Structure of PDB 6wdr Chain N Binding Site BS01

Receptor Information
>6wdr Chain N (length=150) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIG
VLLRDAHGVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKH
LERNRKDKDAKFRLILIESRIHRLARYYRTVAVLPPNWKYESATASALVN
Ligand information
>6wdr Chain 2 (length=1647) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
aucugguugauccugccaguagucauaugcuugucucaaagauuaagcca
ugcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcucau
uaaaucaguuaucguuuauuugauaguuccuuuacuacaugguauaacug
ugguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagag
auguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauuca
uaauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaaa
uuucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuuc
aacggguaacggggaauaaggguucgauuccggagagggagccugagaaa
cggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccua
auucagggagguagugacaauaaauaacgauacagggcccauucgggucu
uguaauuggaaugaguacaauguaaauaccuuaacgaggaacaauuggag
ggcaagucuggugccagcagccgcgguaauuccagcuccaauagcguaua
uuaaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguug
gccggucggauuuccaacggggccuuuccuucuggcuaaccuugaguccu
uguggcucuuggcgaaccaggacuuuuacuuugaaaaaauuagaguguuc
aaagcaggcguauugcucgaauauauuagcauggaauaauagaauaggac
guuugguucuauuuuguugguuucuaggaccaucguaaugauuaauaggg
acggucgggggcauaacuacugcgaaagcauuugccaaggacguuuucau
uaaucuaaccauaaacuaugccgacuagggaucgggugguguuuuuuuaa
ugacccacucggcaccuuacgagaaaucaaagucuuuggguucugggggg
aguauggucgcaaggaugaaacuuaaaggaauugacggaagggcaccacc
aggaguggagccugcggcuuaauuugacucaacacggggaaacucaccag
guccagacacaauaaggauugacagauugagagcucuuucuugauuuugu
gggugguggugcauggccguucuuaguugguggagugauuugucugcuua
auugcgauaacgaacgagaccuuaaccuacuaaauaguggugcuagcauu
ugcugguuauccacuucuuagagggacuaucgguuucaagccgauggaag
uuugaggcaauaacaggucugugaugcccuuagacguucugggccgcacg
cgcgcuacacugacggagccagcgagucuaaccuuggccgagaggucuug
guaaucuugugaaacuccgucgugcuggggauagagcauuguaauuauug
cucuucaacgaggaauuccuaguaagcgcaagucaucagcuugcguugau
uacgucccugcccuuuguacacaccgcccgucgcuaguaccgauugaaug
gcuuagugaggccucaggaucugcuuagagaagggggcaacuccaucuca
gagcggagaauuuggacaaacuuggucauuuagaggaacuaaaaguc
..<<<<<...((((>>>>><<<<.<<<<.....<.<...<.......<<.
<<<..<<....<<....<<..........>>...>>.>>......<<...
.....<<<..<<..<<....<<<..................<.....<<.
<<.......>>.>>......>.........<<<<<..<......>..>>>
>><...<<<<<<......(((.(((.........................
>>>>>>.....>...<<<<..<<<.....>>>.>>>>....>>>...>>>
>..>>>.<<<....<<<....<<<<<<<<.......>>>>>>>>>>>...
...>>>...<<<.<<<<....>>>>....>>>.>>.<<.<<<........
..>>>.>>.<.<<....>>.>...>>>>>..........<<<....<<<.
....>>>..>>>..>....>.>.....<<<<<<<<<.<.......>..>>
>>>>.>>>......<<..<...........>..>>.........<<<<<(
(......<<<<.........)).........>>>>.>>>>>....>>>>>
>>>.........<<.<<................<<....<<<<<<.<<<<
<............>>>>>.>>>>>>.....<<<<<.....<..<<<<...
....>>>>..>.....>>>>>....<<<<<.<<.......<<...<....
...>..<<<.....>>>....>>......>>.>>..>>>.........<<
<..<<<<.<<......))).)))..>>.>>>>.>>>.....>>....<<<
<<<.<<...<<<<........<<....>>...>>>>...>>>>>.>>>..
....................((.((.<<<..<<<<<<<<.<<<.<....>
.>>>>>>>>>>>..>>>...((..>>))...)).....))...>>.<<<.
.......<......>......>>>..)))).....<..<<<<<<......
...<<<..<<..............<<........>>..........<<<<
<......<.<<............<............>..........>>.
.>..................<....<<<.<<<<......>>...<<<...
...>>>...>>.>>>....<<<<..<<..<<<<..<<<<<...<<<....
..>>>.....>>>>>..>>>>.>>....<<<<<<.....>>>>>>.....
...>>>>....>.........................>>>>>........
....>>.....<<<<<<<......<<.....<<..<<<<....>>>>..>
>....>>.......>>>>>>>...........<<<<<<..........>>
>>>>..........>>>.......<<<<...............>>>>...
.........>>>>>>.>.................<<<<.....<<<<<<<
<<<.<<<..<.<<..<...<<<<<<<.<<....<<<....>>>....>>.
>>>>>>>...>..>>.>..>>>.>>>>>>>>>>....>>>>......
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6wdr An open interface in the pre-80S ribosome coordinated by ribosome assembly factors Tsr1 and Dim1 enables temporal regulation of Fap7.
Resolution3.7 Å
Binding residue
(original residue number in PDB)		G2 R3 H5 G8 G10 I11 S12 S14 P17 R55 T61 R64 K70 M72 R73 K94 H101 N105 K107 D108 F113 L117 S120 R121 R124 Y128
Binding residue
(residue number reindexed from 1)		G1 R2 H4 G7 G9 I10 S11 S13 P16 R54 T60 R63 K69 M71 R72 K93 H100 N104 K106 D107 F112 L116 S119 R120 R123 Y127
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0070181 small ribosomal subunit rRNA binding
Biological Process
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0002181 cytoplasmic translation
GO:0006412 translation
Cellular Component
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:0030686 90S preribosome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6wdr, PDBe:6wdr, PDBj:6wdr
PDBsum6wdr
PubMed33219089
UniProtP05756|RS13_YEAST Small ribosomal subunit protein uS15 (Gene Name=RPS13)

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