Gene Name=RPL23A)