Structure of PDB 5i4l Chain n6 Binding Site BS01

Receptor Information

>5i4l Chain n6 (length=126) Species: 559292 (Saccharomyces cerevisiae S288C)

AKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIR
RDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHP
SKLVITKLHLDKDRKALIQRKGGKLE

Ligand information

>5i4l Chain 5 (length=3150)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacauggcugggccag
caucaguuuugguggcaggauaaauccauaggaauguagcuugccucggu
aaguauuauagccugugggaauacugccagcugggacugaggacugcgac
guaagucaaggaugcuggcauaaugguuauaugccgcccgucuugaaaca
cggaccaaggagucuaacgucuaugcgaguguuuggguguaaaacccaua
cgcguaaugaaagugaacguagguuggggccucgcaagaggugcacaauc
gaccgauccugaugucuucggauggauuugaguaagagcauagcuguugg
gacccgaaagauggugaacuaugccugaauagggugaagccagaggaaac
ucugguggaggcucguagcgguucugacgugcaaaucgaucgucgaauuu
ggguauaggggcgaaagacuaaucgaaccaucuaguagcugguuccugcc
gaaguuucccucaggauagcagaagcucguaucaguuuuaugagguaaag
cgaaugauuagagguuccggggucgaaaugaccuugaccuauucucaaac
uuuaaauauguaagaaguccuuguuacuuaauugaacguggacauuugaa
ugaagagcuuuuagugggccauuuuugguaagcagaacuggcgaugcggg
augaaccgaacguagaguuaaggugccggaauacacgcucaucagacacc
acaaaagguguuaguucaucuagacagccggacgguggccauggaagucg
gaauccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccu
gaaaauggauggcgcucaagcguguuaccuauacucuaccgucaggguug
auaugaugcccugacgaguaggcaggcguggaggucagugacgaagccua
gaccguaaggucgggucgaacggccucuagugcagaucuuggugguagua
gcaaauauucaaaugagaacuuugaagacugaaguggggaaagguuccac
gucaacagcaguuggacguggguuagucgauccuaagagauggggaagcu
ccguuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgg
uuaagauuccggaaccuggauauggauucuucacgguaacguaacugaau
guggagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaaca
gcuuaucaccccggaauugguuuauccggagauggggucuuauggcugga
agaggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaa
auccacaggaaggaauaguuuucaugccaggucguacugauaaccgcagc
aggucuccaaggugaacagccucuaguugauagaauaauguagauaaggg
aagucggcaaaauagauccguaacuucgggauaaggauuggcucuaaggg
ucggacgaucaacuuagaacugguacggacaaggggaaucugacugucua
auuaaaacauagcauugcgauggucagaaagugauguugacgcaauguga
uuucugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcg
gguaaacggcgggaguaacuaugacucucuuaagguagccaaaugccucg
ucaucuaauuagugacgcgcaugaauggauuaacgagauucccacugucc
cuaucuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaau
cagcggggaaagaagacccuguugagcuugacucuaguuugacauuguga
agagacguuucuuuacuuauucaaugaagcggagcuggaauucauuuucc
acguucuagcauucaaggucccauucggggcugauccggguugaagacau
ugucagguggggaguuuggcuggggcggcacaucuguuaaacgauaacgc
agauguccuaaggggggcucauggagaacagaaaucuccaguagaacaaa
aggguaaaagcccccuugauuuugauuuucagugugaauacaaaccauga
aaguguggccuaucgauccuuuagucccucggaauuugaggcuagaggug
ccagaaaaguuaccacagggauaacuggcuuguggcagucaagcguucau
agcgacauugcuuuuugauucuucgaugucggcucuuccuaucauaccga
agcagaauucgguaagcguuggauuguucacccacuaauagggaacguga
gcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaau
guuaccgcaauaguaauugaacuuaguacgagaggaacaguucauucgga
uaauugguuuuugcggcugucugaucaggcauugccgcgaagcuaccauc
cgcuggauuauggcugaacgccucuaagucagaauccaugcuagaacgcg
gugauuucuuugcuccacacaauauagauggauacgaauaaggcguccuu
guggcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaag
gccuugggugcuugcuggcgaauugcaaugucauuuugcguggggauaaa
ucauuuguauacgacuuagauguacaacgggguauuguaagcaguagagu
agccuuguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5i4l Amicoumacin A induces cancer cell death by targeting the eukaryotic ribosome.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): A2 K3 Q4 S5 L6 V8 S9 S10 R12 A15 R16 Y19 V29 L30 S32 R40 K46 R60 G61 S62 K87 K89 N91 H100 S102 K103 K122
• Binding residue (residue number reindexed from 1): A1 K2 Q3 S4 L5 V7 S8 S9 R11 A14 R15 Y18 V28 L29 S31 R39 K45 R59 G60 S61 K86 K88 N90 H99 S101 K102 K121

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0032991 protein-containing complex
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5i4l, PDBe:5i4l, PDBj:5i4l
• PDBsum: 5i4l
• PubMed: 27296282
• UniProt: P05743|RL26A_YEAST Large ribosomal subunit protein uL24A (Gene Name=RPL26A)