Structure of PDB 5dgf Chain m0 Binding Site BS01

Receptor Information

>5dgf Chain m0 (length=213) Species: 559292 (Saccharomyces cerevisiae S288C)

ARRPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVH
LVSNELEQLSSEALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINK
MLLQQGMRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYK
FPGQQKIILSKKWGFTNLDRPEYLKKREAGEVKDDGAFVKFLSKKGSLEN
NIREFPEYFAAQA

Ligand information

>5dgf 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: 5dgf Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): R3 R4 A6 R7 C8 K13 N14 K15 Y22 D35 K39 S61 E63 A64 A67 K74 R90 H92 F94 R98 M115 R116 G117 W119 R154 Y157 K158 P160 Q162 D193 G194 F196 K198
• Binding residue (residue number reindexed from 1): R2 R3 A5 R6 C7 K12 N13 K14 Y21 D34 K38 S60 E62 A63 A66 K73 R89 H91 F93 R97 M107 R108 G109 W111 R146 Y149 K150 P152 Q154 D185 G186 F188 K190

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006415 translational termination

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:5dgf, PDBe:5dgf, PDBj:5dgf
• PDBsum: 5dgf
• UniProt: P41805|RL10_YEAST Large ribosomal subunit protein uL16 (Gene Name=RPL10)