Structure of PDB 6ylx Chain L Binding Site BS01

Receptor Information

>6ylx Chain L (length=187) Species: 4932 (Saccharomyces cerevisiae)

PILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPLDLLRPV
VRAPTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQE
IFDANVQRLKEYQSKIIVFPRNGKAPEAEQVLSAAATFPIAQPATDVEAR
AVQDNGESAFRTLRLARSEKKFRGIREKRAREKAEAE

Ligand information

>6ylx Chain 1 (length=2534)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaac
aaguacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaag
uacgugaaauuguugaaagggaagggcauuugaucagacaggccagcauc
aguuuugguggcaggauaaauccauaggaauguagcuugccucgguaagu
auuauagccugugggaauacugccagcugggacugaggacugcgacguaa
gucaaggaugcuggcauaaugguuauaugccgcccgucuugaaacacgga
ccaaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcg
uaaugaaagugaacguagguuggggccucgcaagaggugcacaaucgacc
gauccugaugucuucggauggauuugaguaagagcauagcuguugggacc
cgaaagauggugaacuaugccugaauagggugaagccagaggaaacucug
guggaggcucguagcgguucugacgugcaaaucgaucgucgaauuugggu
auaggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaag
uuucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaa
aacuuuaaauauguaagaagucggacauuugaaugaagagcuuuuagugg
gccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacguagag
uuaaggugccggaauacacgcucaucagacaccacaaaagguguuaguuc
aucuagacagccggacgguggccauggaagucggaauccgcuaaggagug
uguaacaacucaccggccgaaugaacuagcccugaaaauggauggcgcuc
aagcguguuaccuauacucuaccgucaggguugauaugaugcccugacga
guaggcaggcguggaggucagugacgaagccuagaccguaaggucggguc
gaacggccucuagugcagaucuuggugguaguagcaaauauucaaaugag
aacuuugaagacugaaguggggaaagguuccacgucaacagcaguuggac
guggguuagucgauccuaagagauggggaagcuccguuucaaaggccuga
uuuuaugcaggccaccaucgaaagggaauccgguuaagauuccggaaccu
ggauauggauucuucacgguaacguaacugaauguggagacgucggcgcg
agcccugggaggaguuaucuuuucuucuuaacagcuuaucaccccggaau
ugguuuauccggagauggggucuuauggcuggaagaggccagcaccuuug
cuggcuccggugcgcuugugacggcccgugaaaauccacaggaaggaaua
guuuucaugccaggucguacugauaaccgcagcaggucuccaaggugaac
agccucuaguugauagaauaauguagauaagggaagucggcaaaauagau
ccguaacuucgggauaaggauuggcucuaagggucggacgaucaacuuag
aacugguacggacaaggggaaucugacugucuaauuaaaacauagcauug
auuuauggauuaacgagauucccacugucccuaucuacuaucuagcgaaa
ccacagccaagggggcuuggcagaaucagcggggaaacuggcuuguggca
gucaagcguucauagcgacauugcuuuuugauucuucgaugucggcucuu
ccuaucauaccgaagcagaauucgguaagcguuggauuguucacccacua
auagggagugagcuggguuacccuacugaugaauguuaccgcaauaguaa
uugaacuuaguacgagaggaacaguucauucggauaauugguuuuugcgg
cugucugaucaggcauugccgcgaagcuaccauccgcuggauuauggcug
aacgccucuaagucagaauccaugcuagaacgcggugauuucuuugcucc
acacaauauagauggauacgaauaaggcguccuuguggcgucgcugaacc
auagcaggcuagcaacggugcacuuggcggaaaggccuugggugcuugcu
ggcgaauugcaaugucauuuugcguggggauaaaucauuuguauacgacu
uagauguacaacgggguauuguaagcaguagaguagccuuguuguuacga
ucugcugagauuaagccuuuguugucugauuugu

