Structure of PDB 8v87 Chain E Binding Site BS01

Receptor Information

>8v87 Chain E (length=156) Species: 1247190 (Saccharomyces cerevisiae BY4741)

SAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKR
VVYLKHLEDNTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKF
NVEYFAKEEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDK
PHMLKF

Ligand information

>8v87 Chain 1 (length=2489)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaagu
acagugauggaaagaugaaaagaacuuugaaaagagagugaaaaaguacg
ugaaauuguugaaagggaagggcauuugaucagacauggugcacugggcc
agcaucaguuuugguggcaggauaaauccauaggaauguagcuugccucg
guaaguauuauagccugugggaauacugccagcugggacugaggacugcg
acguaagucaaggaugcuggcauaaugguuauaugccgcccgucuugaaa
cacggaccaaggagucuaacgucuaugcgaguguuuggguguaaaaccca
uacgcguaaugaaagugaacguagguuggggccucgcaagaggugcacaa
ucgaccgaguaagagcauagcuguugggacccgaaagauggugaacuaug
ccugaauagggugaagccagaggaaacucugguggaggcucgcgguucga
ucgucgaauuuggguauaggggcgaaagacuaaaaccaucuaguagcugg
uuccugccgaaguuucccucaggauagcagaagcucguaucaguuuuaug
aauguaaaaugaagagcuuuuagugggccauuuuugguaagcagaacugg
cgaugcgggaugaaccgaacguagaguuaaggugccggaauacacgcuca
ucagacacaaaagguguuaguucaucuagacagccggacgguggccaugg
aagucggaauccgcuaaggaguguguaacaacucaccggccgaaugaacu
agcccugaaaauggauggcgcucaagcguguuaccuauacucuaccguca
ggguugaugcccugacgaguaggcaggcguggaggucagugacgaagccu
agaccguaaggucgggucgaacggccucuagugcagaucuuggugguagu
agcaauucaaaugagaacuuugaagacugaaguggggaaagguuccacgu
caacagcaguuggacguggguuagucgauccuaagagauggggaagcucc
guuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgguu
aagauuccggaaccuggauauggauucuucacgguaacguaacugaaugu
ggagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagc
uuaucaccccggaauugguuuauccggagauggggucuuauggcuggaag
aggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaau
ccacaggaaggaauaguuuucaugccaggucguacugaucuccaagguga
acagccucuaguugauagaauaauguagauaagggaagucggggggaauc
uggagauucccacugucccuaucuacuaucuagcgaaaccacagccaagg
gaacgggcuuggcagaaucagcggggaaagaagacccuguugagcuugac
ucuaguuugacauugugaagagacauagaggguguagaauaagugggagc
uucggcgccagugaaauaccacuaccuuuauaguuucuuuacuauuguca
gguggggaguaaaguuaccacagggauaacuggcuuguggcagucaagcg
agcgacauugcuuuuugagaugucggcucuuccuaucauaccgaagcaga
auucgguaagcguuggauuguucacccacuaauagggaacgugagcuggg
uuuagaccgucgugagacagguuaguuuuacccuacugaugaauguuacc
gcaauaguaauugaacuuaguacgagaggaacaguucauucggauaauug
guuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgcugg
auuauggcugaacgccucuaagucagaauccaugcuagaacgcggugauu
ucuuugcuccacacaauauagauggauacgaauaaggcguccuuguggcg
ucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuug
ggugcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauuu
guauacgacuuagauguacaacgggguauuguaagcaguagaguagccgu
uacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8v87 The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
• Resolution: 2.66 Å
• Binding residue (original residue number in PDB): S2 K5 W9 A17 L18 K19 K20 T21 R22 K23 A24 R26 Q28 K29 G45 R46 R48 N61 T62 F69 K70 N72 G73 P75 R77 R78 N80 R82 Y83 K108 I130 K131 R134 Q157 A161 S162 N167
• Binding residue (residue number reindexed from 1): S1 K4 W8 A16 L17 K18 K19 T20 R21 K22 A23 R25 Q27 K28 G44 R45 R47 N60 T61 F68 K69 N71 G72 P74 R76 R77 N79 R81 Y82 K107 I110 K111 R114 Q137 A141 S142 N147

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000027 ribosomal large subunit assembly
• 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:8v87, PDBe:8v87, PDBj:8v87
• PDBsum: 8v87
• PubMed: 38632236
• UniProt: Q02326|RL6A_YEAST Large ribosomal subunit protein eL6A (Gene Name=RPL6A)