Structure of PDB 5dge Chain O2 Binding Site BS01

Receptor Information

>5dge Chain O2 (length=127) Species: 559292 (Saccharomyces cerevisiae S288C)

ASLPHPKIVKKHTKKFKRHHSDRYHRVAENWRKQKGIDSVVRRRFRGNIS
QPKIGYGSNKKTKFLSPSGHKTFLVANVKDLETLTMHTKTYAAEIAHNIS
AKNRVVILARAKALGIKVTNPKGRLAL

Ligand information

>5dge Chain 1 (length=3149)

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
acauaguuucuuuacuuauucaaugaagcggagcuggaauucauuuucca
cguucuagcauucaaggucccauucggggcugauccggguugaagacauu
gucagguggggaguuuggcuggggcggcacaucuguuaaacgauaacgca
gauguccuaaggggggcucauggagaacagaaaucuccaguagaacaaaa
ggguaaaagcccccuugauuuugauuuucagugugaauacaaaccaugaa
aguguggccuaucgauccuuuagucccucggaauuugaggcuagaggugc
cagaaaaguuaccacagggauaacuggcuuguggcagucaagcguucaua
gcgacauugcuuuuugauucuucgaugucggcucuuccuaucauaccgaa
gcagaauucgguaagcguuggauuguucacccacuaauagggaacgugag
cuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaaug
uuaccgcaauaguaauugaacuuaguacgagaggaacaguucauucggau
aauugguuuuugcggcugucugaucaggcauugccgcgaagcuaccaucc
gcuggauuauggcugaacgccucuaagucagaauccaugcuagaacgcgg
ugauuucuuugcuccacacaauauagauggauacgaauaaggcguccuug
uggcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaagg
ccuugggugcuugcuggcgaauugcaaugucauuuugcguggggauaaau
cauuuguauacgacuuagauguacaacgggguauuguaagcaguagagua
gccuuguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dge Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome
• Resolution: 3.45 Å
• Binding residue (original residue number in PDB): K11 K12 T14 K15 F17 R19 H21 D23 R24 Y25 H26 R27 N31 W32 R33 K36 G37 I38 D39 S40 R43 R44 R45 F46 R47 G48 I50 P53 K54 I55 G56 Y57 G58 S59 N60 K61 K64 F65 S69 N78 K80 E95 H98 N99 I100 S101 A102 K103 N104 R105 N121 R125
• Binding residue (residue number reindexed from 1): K10 K11 T13 K14 F16 R18 H20 D22 R23 Y24 H25 R26 N30 W31 R32 K35 G36 I37 D38 S39 R42 R43 R44 F45 R46 G47 I49 P52 K53 I54 G55 Y56 G57 S58 N59 K60 K63 F64 S68 N77 K79 E94 H97 N98 I99 S100 A101 K102 N103 R104 N120 R124

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:5dge, PDBe:5dge, PDBj:5dge
• PDBsum: 5dge
• UniProt: P38061|RL32_YEAST Large ribosomal subunit protein eL32 (Gene Name=RPL32)