Structure of PDB 6rbd Chain l Binding Site BS01

Receptor Information

>6rbd Chain l (length=271) Species: 559292 (Saccharomyces cerevisiae S288C)

TDDFRVLQAVEQGSRSHEVVPTPLIHQISGMRSQSGTNRAISDLAKLSLI
SKMRNVKYDGYRLTYNGIDYLALKTMLNRDTVYSVGNTIGVGKESDIYKV
SDKNGNPRVMKIHRLQGANWMHLSRLAANKEYQFMSMLYSKGFKVPEPFD
NSRHIVVMELIEGYPMRRLRKHKNIPKLYSDLMCFIVDLANSGLIHCDFN
EFNIMIKDKLEDENDCGFVVIDFPQCISIQHQDADYYFQRDVDCIRRFFK
KKLKYEPKPDSSMLDTEGFGD

Ligand information

>6rbd Chain 2 (length=1777)

aucugguugauccugccaguagucauaugcuugucucaaagauuaagcca
ugcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcucau
uaaaucaguuaucguuuauuugauaguuccuuuacuacaugguauaacug
ugguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagag
auguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauuca
uaauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaaa
uuucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuuc
aacggguaacggggaauaaggguucgauuccggagagggagccugagaaa
cggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccua
auucagggagguagugacaauaaauaacgauacagggcccauucgggucu
uguaauuggaaugaguacaauguaaauaccuuaacgaggaacaauuggag
ggcaagucuggugccagcagccgcgguaauuccagcuccaauagcguaua
uuaaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguug
gccggucggauuuccaacggggccuuuccuucuggcuaaccuugaguccu
uguggcucuuggcgaaccaggacuuuuacuuugaaaaaauuagaguguuc
aaagcaggcguauugcucgaauauauuagcauggaauaauagaauaggac
guuugguucuauuuuguugguuucuaggaccaucguaaugauuaauaggg
acggucgggggcaucaguauucaauugucagaggugaaauucuuggauuu
auugaagacuaacuacugcgaaagcauuugccaaggacguuuucauuaau
caagaacgaaaguuaggggaucgaagaugaucagauaccgucguagucuu
aaccauaaacuaugccgacuagggaucgggugguguuuuuuuaaugaccc
acucggcaccuuacgagaaaucaaagucuuuggguucuggggggaguaug
gucgcaaggcugaaacuuaaaggaauugacggaagggcaccaccaggagu
ggagccugcggcuuaauuugacggggaaacucaccagguccagacacaau
aaggauugacagauugagagcucuuucuugauuuugugggugguggugca
uggccguucuuaguugguggagugauuugucugcuuaauugcgauaacga
acgagaccuuaaccuacuaaauaguggugcuagcauuugcugguuaucca
cuucuuagagggacuaucgguuucaagccgauggaaguuugaggcaauaa
caggucugugaugcccuuagacguucugggccgcacgcgcgcuacacuga
cggagccagcgagucuaaccuuggccgagaggucuugguaaucuugugaa
acuccgucgugcuggggauagagcauuguaauuauugcucuucaacgagg
aauuccuaguaagcgcaagucaucagcuugcguugauuacgucccugccc
uuuguacacaccgcccgucgcuaguaccgauugaauggcuuagugaggcc
ucaggaucugcuuagagaagggggcaacuccaucucagagcggagaauuu
ggacaaacuuggucauuuagaggaacuaaaagucguaacaagguuuccgu
aggugaaccugcggaaggaucauuaaa

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6rbd Conformational proofreading of distant 40S ribosomal subunit maturation events by a long-range communication mechanism.
• Resolution: 3.47 Å
• Binding residue (original residue number in PDB): R17 Q24 E30 S47 R51 N67 V68 T100 I101 G102 V103 K105 R198 D229 N231 F233 K282
• Binding residue (residue number reindexed from 1): R5 Q12 E18 S35 R39 N55 V56 T88 I89 G90 V91 K93 R167 D198 N200 F202 K251

Enzymatic activity

• Enzyme Commision number: 2.7.11.1: non-specific serine/threonine protein kinase.

Gene Ontology

Molecular Function

• GO:0004672 protein kinase activity
• GO:0004674 protein serine/threonine kinase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0044024 histone H2AS1 kinase activity
• GO:0046872 metal ion binding
• GO:0106310 protein serine kinase activity

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006338 chromatin remodeling
• GO:0006468 protein phosphorylation
• GO:0016310 phosphorylation
• GO:0030490 maturation of SSU-rRNA
• GO:0042254 ribosome biogenesis
• GO:0046830 positive regulation of RNA import into nucleus

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0010494 cytoplasmic stress granule
• GO:0030688 preribosome, small subunit precursor

External links

• PDB: RCSB:6rbd, PDBe:6rbd, PDBj:6rbd
• PDBsum: 6rbd
• PubMed: 31227701
• UniProt: P40160|RIO2_YEAST Serine/threonine-protein kinase RIO2 (Gene Name=RIO2)