Structure of PDB 5h4p Chain d Binding Site BS01

Receptor Information

>5h4p Chain d (length=109) Species: 559292 (Saccharomyces cerevisiae S288C)

LKDVVTREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAP
ELNQAIWKRGVKGVEYRLRLRISRKRNEEEDAKNPLFSYVEPVLVASAKG
LQTVVVEED

Ligand information

>5h4p Chain 1 (length=3091)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaaguuaaau
auguaagaaguccuuguuacuuaauugaacguggacauuugaaugaagag
cuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaacc
gaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaag
guguuaguucaucuagacagccggacgguggccauggaagucggaauccg
cuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaaug
gauggcgcucaagcguguuaccuauacucuaccgucaggguugauaugau
gcccugacgaguaggcaggcguggaggucagugacgaagccuagaccgua
aggucgggucgaacggccucuagugcagaucuuggugguaguagcaaaua
uucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaaca
gcaguuggacguggguuagucgauccuaagagauggggaagcuccguuuc
aaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaagau
uccggaaccuggauauggauucuucacgguaacguaacugaauguggaga
cgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuauc
accccggaauugguuuauccggagauggggucuuauggcuggaagaggcc
agcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccaca
ggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucuc
caaggugaacagccucuaguugauagaauaauguagauaagggaagucgg
caaaauagauccguaacuucgggauaaggauuggcucuaagggucgggua
cgaucaacuuagaacugguacggacaaggggaaucugacugucuaauuaa
aacauagcauugcgauggucagaaagugauguugacgcaaugugauuucu
gcccagugcucugaaugucaaagugaagaaauucaaccaagcgcggguaa
acggcgggaguaacuaugacucucuuaagguagccaaaugccucgucauc
uaauuagugacgcgcaugaauggauuaacgagauucccacugucccuauc
uacuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcg
gggaaagaagacccuguugagcuugacucuaguuugacauugugaagaga
ucuuuacuuauucaaugaagcggagcuggaauucauuuuccacguucuag
cauucaaggucccauucggggcugauccggguugaagacauugucaggug
gggaguuuggcuggggcggcacaucuguuaaacgauaacgcagauguccu
aaggggggcucauggagaacagaaaucuccaguagaacaaaaggguaaaa
gcccccuugauuuugauuuucagugugaauacaaaccaugaaaguguggc
cuaucgauccuuuagucccucggaauuugaggcuagaggugccagaaaag
uuaccacagggauaacuggcuuguggcagucaagcguucauagcgacauu
gcuuuuugauucuucgaugucggcucuuccuaucauaccgaagcagaauu
cgguaagcguuggauuguucacccacuaauagggaacgugagcuggguuu
agaccgucgugagacagguuaguuuuacccuacugaugaauguuaccgca
auaguaauugaacuuaguacgagaggaacaguucauucggauaauugguu
uuugcggcugucugaucaggcauugccgcgaagcuaccauccgcuggauu
auggcugaacgccucuaagucagaauccaugcuagaacgcggugauuucu
uugcuccacacaauauagauggauacgaauaaggcguccuuguggcgucg
cugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuugggu
gcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauuugua
uacgacuuagauguacaacgggguauuguaagcaguagaguagccuuguu
guuacgaucugcugagauuaagccuuuguugucugauuugu

