Structure of PDB 6m62 Chain e Binding Site BS01

Receptor Information

>6m62 Chain e (length=127) Species: 559292 (Saccharomyces cerevisiae S288C)

ASLPHPKIVKKHTKKFKRHHSDRYHRVAENWRKQKGIDSVVRRRFRGNIS
QPKIGYGSNKKTKFLSPSGHKTFLVANVKDLETLTMHTKTYAAEIAHNIS
AKNRVVILARAKALGIKVTNPKGRLAL

Ligand information

>6m62 Chain 1 (length=2972)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaac
aaguacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaag
uacgugaaauuguugaaagggaagggcauuugaucagacaggccagcauc
aguuuugguggcaggauaaauccauaggaauguagcuugccucgguaagu
auuauagccugugggaauacugccagcugggacugaggacugcgacguaa
gucaaggaugcuggcauaaugguuauaugccgcccgucuugaaacacgga
ccaaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcg
uaaugaaagugaacguagguuggggccucgcaagaggugcacaaucgacc
gauccugaugucuucggauggauuugaguaagagcauagcuguugggacc
cgaaagauggugaacuaugccugaauagggugaagccagaggaaacucug
guggaggcucguagcgguucugacgugcaaaucgaucgucgaauuugggu
auaggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaag
uuucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaa
aacuuuaaauauguaagaaguccuuguuugaacguggacauuugaaugaa
gagcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggauga
accgaacguagaguuaaggugccggaauacacgcucaucagacaccacaa
aagguguuaguucaucuagacagccggacgguggccauggaagucggaau
ccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaa
auggauggcgcucaagcguguuaccuauacucuaccgucaggguugauau
gaugcccugacgaguaggcaggcguggaggucagugacgaagccuagacc
guaaggucgggucgaacggccucuagugcagaucuuggugguaguagcaa
auauucaaaugagaacuuugaagacugaaguggggaaagguuccacguca
acagcaguuggacguggguuagucgauccuaagagauggggaagcuccgu
uucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaa
gauuccggaaccuggauauggauucuucacgguaacguaacugaaugugg
agacgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuu
aucaccccggaauugguuuauccggagauggggucuuauggcuggaagag
gccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaaucc
acaggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggu
cuccaaggugaacagccucuaguugauagaauaauguagauaagggaagu
cggcaaaauagauccguaacuucgggauaaggauuggcucuaagggucgg
acgaucaacuuagaacugguacggacaaggggaaucugacugucuaauua
aaacauagcauugcgauggucagaaagugauguugacgcaaugugauuuc
ugcuggauuaacgagauucccacugucccuaucuacuaucuagcgaaacc
acagccaagggggcuuggcagaaucagcggggaaagaagacccuguugag
cuugacucuaguuugacauugugaagagacauaguuucuuuacuuauuca
augaagcggagcuggaauucauuuuccacguucuagcauucaagguccca
uucggggcugauccggguugaagacauugucagguggggaguuugggggc
ggcacaucuguuaaacgauaacgcagauguccuaaggggggcucauggag
aacagaaaucuccaguagaacaaaaggguaaaagcccccuugauuuugau
uuucagugugaauacaaaccaugaaaguguggccuaucgauccuuuaguc
ccucggaauuugaggcuagaggugccagaaaaguuaccacagggauaacu
ggcuuguggcagucaagcguucauagcgacauugcuuuuugauucuucga
ugucggcucuuccuaucauaccgaagcagaauucgguaagcguuggauug
uucacccacuaauagggagugagcuggguuuagaccgucgugagacaggu
uaguuuuacccuacugaugaauguuaccgcaauaguaauugaacuuagua
cgagaggaacaguucauucggauaauugguuuuugcggcugucugaucag
gcauugccgcgaagcuaccauccgcuggauuauggcugaacgccucuaag
ucagaauccaugcuagaacgcggugauuucuuugcuccacacaauauaga
uggauacgaauaaggcguccuuguggcgucgcugaaccauagcaggcuag
caacggugcacuuggcggaaaggccuugggugcuugcuggcgaauugcaa
ugucauuuugcguggggauaaaucauuuguauacgacuuagauguacaac
gggguauuguaagcaguagaguagccuuguuguuacgaucugcugagauu
aagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6m62 Coupling of 5S RNP rotation with maturation of functional centers during large ribosomal subunit assembly.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): K12 F17 R19 H21 D23 Y25 H26 R27 V28 N31 W32 R33 K34 I38 S40 R43 R44 R45 F46 R47 P53 K54 I55 G56 Y57 G58 S59 K61 K62 K64 F65 E95 A97 H98 N99 S101 K103 R105 N121 R125
• Binding residue (residue number reindexed from 1): K11 F16 R18 H20 D22 Y24 H25 R26 V27 N30 W31 R32 K33 I37 S39 R42 R43 R44 F45 R46 P52 K53 I54 G55 Y56 G57 S58 K60 K61 K63 F64 E94 A96 H97 N98 S100 K102 R104 N120 R124

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:6m62, PDBe:6m62, PDBj:6m62
• PDBsum: 6m62
• PubMed: 32719344
• UniProt: P38061|RL32_YEAST Large ribosomal subunit protein eL32 (Gene Name=RPL32)