Structure of PDB 8v87 Chain f Binding Site BS01

Receptor Information

>8v87 Chain f (length=106) Species: 1247190 (Saccharomyces cerevisiae BY4741)

AESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAY
VYRASKEVRGSKIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIF
LYPSNI

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): A2 S4 H5 R6 Y8 K10 Q17 R18 S19 K20 R21 N23 L45 G46 R48 V52 Y53 R54 S56 K57 R60 S62 I64 R65 V66 M67 W68 K70 R73 H75 G76 N77 S78 R82 R86 N87 N88 P90 A91 K92 A96 S97 R99 N106
• Binding residue (residue number reindexed from 1): A1 S3 H4 R5 Y7 K9 Q16 R17 S18 K19 R20 N22 L44 G45 R47 V51 Y52 R53 S55 K56 R59 S61 I63 R64 V65 M66 W67 K69 R72 H74 G75 N76 S77 R81 R85 N86 N87 P89 A90 K91 A95 S96 R98 N105

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

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: P05744|RL33A_YEAST Large ribosomal subunit protein eL33A (Gene Name=RPL33A)