Structure of PDB 5dc3 Chain n1 Binding Site BS01

Receptor Information

>5dc3 Chain n1 (length=159) Species: 559292 (Saccharomyces cerevisiae S288C)

GKSHGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKG
MPHKFYQGKTGVVYNVTKSSVGVIINKMVGNRYLEKRLNLRVEHIKHSKC
RQEFLERVKANAAKRAEAKAQGVAVQLKRQPAQPRESRIVSTEGNVPQTL
APVPYETFI

Ligand information

>5dc3 Chain 5 (length=3169)

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
agagacauagagggcuaccuuuauaguuucuuuacuuauucaaugaagcg
gagcuggaauucauuuuccacguucuagcauucaaggucccauucggggc
ugauccggguugaagacauugucagguggggaguuuggcuggggcggcac
aucuguuaaacgauaacgcagauguccuaaggggggcucauggagaacag
aaaucuccaguagaacaaaaggguaaaagcccccuugauuuugauuuuca
gugugaauacaaaccaugaaaguguggccuaucgauccuuuagucccucg
gaauuugaggcuagaggugccagaaaaguuaccacagggauaacuggcuu
guggcagucaagcguucauagcgacauugcuuuuugauucuucgaugucg
gcucuuccuaucauaccgaagcagaauucgguaagcguuggauuguucac
ccacuaauagggaacgugagcuggguuuagaccgucgugagacagguuag
uuuuacccuacugaugaauguuaccgcaauaguaauugaacuuaguacga
gaggaacaguucauucggauaauugguuuuugcggcugucugaucaggca
uugccgcgaagcuaccauccgcuggauuauggcugaacgccucuaaguca
gaauccaugcuagaacgcggugauuucuuugcuccacacaauauagaugg
auacgaauaaggcguccuuguggcgucgcugaaccauagcaggcuagcaa
cggugcacuuggcggaaaggccuugggugcuugcuggcgaauugcaaugu
cauuuugcguggggauaaaucauuuguauacgacuuagauguacaacggg
guauuguaagcaguagaguagccuuguuguuacgaucugcugagauuaag
ccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dc3 Crystal Structure of Hypusine-Containing Translation Factor eIF5A Bound to a Rotated Eukaryotic Ribosome.
• Resolution: 3.25 Å
• Binding residue (original residue number in PDB): G2 K3 S4 H5 G6 Y7 R8 S9 R10 R12 Y13 M14 F15 Q16 R17 F19 H22 G23 K35 K43 G46 S47 Q49 K50 G51 H54 Y57 Q58 G59 K60 T61 T68 K69 S70 S71 K78 V80 L85 K87 R88 N90 R92 K100 C101 R102 F105 R108 N112 R116 Q127 K129 R130 Q131
• Binding residue (residue number reindexed from 1): G1 K2 S3 H4 G5 Y6 R7 S8 R9 R11 Y12 M13 F14 Q15 R16 F18 H21 G22 K34 K42 G45 S46 Q48 K49 G50 H53 Y56 Q57 G58 K59 T60 T67 K68 S69 S70 K77 V79 L84 K86 R87 N89 R91 K99 C100 R101 F104 R107 N111 R115 Q126 K128 R129 Q130

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

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:5dc3, PDBe:5dc3, PDBj:5dc3
• PDBsum: 5dc3
• PubMed: 27196944
• UniProt: Q02753|RL21A_YEAST Large ribosomal subunit protein eL21A (Gene Name=RPL21A)