Structure of PDB 5h4p Chain b Binding Site BS01

Receptor Information

>5h4p Chain b (length=58) Species: 559292 (Saccharomyces cerevisiae S288C)

AKSKNHTAHNQTRKAHRNGIKKPKTYKYPSLKGVDPKFRRNHKHALHGTA
KALAAAKK

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): K3 K5 H7 T8 A9 H10 N11 Q12 R14 K15 H17 R18 N19 K25 T26 Y27 K28 Y29 S31 L32 K33 G34 K38 F39 R41 N42 H43 K44 H45 A46
• Binding residue (residue number reindexed from 1): K2 K4 H6 T7 A8 H9 N10 Q11 R13 K14 H16 R17 N18 K24 T25 Y26 K27 Y28 S30 L31 K32 G33 K37 F38 R40 N41 H42 K43 H44 A45

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:5h4p, PDBe:5h4p, PDBj:5h4p
• PDBsum: 5h4p
• PubMed: 28112732
• UniProt: P05747|RL29_YEAST Large ribosomal subunit protein eL29 (Gene Name=RPL29)