........................<<<<<<.....<......>......>
>>>>.>.........<<....>>..<<<<<......<<.....>>.....
>>>>>..<<<...<.......<<.<<<<<<...>>>>>>.>>.......>
.....<<<<<<<.<<<<<<<<<<<<<<<<<<<<<....<<<<......>>
>>.(.......<<<......)>>>..>.>>>>>>>>..>>>>>>>>....
>>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<<<
<..((((((>>>>>..>>>...............................
...<<....>>...............<<<......>>>............
......................<<<<<.<<<<<......<<<<<<<.<<<
<<<<<<<<<<<<.....<<<<<<<<<......<<<<<......>>>>>..
.....>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>>
>.....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<<
<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>...
<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<<
<<<....<....>....>>>.>>>.>>....>>>>>>.>>>>>>..<<.<
..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>
.....>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>>>
...<<.......>>......>>>>>>...>..>.>>..<<<<<<....<.
<<<....>>>.><<<<<<<<<<...<<<.<<<<<<<.....<<.>>....
.>>>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>>>>.>>>
>>>>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>
>...<<<<<<<..<<<<(((.....<<<<<<......<..........<<
<.<<<<<<<<<........<<<<<.<<....<<.........>>....>>
.........<<......>>...>>>>>....>>>>>>>>>>>>.......
...))).>....>>>>>>.>>>>..>>>>>>><<<<<<<<<.........
>>>>>>>>>....>>>>>><.<<<<<<<..<<......<<<<.<<<<...
.>>>>>>>>...>>.>>>>>>>..>.....>>>>>><<.....<<.....
<<<<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<<...<<
.....>>.>>>>>>....((<<<<<<...<<....<<<....>>>.....
...<<<<<<........>>>>>>....>>....>>...<<<<<.......
.>>>>>))<<<<.<<<<<<<.....<<<....>>>.......<<<<<<..
.<<<<.<<<<<<<.<<<<<<<<<<..[[[..>>>>>><...<<<<<....
<<<<<<....<<<.....>>>....>>>>>>.....>>>>>....><<<<
<<<......>>>>>>>>>>>...>>>>>>>.>>>>.........>>>>>>
..........>>>..>>>>>>>>>>>>..>>.....<<......>>>>>>
>.<<<<.....>>>>..>>>>..<<<<.....<<<<<<<.<<........
.<.....<<<<<....<....>.....>>>>><<.<<<<<<<<<<.<...
>>>>>..>>>>>>.>>............<<<<<<<<<..<<<........
.>>>..<<<<<<<....<<<<.....>>>>......>>>>>>>...<<..
<<<..<<<<<<.<...<<....<<<<<....>>>>.>...>>.>>>>>..
>>>>><<<<<.........>>>>>........<...........<<<<<.
......>>>>>.....>.....>>....>>.>>>>>>>..>..>>.>>>>
>>>..>>>>>>....>>....<<<<<........>>>>>....<<<<<..
<<<.<<......<<<<.<<<<<<..<<<<<.<<<<<<<<..<<<<<<<..
>>>>>>>...<<<<<.....<<<<..<<<<<......>>>>>........
.......<<<<<<....>>>>>>..>>>>..>>>>>.....>>>>>>>>.
.>>>>>...<<<.....>>>..<<<<<<...........>>>>>>..<<.
..<<<<<<<...<<<<<<.......>>>>>>.....<<...(((>>....
>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<<....>>>.>>)
))......<<<<<<<..<<<<.))))))>>>>>>>>>>>.........>>
>>..>>>>>>.......<<.<...<<<<<<...<<.......>>...>>>
>>>....>.>.>.......<.<<<.<<<<<<..<.<<<<<<<......>>
>>>>>...>.<<<.........>>>.....>>>>>..>...>>>..>...
.<<<<<<<....>>>.>>>>....>>..>>>.>>>>>....<<<<<<<<.
.<<<<...<<<<<<...............>>>>>>..<<<<<...<<<<.
...<<<<<<<<<.]]]..>>>>..>>>>>...>>>>..>>>>>.<<<<..
.<<<<<...........>>>>>...>>>>.>>>>....>>>>>>>>....
...<<<<<<.<<<.<<....<<..........<<<<<<.....>>>>>>.
.....>>.......<<<<<<...<<<<<.<..<<<......>>>..>.>>
>>>.>>>>>>.............>>.>>>.>>>>>>..<<<<<.<.....
........>.....<<<<<<<<<.<<<....<<<<....<<<<<......
>>>>>...>>>>...>>>....>>>>.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5h4p Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1
• Resolution: 3.07 Å
• Binding residue (original residue number in PDB): R10 T13 H17 K18 R19 H21 G22 S24 F25 K26 V33 K34 H43 L51 A52 P53 N56 W60 V64 K65 Y69 R70 L104 Q105 T106
• Binding residue (residue number reindexed from 1): R7 T10 H14 K15 R16 H18 G19 S21 F22 K23 V30 K31 H40 L48 A49 P50 N53 W57 V61 K62 Y66 R67 L101 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:5h4p, PDBe:5h4p, PDBj:5h4p
• PDBsum: 5h4p
• PubMed: 28112732
• UniProt: P0C2H8|RL31A_YEAST Large ribosomal subunit protein eL31A (Gene Name=RPL31A)