Structure of PDB 5gak Chain f Binding Site BS01

Receptor Information

>5gak Chain f (length=109) Species: 4932 (Saccharomyces cerevisiae)

LKDVVTREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAP
ELNQAIWKRGVKGVEYRLRLRISRKRNEEEDAKNPLFSYVEPVLVASAKG
LQTVVVEED

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): R10 T13 N15 H17 K18 R19 H21 G22 S24 F25 K26 K27 R28 P30 R31 K34 K37 H43 L51 P53 N56 Q57 W60 R62 V64 K65 Y69 R70 G103 Q105 T106
• Binding residue (residue number reindexed from 1): R7 T10 N12 H14 K15 R16 H18 G19 S21 F22 K23 K24 R25 P27 R28 K31 K34 H40 L48 P50 N53 Q54 W57 R59 V61 K62 Y66 R67 G100 Q102 T103

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006450 regulation of translational fidelity

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: P0C2H8|RL31A_YEAST Large ribosomal subunit protein eL31A (Gene Name=RPL31A)