Structure of PDB 8v83 Chain e Binding Site BS01

Receptor Information

>8v83 Chain e (length=126) Species: 1247190 (Saccharomyces cerevisiae BY4741)

LPHPKIVKKHTKKFKRHHSDRYHRVAENWRKQKGIDSVVRRRFRGNISQP
KIGYGSNKKTKFLSPSGHKTFLVANVKDLETLTMHTKTYAAEIAHNISAK
NRVVILARAKALGIKVTNPKGRLALE

Ligand information

>8v83 Chain 1 (length=2015)

guuugaccucaaaucagguaggaguacccgcugaacaauaagcggaggaa
aagaaaccaaccgggauugccuuaguaacggcgagugaagcggcaaaagc
ucaaauuugaaaucugguaccuucggugcccgaguuguaauuuggagagg
gcaacuuuggggccguuccuugucuauguuccuuggaacaggacgucaua
gagggugagaaucccguguggcgaggagugcgguucuuuguaaagugccu
ucgaagagucgaguuguaugcagcucuaagugggugguaaauuccaucua
aagcuaaauauuggcgagagaccgauagcgaacaaguacagugauggaaa
gaugaaaagaacuuugaaaagagagugaaaaaguacgugaaauuguugaa
agggaagggcauuugaucagacaugguguuuugugcccucugcuccuugu
ggguaggggaaucucgcauuucacugggccagcaucaguuuugguggcag
gauaaauccauaggaauguagcuugccucgguaaguauuauagccugugg
gaauacugccagcugggacugaggacugcgacguaagucaaggaugcugg
cauaaugguuauaugccgcccgucuugaaacacggaccaaggagucuaac
gucuaugcgaguguuuggguguaaaacccauacgcguaaugaaagugaac
guagguuggggccucgcaagaggugcacaaucgaccgauccugaggaugg
auuugaguaagagcauagcuguugggacccgaaagauggugaacuaugcc
ugaaggguauaggggcaagacaccaucuaguagcugguuccugccgaagu
uucccucaggauagcagaagcucguaucaguuuuagaaugaagagcuuuu
agugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacg
uagaguuaaggugccggaauacacgcucaucagacaccacaaaagguguu
aguucaucuagacagccggacgguggccauggaagucggaauccgcuaag
gaguguguaacaacucaccggccgaaugaacuagcccugaaaauggaugg
cgcucaagcguguuaccuauacucuaccgucaggguugauaugaugcccu
gacgaguaggcaggcguggaggucagugacgaagccuagaccguaagguc
gggucgaacggccucuagugcagaucuuggugguaguagcaaauauucaa
augaggaacagccucuaguugauagaauaauguagauauaucuacuaucu
agcgaaaccacagccaagggaacgggcuuggcagaaucagcggggaaaga
agacccuguugagcuugacucuaguuugacauugugaagagacauagagg
guguagaauaagugggagcuucggcgccagugaaauaccacuaccuuuau
aguuucuuuacuauugucagguggggaguaaaguuaccacagggauaacu
ggcuuguggcagucaagcguucauagcgacauugcuugauucucggcucu
uccuaucauaccgaagcagaauucgguaagcguuggauuguucaccggga
acgugagcugggucgucgugagacaggccuacugaguuaccgcaauagua
auugaacuuaguacgagaggaacaguucauucggauaauugguuuugcgg
cugucugaucaggcauugccgcgaagcuaccauccgcuggauuauggcug
aacgccucuaagucagaauccaugcuagaacgcggugaugcuccacacag
auggauacgaauaaggcguccuuguggcgucgcugaaccauagcaggcua
gcaacggugcacuuggcggaaaggccuugggugcuugcuggcgaauugca
augcguggggauaaaucauuuguauacgacuuagauguacaacgggguau
uguaagcaguagaguagccuuguuguuacgaucugcugagauuaagccuu
uguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8v83 The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
• Resolution: 2.53 Å
• Binding residue (original residue number in PDB): L4 P5 K11 K12 K15 K16 F17 R19 D23 R24 Y25 H26 R27 V28 N31 W32 R33 K34 I38 S40 R43 R44 R45 F46 R47 G48 P53 K54 I55 G56 Y57 G58 S59 N60 K61 K64 F65 L66 P68 L75 N78 K80 E95 A97 H98 N99 I100 S101 K103 N104 R105 K113 N121 K123 G124 R125 L128
• Binding residue (residue number reindexed from 1): L1 P2 K8 K9 K12 K13 F14 R16 D20 R21 Y22 H23 R24 V25 N28 W29 R30 K31 I35 S37 R40 R41 R42 F43 R44 G45 P50 K51 I52 G53 Y54 G55 S56 N57 K58 K61 F62 L63 P65 L72 N75 K77 E92 A94 H95 N96 I97 S98 K100 N101 R102 K110 N118 K120 G121 R122 L125

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:8v83, PDBe:8v83, PDBj:8v83
• PDBsum: 8v83
• PubMed: 38632236
• UniProt: P38061|RL32_YEAST Large ribosomal subunit protein eL32 (Gene Name=RPL32)