Structure of PDB 5gak Chain Y Binding Site BS01

Receptor Information

>5gak Chain Y (length=98) Species: 4932 (Saccharomyces cerevisiae)

MKVEIDSFSGAKIYPGRGTLFVRGDSKIFRFQNSKSASLFKQRKNPRRIA
WTVLFRKHHKKGITEEVAKKRSRKTVKAQRPITGASLDLIKERRSLKP

Ligand information

>5gak Chain 1 (length=3165)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaa
uauguaagaaguccuuguuacuuaauugaacguggacauuugaaugaaga
gcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaac
cgaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaa
gguguuaguucaucuagacagccggacgguggccauggaagucggaaucc
gcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaau
ggauggcgcucaagcguguuaccuauacucuaccgucaggguugauauga
ugcccugacgaguaggcaggcguggaggucagugacgaagccuagaccgu
aaggucgggucgaacggccucuagugcagaucuuggugguaguagcaaau
auucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaac
agcaguuggacguggguuagucgauccuaagagauggggaagcuccguuu
caaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaaga
uuccggaaccuggauauggauucuucacgguaacguaacugaauguggag
acgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuau
caccccggaauugguuuauccggagauggggucuuauggcuggaagaggc
cagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccac
aggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucu
ccaaggugaacagccucuaguugauagaauaauguagauaagggaagucg
gcaaaauagauccguaacuucgggauaaggauuggcucuaagggucgggu
acgaucaacuuagaacugguacggacaaggggaaucugacugucuaauua
aaacauagcauugcgauggucagaaagugauguugacgcaaugugauuuc
ugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcgggua
aacggcgggaguaacuaugacucucuuaagguagccaaaugccucgucau
cuaauuagugacgcgcaugaauggauuaacgagauucccacugucccuau
cuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagc
ggggaaagaagacccuguugagcuugacucuaguuugacauugugaagag
acauagagggcuaccuuuauaguuucuuuacuuauucaaugaagcggagc
uggaauucauuuuccacguucuagcauucaaggucccauucggggcugau
ccggguugaagacauugucagguggggaguuuggcuggggcggcacaucu
guuaaacgauaacgcagauguccuaaggggggcucauggagaacagaaau
cuccaguagaacaaaaggguaaaagcccccuugauuuugauuuucagugu
gaauacaaaccaugaaaguguggccuaucgauccuuuagucccucggaau
uugaggcuagaggugccagaaaaguuaccacagggauaacuggcuugugg
cagucaagcguucauagcgacauugcuuuuugauucuucgaugucggcuc
uuccuaucauaccgaagcagaauucgguaagcguuggauuguucacccac
uaauagggaacgugagcuggguuuagaccgucgugagacagguuaguuuu
acccuacugaugaauguuaccgcaauaguaauugaacuuaguacgagagg
aacaguucauucggauaauugguuuuugcggcugucugaucaggcauugc
cgcgaagcuaccauccgcuggauuauggcugaacgccucuaagucagaau
ccaugcuagaacgcggugauuucuuugcuccacacaauauagauggauac
gaauaaggcguccuuguggcgucgcugaaccauagcaggcuagcaacggu
gcacuuggcggaaaggccuugggugcuugcuggcgaauugcaaugucauu
uugcguggggauaaaucauuuguauacgacuuagauguacaacgggguau
uguaagcaguagaguagccuuguuguuacgaucugcugagauuaagccuu
uguugucugauuugu

