Structure of PDB 5m1j Chain D5 Binding Site BS01

Receptor Information

>5m1j Chain D5 (length=296) Species: 4932 (Saccharomyces cerevisiae)

AFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRL
VVRFTNKDIICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYAT
GLLIARRTLQKLGLDETYKGVEEVEGEYELTEAVEDGPRPFKVFLDIGLQ
RTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEEIDPELLRSYIFG
GHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIYTSAHEAIRADP
AFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ

Ligand information

>5m1j Chain 14 (length=3295)

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
agugagggccuuggucagacgcagcgggcgugcgugccuuguuguagacg
gccuugguaggucucuuguagaccgucgcuugcuacaauuaacgaucaac
uuagaacugguacggacaaggggaaucugacugucuaauuaaaacauagc
auugcgauggucagaaagugauguugacgcaaugugauuucugcccagug
cucugaaugucaaagugaagaaauucaaccaagcgcggguaaacggcggg
aguaacuaugacucucuuaagguagccaaaugccucgucaucuaauuagu
gacgcgcaugaauggauuaacgagauucccacugucccuaucuacuaucu
agcgaaaccacagccaagggaacgggcuuggcagaaucagcggggaaaga
agacccuguugagcuugacucuaguuugacauugugaagagacauagagg
guguagaauaagugggagcuucggcgccagugaaauaccacuaccuuuau
aguuucuuuacuuauucaaugaagcggagcuggaauucauuuuccacguu
cuagcauucaaggucccauucggggcugauccggguugaagacauuguca
gguggggaguuuggcuggggcggcacaucuguuaaacgauaacgcagaug
uccuaaggggggcucauggagaacagaaaucuccaguagaacaaaagggu
aaaagcccccuugauuuugauuuucagugugaauacaaaccaugaaagug
uggccuaucgauccuuuagucccucggaauuugaggcuagaggugccaga
aaaguuaccacagggauaacuggcuuguggcagucaagcguucauagcga
cauugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagcag
aauucgguaagcguuggauuguucacccacuaauagggaacgugagcugg
guuuagaccgucgugagacagguuaguuuuacccuacugaugaauguuac
cgcaauaguaauugaacuuaguacgagaggaacaguucauucggauaauu
gguuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgcug
gauuauggcugaacgccucuaagucagaauccaugcuagaacgcggugau
uucuuugcuccacacaauauagauggauacgaauaaggcguccuuguggc
gucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuu
gggugcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauu
uguauacgacuuagauguacaacgggguauuguaagcaguagaguagccu
uguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5m1j Structural insights into ribosomal rescue by Dom34 and Hbs1 at near-atomic resolution.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): K5 K8 Y12 R15 F16 Q17 P19 R23 G26 D29 Y31 R35 L36 K43 N45 L113 R140 P141 F142 F145 L146 I148 L150 R152 T153 H175 S176 N178 R179
• Binding residue (residue number reindexed from 1): K4 K7 Y11 R14 F15 Q16 P18 R22 G25 D28 Y30 R34 L35 K42 N44 L112 R139 P140 F141 F144 L145 I147 L149 R151 T152 H174 S175 N177 R178

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

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

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5m1j, PDBe:5m1j, PDBj:5m1j
• PDBsum: 5m1j
• PubMed: 27995908
• UniProt: P26321|RL5_YEAST Large ribosomal subunit protein uL18 (Gene Name=RPL5)