Structure of PDB 5apn Chain a Binding Site BS01

Receptor Information

>5apn Chain a (length=148) Species: 559292 (Saccharomyces cerevisiae S288C)

PSRFTKTRKHRGHVSAGKGRIGKHRKHPGGRGMAGGQHHHRINMDKYHPG
YFGKVGMRYFHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPV
IDTLAAGYGKILGKGRIPNVPVIVKARFVSKLAEEKIRAAGGVVELIA

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): P2 S3 R4 T6 K7 T8 R9 K10 H11 R12 G13 H14 V15 S16 G18 K19 G20 R21 I22 G23 H25 R26 K27 H28 P29 G30 G31 R32 M34 A35 G36 H39 H40 H41 R42 I43 N44 Y52 G54 K55 G57 M58 R59 Y60 F61 H62 K63 Q64 N74 K111 L113 G114 K115 R117 S131 K132 L133
• Binding residue (residue number reindexed from 1): P1 S2 R3 T5 K6 T7 R8 K9 H10 R11 G12 H13 V14 S15 G17 K18 G19 R20 I21 G22 H24 R25 K26 H27 P28 G29 G30 R31 M33 A34 G35 H38 H39 H40 R41 I42 N43 Y51 G53 K54 G56 M57 R58 Y59 F60 H61 K62 Q63 N73 K110 L112 G113 K114 R116 S130 K131 L132

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:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5apn, PDBe:5apn, PDBj:5apn
• PDBsum: 5apn
• PubMed: 26709046
• UniProt: P02406|RL28_YEAST Large ribosomal subunit protein uL15 (Gene Name=RPL28)