Structure of PDB 6ylx Chain Z Binding Site BS01

Receptor Information

>6ylx Chain Z (length=135) Species: 4932 (Saccharomyces cerevisiae)

AKFLKAGKVAVVVRGRYAGKKVVIVKPHDEGSKSHPFGHALVAGIERYPL
KVTKKHGAKKVAKRTKIKPFIKVVNYNHLLPTRYTLDVEAFKSVVSTETF
EQPSQREEAKKVVKKAFEERHQAGKNQWFFSKLRF

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): R15 G16 R17 H36 F38 R48 K64 K67 K69 K73 V74 N76 N78 H79 R107 E108 K111 K112 K115 R135
• Binding residue (residue number reindexed from 1): R14 G15 R16 H35 F37 R47 K63 K66 K68 K72 V73 N75 N77 H78 R106 E107 K110 K111 K114 R134

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:6ylx, PDBe:6ylx, PDBj:6ylx
• PDBsum: 6ylx
• PubMed: 32668200
• UniProt: P0C2H6|RL27A_YEAST Large ribosomal subunit protein eL27A (Gene Name=RPL27A)