Structure of PDB 6hhq Chain CM Binding Site BS01

Receptor Information

>6hhq Chain CM (length=169) Species: 4932 (Saccharomyces cerevisiae)

QNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVR
TFGIRRNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFG
IDEHIDLGIKYDPSIGIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTT
KEDTVSWFKQKYDADVLDK

Ligand information

>6hhq Chain AR (length=3147)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagaggccagcaucaguu
uugguggcaggauaaauccauaggaauguagcuugccucgguaaguauua
uagccugugggaauacugccagcugggacugaggacugcgacguaaguca
aggaugcuggcauaaugguuauaugccgcccgucuugaaacacggaccaa
ggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaau
gaaagugaacguagguuggggccucgcaagaggugcacaaucgaccgauc
cugaugucuucggauggauuugaguaagagcauagcuguugggacccgaa
agauggugaacuaugccugaauagggugaagccagaggaaacucuggugg
aggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguauag
gggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguuuc
ccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaugau
uagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaaua
uguaagaaguccuuguuacuuaauugaacguggacauuugaaugaagagc
uuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaaccg
aacguagaguuaaggugccggaauacacgcucaucagacaccacaaaagg
uguuaguucaucuagacagccggacgguggccauggaagucggaauccgc
uaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaaugg
auggcgcucaagcguguuaccuauacucuaccgucaggguugauaugaug
cccugacgaguaggcaggcguggaggucagugacgaagccuagaccguaa
ggucgggucgaacggccucuagugcagaucuuggugguaguagcaaauau
ucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaacag
caguuggacguggguuagucgauccuaagagauggggaagcuccguuuca
aaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaagauu
ccggaaccuggauauggauucuucacgguaacguaacugaauguggagac
gucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuauca
ccccggaauugguuuauccggagauggggucuuauggcuggaagaggcca
gcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccacag
gaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucucc
aaggugaacagccucuaguugauagaauaauguagauaagggaagucggc
aaaauagauccguaacuucgggauaaggauuggcucuaagggucggguac
gaucaacuuagaacugguacggacaaggggaaucugacugucuaauuaaa
acauagcauugcgauggucagaaagugauguugacgcaaugugauuucug
cccagugcucugaaugucaaagugaagaaauucaaccaagcgcggguaaa
cggcgggaguaacuaugacucucuuaagguagccaaaugccucgucaucu
aauuagugacgcgcaugaauggauuaacgagauucccacugucccuaucu
acuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcgg
ggaaagaagacccuguugagcuugacucuaguuugacauugugaagagac
auaguuucuuuacuuauucaaugaagcggagcuggaauucauuuuccacg
uucuagcauucaaggucccauucggggcugauccggguugaagacauugu
cagguggggaguuuggcuggggcggcacaucuguuaaacgauaacgcaga
uguccuaaggggggcucauggagaacagaaaucuccaguagaacaaaagg
guaaaagcccccuugauuuugauuuucagugugaauacaaaccaugaaag
uguggccuaucgauccuuuagucccucggaauuugaggcuagaggugcca
gaaaaguuaccacagggauaacuggcuuguggcagucaagcguucauagc
gacauugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagc
agaauucgguaagcguuggauuguucacccacuaauagggaacgugagcu
ggguuuagaccgucgugagacagguuaguuuuacccuacugaugaauguu
accgcaauaguaauugaacuuaguacgagaggaacaguucauucggauaa
uugguuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgc
uggauuauggcugaacgccucuaagucagaauccaugcuagaacgcggug
auuucuuugcuccacacaauauagauggauacgaauaaggcguccuugug
gcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggcc
uugggugcuugcuggcgaauugcaaugucauuuugcguggggauaaauca
uuuguauacgacuuagauguacaacgggguauuguaagcaguagaguagc
cuuguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6hhq Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): K16 V18 N20 S22 G24 S48 A50 R51 Y52 F57 I59 H68 R94 N95 S97 A98 T99 N101 G103 F104 G105 I106 G124 M125 D126 Y128 K142
• Binding residue (residue number reindexed from 1): K11 V13 N15 S17 G19 S43 A45 R46 Y47 F52 I54 H63 R89 N90 S92 A93 T94 N96 G98 F99 G100 I101 G119 M120 D121 Y123 K137

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• 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:6hhq, PDBe:6hhq, PDBj:6hhq
• PDBsum: 6hhq
• PubMed: 30759226
• UniProt: Q3E757|RL11B_YEAST Large ribosomal subunit protein uL5B (Gene Name=RPL11B)