Structure of PDB 5gak Chain Q Binding Site BS01

Receptor Information

>5gak Chain Q (length=197) Species: 4932 (Saccharomyces cerevisiae)

VEPVVVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKL
KYHDFLRKATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERL
KVFEGIPPPYDKKKRVVVPQALRVLRLKPGRKYTTLGKLSTSVGWKYEDV
VAKLEAKRKVSSAEYYAKKRAFTKKVASANATAAESDVAKQLAALGY

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): E4 K12 G17 R18 S21 K32 R37 S44 F48 R49 R59 K60 T62 K66 R68 P70 F71 H72 F73 R74 A83 R85 M87 S89 K91 T92 A93 R94 K96 R101 F105 I108 P110 K114 K115 K116 R117 Q122 V126 R128 L129 K130 R133 G146 K148 Y149 L156 R160 K161 S164 Y167 Y168 K171 R172
• Binding residue (residue number reindexed from 1): E2 K10 G15 R16 S19 K30 R35 S42 F46 R47 R57 K58 T60 K64 R66 P68 F69 H70 F71 R72 A81 R83 M85 S87 K89 T90 A91 R92 K94 R99 F103 I106 P108 K112 K113 K114 R115 Q120 V124 R126 L127 K128 R131 G144 K146 Y147 L154 R158 K159 S162 Y165 Y166 K169 R170

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5gak, PDBe:5gak, PDBj:5gak
• PDBsum: 5gak
• PubMed: 26715760
• UniProt: P26784|RL16A_YEAST Large ribosomal subunit protein uL13A (Gene Name=RPL16A)