Structure of PDB 5apn Chain L Binding Site BS01

Receptor Information

>5apn Chain L (length=194) Species: 559292 (Saccharomyces cerevisiae S288C)

AISKNLPILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPL
DLLRPVVRAPTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRR
QNRNQEIFDANVQRLKEYQSKIIVFPRNGKAPEAEQVLSAAATFPIAQPA
TDVEARAVQDNGESAFRTLRLARSEKKFRGIREKRAREKAEAEA

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): A2 I3 K5 L10 K11 N12 H13 F14 R15 K16 H17 W18 K23 Q28 A29 K31 K32 R35 R36 R39 R42 L53 R55 V58 R59 A60 P61 T62 Y65 N66 R70 G72 R73 R91 D98 H99 R100 R101 R104 R171 R174 S175 K178 F179 R180 K185 R186
• Binding residue (residue number reindexed from 1): A1 I2 K4 L9 K10 N11 H12 F13 R14 K15 H16 W17 K22 Q27 A28 K30 K31 R34 R35 R38 R41 L52 R54 V57 R58 A59 P60 T61 Y64 N65 R69 G71 R72 R90 D97 H98 R99 R100 R103 R170 R173 S174 K177 F178 R179 K184 R185

Gene Ontology

Molecular Function

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

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: Q12690|RL13A_YEAST Large ribosomal subunit protein eL13A (Gene Name=RPL13A)