...........................<<<<<.....<<....>>.....
.>>>>>.....<.....<<....>>..<<<<<......<<.....>>...
..>>>>>..<<<...........<<.<<<<<<...>>>>>>.>>......
.......<<<<<<.<<<<<<<<<<<<<<<<<<<<<.....<<<<......
>>>>.(.......<<<......)>>>....>>>>>>>>..>>>>>>>>..
..>>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<
<<<........>>>>>..>>>....>........................
.....<<....>>...............<<<<....>>>>..........
........................<<<<<.<<<<<......<<<<<<<.<
<<<<<<<<<<<<<<.....<<<<<<<<<......<<<<<......>>>>>
.......>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....
>>>.....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><
<<<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>.
..<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<
<<<<<...<<....>>...>>>.>>>.>>....>>>>>>.>>>>>>..<<
.<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>
>>.....>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>
>>...<<.......>>......>>>>>>......>.>>..<<<<<<....
<.<<<....>>>.><<<<<<<<.....<<<.<<<<<<.............
............>>>>...<<<.>>>.....>>>>>...>>>>>>.>>..
<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<
<..<<<<(((.....<<<<<<......<..........<<<.<<<<<<<<
<<.......<<<<<.<<....<<.........>>....>>.........<
<......>>...>>>>>...>>>>>>>>>>>>>..........))).>..
..>>>>>>.>>>>..>>>>>>><<<<<<<<<.........>>>>>>>>>.
...>>>>>><<.<<<<<<..<<......<<<<.<<<<....>>>>>>>>.
..>>.>>>>>>..>>.....>>>>>><<.....<<.....<<<<<<....
...>>>>>><<<<.....<<<<<.<<...<<<<<<...<<.....>>.>>
>>>>....((<<<<<<...<<....<<<....>>>........<<<<<<.
.......>>>>>>....>>....>>...<<<<<........>>>>>))<<
<<.<<<<<<<.....<<<....>>>.......<<<<<<...<<<<.<<<<
<<<<<<<<<<<<<<..(((..>>>>>><...<<<<<....<<<<<<....
<<<.....>>>....>>>>>>.....>>>>>....><<<<<<<<....>>
>>>>>>>>>>.>.>>>>>>>.>>>>.........>>>>>>..........
>>>..>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<....
.>>>>..>>>>..<<<<.....<<<<<<<.<<...............<<<
<<...............>>>>><<.<<<<<<<<<<....>>>>..>>>>>
>.>>............<<<<<<<....<<<.........>>>..<...>.
................>>>>>>>.....>>.>>>>>>>..>>>>>>....
>>....<<<<<....>>>>>....<<<<<..<<.............<<<<
<<...<<.......>>...>>>>>>......................<<<
<<<..<.<<<<<<<......>>>>>>>...>.<<<.........>>>...
..>>>>>>..............>>.>>>>>....<<<<<<<<..<<<<.<
.<<<<<<...............>>>>>>.><<<<<....<<<...<<<<<
<<<<<<))).>>>>>..>>>>>>..>>>...>>>>>.<<<<...<<<<<.
..........>>>>>...>>>>.>>>>....>>>>>>>>.......<<<<
<<.<<<.<<....<<..........<<<<<<.....>>>>>>......>>
.......<<<<<<...<<<<<.<..<<<......>>>..>.>>>>>.>>>
>>>.............>>.>>>.>>>>>>..<<<<<.<............
.>.....<<<<<<<<<.<<<....<<<<....<<<<........>>>>..
.>>>>...>>>....>>>>.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ylx Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): L10 K11 N12 H13 F14 R15 K16 H17 W18 Q19 Q28 A29 K31 R35 R36 R39 R42 R55 V58 R59 P61 T62 Y65 N66 K68 R70 G72 R73 L77 R91 D98 H99 R100 R101 R128 F167 R168 R171 R174 S175 K178 F179 R183 R186
• Binding residue (residue number reindexed from 1): L3 K4 N5 H6 F7 R8 K9 H10 W11 Q12 Q21 A22 K24 R28 R29 R32 R35 R48 V51 R52 P54 T55 Y58 N59 K61 R63 G65 R66 L70 R84 D91 H92 R93 R94 R121 F160 R161 R164 R167 S168 K171 F172 R176 R179

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• 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:6ylx, PDBe:6ylx, PDBj:6ylx
• PDBsum: 6ylx
• PubMed: 32668200
• UniProt: Q12690|RL13A_YEAST Large ribosomal subunit protein eL13A (Gene Name=RPL13A)