........................<<<<<<.....<......>......>
>>>>.>.........<<....>>..<<<<<......<<.....>>.....
>>>>>..[[[..<<.......<<.<<<<<<...>>>>>>.>>.......>
>....<<<<<<.<<<<<<<<<<<<<<<<<<<<<.....<<<<......>>
>>.((......<<<.....))>>>....>>>>>>>>..>>>>>>>>....
>>>>>>>>>>>........<<<<<<<........>>>>>>>.....((((
(..<<<<<<)))))..]]]...............................
...<<....>>...............<<<<....>>>>............
......................<<<<<.<<<<<......<<<<<<<<<<<
<<<<<<<<<<<<.....<<<<<<<<<......<<<<<<<..>>>>>>>..
.....>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>>
>....>>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<<
<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>...
<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<<
<<<...<<....>>...>>>.>>>.>>....>>>>>>.>>>>>>..<<.<
...<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>
.....>>>...<<<<.<<.<<........>>>>>>>>....>>>>>>>>>
...<<.......>>......>>>>>>......>.>>..<<<<<<....<.
<<<....>>>.><<<<<<<<<<...<<<.<<<<<<<.....<<<....<<
<..<.<<<<<..<<<<<<.....>>>>>>>>>>>.>..>>>..>>.>...
..>>>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>>>>.>>
>>>>>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>
>>...<<<<<<<..<<<<(((.....<<<<<<.....<<..........<
<<.<<<<<<<<<........<<<<<.<<<...<<.........>>...>>
>......................>>>>>....>>>>>>>>>>>>......
....))).>>...>>>>>>.>>>>..>>>>>>><<<<<<<<<........
.>>>>>>>>>....>>>>>><<<<<<<<<<.<<......<<<<.<<<<..
..>>>>>>>>...>>>>>>>>>>.>>.....>>>>>><<.....<<....
.<<<<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<<...<
<.....>>.>>>>>>....((<<<<<<...<<....<<<....>>>....
....<<<<<<........>>>>>>....>>....>>...<<<<<......
..>>>>>))<<<<.<<<<<.<.....<<<....>>>...<...<<<<<<.
..<<<<.<<<<<<<<<<<<<<<<<<..{{{..>>>>>>....<<<<<...
.<<<<<<....<<<.....>>>....>>>>>>.....>>>>>.....<<<
<<<<<....>>>>>>>>>>>>.>.>>>>>>>.>>>>.........>>>>>
>...>......>.>..>>>>>>>>>>>>..>>.....<<......>>>>>
>>.<<<<.....>>>>..>>>>..<<<<.....<<<<<<<.<<.......
........<<<<<....<....>.....>>>>><<.<<<<<<<<<<<...
.>>>>>..>>>>>>.>>............<<<<<<<<<..<<<.......
..>>>..<<<<<<<....<<<<.....>>>>......>>>>>>>...<<.
.<<<..<<<<<<.<...<<....<<<<<....>>>>.>...>>.>>>>>.
.>>>>><<<<<<.......>>>>>>........<...........<<<<<
.......>>>>>.....>.....>>....>>.>>>>>>>.....>>.>>>
>>>>..>>>>>>....>>....<<<<<........>>>>>....[[[[[.
.{{{.{{......[[[[.{{[[[[..<<<<<.<<<<<<<<..<<<<<<<<
<<<<<<<<<..>..>>>>>>.>>>>>>>>>>...<<<<<.....<<<<..
<<<<<......>>>>>...............<<<<<......>>>>>..>
>>>..>>>>>.....>>>>>>>>..>>>>>...<<<.....>>>..<<<<
<<...........>>>>>>..<<...<<<<<<<...<<<<<<.......>
>>>>>.....<<...(((>>....>>>>>>>...<<<.<<<<<.......
>>>>.>>>>.<<<....>>>.>>))).......((((((..((((.>>>>
>>))))))))))..........]]]]..}}]]]].......<<.<.<.<<
<<<<...<<.......>>...>>>>>>...>>.>.>.......<<<<<.<
<<<<<..<.<<<<<<<......>>>>>>>...>.<<<.........>>>.
....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>....}}
..}}}.]]]]]....<<<<<<<<..<<<<.<.<<<<<<............
...>>>>>>.><<<<<...<<<<<...<<<<<<<<<<}}}.>>>>>..>>
>>>..>>>>>..>>>>>.<<<<...<<<<<...........>>>>>...>
>>>.>>>>....>>>>>>>>.......<<<<<<.<<<.<<....<<....
......<<<<<<.....>>>>>>......>>.......<<<<<<...<<<
<<.<..<<<......>>>..>.>>>>>.>>>>>>.............>>.
>>>.>>>>>>..<<<<<.<.............>.....<<<<<<<<<.<<
<....<<<<.<..<<<<<......>>>>>..>>>>>...>>>....>>>>
.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5gak Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome.
• Resolution: 3.88 Å
• Binding residue (original residue number in PDB): R17 S34 K35 S38 L39 Q42 K44 R48 I49 A50 W51 R56 K61
• Binding residue (residue number reindexed from 1): R17 S34 K35 S38 L39 Q42 K44 R48 I49 A50 W51 R56 K61

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006413 translational initiation
• GO:0006414 translational elongation

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:5gak, PDBe:5gak, PDBj:5gak
• PDBsum: 5gak
• PubMed: 26715760
• UniProt: P04449|RL24A_YEAST Large ribosomal subunit protein eL24A (Gene Name=RPL24A)