Structure of PDB 6yly Chain p Binding Site BS01

Receptor Information

>6yly Chain p (length=91) Species: 4932 (Saccharomyces cerevisiae)

AKRTKKVGITGKYGVRYGSSLRRQVKKLEIQQHARYDCSFCGKKTVKRGA
AGIWTCSCCKKTVAGGAYTVSTAAAATVRSTIRRLREMVEA

Ligand information

>6yly Chain 1 (length=2676)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucucacggaccaagga
gucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaaugaa
agugaacguagguuggggccucgcaagaggugcacaaucgaccgauccug
augucuucggauggauuugaguaagagcauagcuguugggacccgaaaga
uggugaacuaugccugaauagggugaagccagaggaaacucugguggagg
cucguagcgguucugacgugcaaaucgaucgucgaauuuggguauagggg
cgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguuucccu
caggauagcagaagcucguaucaguuuuaugagaauauguaagaaguccg
acauuugaaugaagagcuuuuagugggccauuuuugguaagcagaacugg
cgaugcgggaugaaccgaacguagaguuaaggugccggaauacacgcuca
ucagacaccacaaaagguguuaguucaucuagacagccggacgguggcca
uggaagucggaauccgcuaaggaguguguaacaacucaccggccgaauga
acuagcccugaaaauggauggcgcucaagcguguuaccuauacucuaccg
ucaggguugauaugaugcccugacgaguaggcaggcguggaggucaguga
cgaagccuagaccguaaggucgggucgaacggccucuagugcagaucuug
gugguaguagcaaauauucaaaugagaacuuugaagacugaaguggggaa
agguuccacgucaacagcaguuggacguggguuagucgauccuaagagau
ggggaagcuccguuucaaaggccugacaggccaccaucgaaagggaaucc
gguuaagauuccggaaccuggauauggauucuucacgguaacguaacuga
auguggagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaa
cagcuuaucaccccggaauugguuuauccggagauggggucuuauggcug
gaagaggccagcaccuuugcuggcuccggugcgcuugugacggcccguga
aaauccacaggaaggaauaguuuucaugccaggucguacugauaaccgca
gcaggucuccaaggugaacagccucuaguugauagaauaauguagauaag
ggaagucggcaaaauagauccguaacuucgggauaaggauuggcucuaag
ggucggacgaucaacuuagaacugguacggacaaggggaaucugacuguc
uaauuaaaacauagcauugcgauggucagaaagugauguugacgcaaugu
gauuuauggauuaacgagauucccacugucccuaucuacuaucuagcgaa
accacagccaaggggcuuggcagaaucagcggggacuaguuugacauugu
gaagagacauaguuucuuuacuuauucaaugaagcggagcuggaauucau
uuuccacguucuagcauucaaggucccauucggggcugauccggguugaa
gacauugucaggugguagucccucggaauuugaggcuaaacuggcuugug
gcagucaagcguucauagcgacauugcuuuuugauucuucgaugucggcu
cuuccuaucauaccgaagcagaauucgguaagcguuggauuguucaccca
cuaauagggauacccuacugaugaauguuaccgcaauaguaauugaacuu
aguacgagaggaacaguucauucggauaauugguuuuugcggcugucuga
ucaggcauugccgcgaagcuaccauccgcuggauuauggcugaacgccuc
uaagucagaauccaugcuagaacgcggugauuucuuugcuccacacaaua
uagauggauacgaauaaggcguccuuguggcgucgcugaaccauagcagg
cuagcaacggugcacuuggcggaaaggccuugggugcuugcuggcgaauu
gcaaugucauuuugcguggggauaaaucauuuguauacgacuuagaugua
caacgggguauuguaagcaguagaguagccuuguuguuacgaucugcuga
gauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6yly Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): A2 K3 R4 K6 K7 V8 G9 I10 K13 Y14 G15 V16 R17 Y18 S20 S21 R23 H34 F41 K44 T46 A51 Y69
• Binding residue (residue number reindexed from 1): A1 K2 R3 K5 K6 V7 G8 I9 K12 Y13 G14 V15 R16 Y17 S19 S20 R22 H33 F40 K43 T45 A50 Y68

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0046872 metal ion binding
• GO:0070180 large ribosomal subunit rRNA binding

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:0044391 ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6yly, PDBe:6yly, PDBj:6yly
• PDBsum: 6yly
• PubMed: 32668200
• UniProt: P0CX25|RL43A_YEAST Large ribosomal subunit protein eL43A (Gene Name=RPL43A)