Structure of PDB 5dgv Chain c5 Binding Site BS01

Receptor Information
>5dgv Chain c5 (length=135) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVNAKKRVFKTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKP
AGFMKKLRAAKLAAPENEKPAPVRTHMRNMIIVPEMIGSVVGIYNGKAFN
QVEIRPEMLGHYLGEFSITYTPVRHGRAGATTSRF
Ligand information
>5dgv Chain 6 (length=1795) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccucuacaugguauaacugug
guaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagagau
guauuuauuagauaaaaaaucaaugucuucggacucuuugaugauucaua
auaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaaauu
ucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuucaa
cggguaacggggaauaaggguucgauuccggagagggagccugagaaacg
gcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccuaau
ucagggagguagugacaauaaauaacgauacagggcccauucgggucuug
uaauuggaaugaguacaauguaaauaccuuaacgaggaacaauuggaggg
caagucuggugccagcagccgcgguaauuccagcuccaauagcguauauu
aaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguuggc
cgguccgauuuuuucguacuggauuuccaacggggccuuuccuucuggcu
aaccuugaguccuuguggcucuuggcgaaccaggacuuuuacuuugaaaa
aauuagaguguucaaagcaggcguauugcucgaauauauuagcauggaau
aauagaauaggacguuugguucuauuuuguugguuucuaggaccaucgua
augauuaauagggacggucgggggcaucaguauucaauugucagagguga
aauucuuggauuuauugaagacuaacuacugcgaaagcauuugccaagga
cguuuucauuaaucaagaacgaaaguuaggggaucgaagaugaucagaua
ccgucguagucuuaaccauaaacuaugccgacuagggaucgggugguguu
uuuuuaaugacccacucggcaccuuacgagaaaucaaagucuuuggguuc
uggggggaguauggucgcaaggcugaaacuuaaaggaauugacggaaggg
caccaccaggaguggagccugcggcuuaauuugacucaacacggggaaac
ucaccagguccagacacaauaaggauugacagauugagagcucuuucuug
auuuugugggugguggugcauggccguucuuaguugguggagugauuugu
cugcuuaauugcgauaacgaacgagaccuuaaccuacuaaauaguggugc
uagcauuugcugguuauccacuucuuagagggacuaucgguuucaagccg
auggaaguuugaggcaauaacaggucugugaugcccuuagacguucuggg
ccgcacgcgcgcuacacugacggagccagcgagucuaaccuuggccgaga
ggucuugguaaucuugugaaacuccgucgugcuggggauagagcauugua
auuauugcucuucaacgaggaauuccuaguaagcgcaagucaucagcuug
cguugauuacgucccugcccuuuguacacaccgcccgucgcuaguaccga
uugaauggcuuagugaggccucaggaucugcuuagagaagggggcaacuc
caucucagagcggagaauuuggacaaacuuggucauuuagaggaacuaaa
agucguaacaagguuuccguaggugaaccugcggaaggaucauua
...<<<<<...[[[[>>>>>[[[[.((((((................[[[
.[[[..<<....<<....<<..........>>...>>.>>......{{..
......[[[..{{..{{....[[[...............<.....<<.<<
.......>>.>>......>.........<<<<<..<......>..>>>>>
[...((((((......<<<<<<<<<<<<..>>>>..............))
)))).....]...<<<<..<<<.....>>>.>>>>....]]]...}}}}.
.]]].<<<....<<<....<<<<<<<<.......>>>>>>>>>>>.....
.>>>...<<<.<<<<....>>>>....>>>.}}.<<.<<<..........
>>>.>>.<.<<....>>.>...]]]]]].........<<<....<<<...
..>>>..>>>...............<<<<<<<<..............>>>
>>.>>>......<<..<...........>..>>.........<<<<<((.
.....<<<<.....<<..))>>.......>>>>.>>>>>..))))))]]]
].........[[[{{.......{{...[[[.{{....<<<<<<.<<<..<
<<<...............>>>>......>>>.>>>>>>....<<<<<<..
..<<..<<<<.......>>>>..>>....>>>>>>...<<<<<.<<....
...<<...<.......>..<<<.....>>>....>>......>>.>>..>
>>.........[[[..((((((((....>>>>>>>>.)))))))).]]].
....}}....<<<<<<.<<...<<<<..<<..<<<<<<.<...<<<....
..>>>......>.>>>>>>..>>.......<<....>>...>>>>...>>
>>>.>>>...]]]...}}......<<<<<<<...<...<<<<........
.>>>>...>>>>>>>>..........<<<.<<.<<<..<<<<<<<<.<<<
........>>>>>>>>>>>..>>>...<<..}}>>...>>.....>>>.]
]].<<<......<<<<....>>>>....>>>..]]]]..<<<<<.<<<<<
<<..<<.<<<<<<..<<<.<<<<<.......<<........>>.......
...<<<<<.<....<<<<<........<<.<<<........>>>.>>...
...>>>>>.<.<<.<<<..<<.<<<<<<....<<<.<<<<<....>>>..
.<<<......>>>...>>.>>>....<<<<<.<<..<<<<..<<<<<.<<
<<<<....>>>>>>...>>>>>..>>>>.>>....<<<<<<.....>>>>
>>.......>>>>>....>>>.>>>.....>>>>>>>>....>.>>>>>.
...>.>>>>.>>>.....<<<<<<<......<<.....<<..<<<<....
>>>>..>>....>>.......>>>>>>>...........<<<<<<.....
.....>>>>>>..........>>>>>>....<<<<<<<<.......>>>>
>>>>......>>...>>>>>>>>>>.>>....<..<<.<..<<<<.<<..
..<<<<<<<<.<<<..<.<<..<...<<<<<<<.<<<..<.........>
...>>>.>>>>>>>...>..>>.>..>>>.>>>>>>>>...>>.>>>>..
.>.>>...>.....<<<<<<<<<....>>>>>>>>>.........
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5dgv Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome
Resolution3.1 Å
Binding residue
(original residue number in PDB)		R18 P38 A39 R40 R42 R43 R44 R47 K59 R77 H79 R81 N82 Y97 N98 G99 K100 F102 Y115 E118 T122 Y123 T124 V126 H128 R137 F138
Binding residue
(residue number reindexed from 1)		R15 P35 A36 R37 R39 R40 R41 R44 K56 R74 H76 R78 N79 Y94 N95 G96 K97 F99 Y112 E115 T119 Y120 T121 V123 H125 R134 F135
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
Biological Process
GO:0000028 ribosomal small subunit assembly
GO:0000054 ribosomal subunit export from nucleus
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:0042254 ribosome biogenesis
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0015935 small ribosomal subunit
GO:0022627 cytosolic small ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5dgv, PDBe:5dgv, PDBj:5dgv
PDBsum5dgv
PubMed
UniProtQ01855|RS15_YEAST Small ribosomal subunit protein uS19 (Gene Name=RPS15)

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