Structure of PDB 6z6k Chain LD Binding Site BS01

Receptor Information

>6z6k Chain LD (length=294) Species: 559292 (Saccharomyces cerevisiae S288C)

QKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVV
RFTNKDIICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGL
LIARRTLQKLGLDETYKGVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRT
TTGARVFGALKGASDGGLYVPHSENRFPGWDFETEEIDPELLRSYIFGGH
VSQYMEELADDDEERFSELFKGYLADDIDADSLEDIYTSAHEAIRADPAF
KPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ

Ligand information

>6z6k Chain C1 (length=3127)

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
ggauggcgcucaagcguguuaccuauacucuaccgucaggguuaugaugc
ccugacgaguaggcaggcguggaggucagugacgaagccuagaccguaag
gucgggucgaacggccucuagugcagaucuuggugguaguagcaaauauu
caaaugagaacuuugaagacugaaguggggaaagguuccacgucaacagc
aguuggacguggguuagucgauccuaagagauggggaagcuccguuucaa
aggccugcaggccaccaucgaaagggaauccgguuaagauuccggaaccu
ggauauggauucuucacgguaacguaacugaauguggagacgucggcgcg
agcccugggaggaguuaucuuuucuucuuaacagcuuaucaccccggaau
ugguuuauccggagauggggucuuauggcuggaagaggccagcaccuuug
cuggcuccggugcgcuugugacggcccgugaaaauccacaggaaggaaua
guuuucaugccaggucguacugauaaccgcagcaggucuccaaggugaac
agccucuaguugauagaauaauguagauaagggaagucggcaaaauagau
ccguaacuucgggauaaggauuggcucuaagggucggacgaucaacuuag
aacugguacggacaaggggaaucugacugucuaauuaaaacauagcauug
cgauggucagaaagugauguugacgcaaugugauuucugcccagugcucu
gaaugucaaagugaagaaauucaaccaagcgcggguaaacggcgggagua
acuaugacucucuuaagguagccaaaugccucgucaucuaauuagugacg
cgcaugaauggauuaacgagauucccacugucccuaucuacuaucuagcg
aaaccacagccaagggaacgggcuuggcagaaucagcggggaaagaagac
ccuguugagcuugacucuaguuugacauugugaagaguuucuuuacuuau
ucaaugaagcggagcuggaauucauuuuccacguucuagcauucaagguc
ccauucggggcugauccggguugaagacauugucagguggggaguuuggc
uggggcggcacaucuguuaaacgauaacgcagauguccuaaggggggcuc
auggagaacagaaaucuccaguagaacaaaaggguaaaagcccccuugau
uuugauuuucagugugaauacaaaccaugaaaguguggccuaucgauccu
uuagucccucggaauuugaggcuagaggugccagaaaaguuaccacaggg
auaacuggcuuguggcagucaagcguucauagcgacauugcuuuuugauu
cuucgaugucggcucuuccuaucauaccgaagcagaauucgguaagcguu
ggauuguucacccacuaauagggaacgugagcuggguuuagaccgucgug
agacagguuaguuuuacccuacugaugaauguuaccgcaauaguaauuga
acuuaguacgagaggaacaguucauucggauaauugguuuuugcggcugu
cugaucaggcauugccgcgaagcuaccauccgcuggauuauggcugaacg
ccucuaagucagaauccaugcuagaacgcggugauuuugcuccacacaau
auagauggauacgaauaaggcguccuuguggcgucgcugaaccauagcag
gcuagcaacggugcacuuggcggaaaggccuugggugcuugcuggcgaau
ugcaaugucauuuugcguggggauaaaucauuuguauacgacuuagaugu
acaacgggguauuguaagcaguagaguagccuuguuguuacgaucugcug
agauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6z6k Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): Y12 R15 F16 Q17 R23 T28 D29 Y31 R35 L36 K43 K48 R140 P141 F145 L146 I148 L150 T153 F160 P174 H175 S176 R179
• Binding residue (residue number reindexed from 1): Y9 R12 F13 Q14 R20 T25 D26 Y28 R32 L33 K40 K45 R137 P138 F142 L143 I145 L147 T150 F157 P171 H172 S173 R176

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:6z6k, PDBe:6z6k, PDBj:6z6k
• PDBsum: 6z6k
• PubMed: 32687489
• UniProt: P26321|RL5_YEAST Large ribosomal subunit protein uL18 (Gene Name=RPL5)