Structure of PDB 4u4o Chain S2 Binding Site BS01

Receptor Information

>4u4o Chain S2 (length=217) Species: 559292 (Saccharomyces cerevisiae S288C)

GWVPVTKLGRLVKAGKITTIEEIFLHSLPVKEFQIIDTLLPGLQDEVMNI
KPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAK
LSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVASPA
VKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQ
PLPVSPLDIYSDEASAQ

Ligand information

>4u4o Chain 2 (length=1750)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuuuacuacaugguauaacu
gugguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaaga
gauguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauuc
auaauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaa
auuucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuu
caacggguaacggggaauaaggguucgauuccggagagggagccugagaa
acggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccu
aauucagggagguagugacaauaaauaacgauacagggcccauucggguc
uuguaauuggaaugaguacaauguaaauaccuuaacgaggaacaauugga
gggcaagucuggugccagcagccgcgguaauuccagcuccaauagcguau
auuaaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguu
ggccggucggauuuccaacggggccuuuccuucuggcuaaccuugagucc
uuguggcucuuggcgaaccaggacuuuuacuuugaaaaaauuagaguguu
caaagcaggcguauugcucgaauauauuagcauggaauaauagaauagga
cguuugguucuauuuuguugguuucuaggaccaucguaaugauuaauagg
gacggucgggggcaucaguauucaauugucagaggugaaauucuuggauu
uauugaagacuaacuacugcgaaagcauuugccaaggacguuuucauuaa
ucaagaacgaaaguuaggggaucgaagaugaucagauaccgucguagucu
uaaccauaaacuaugccgacuagggaucgggugguguuuuuuuaaugacc
cacucggcaccuuacgagaaaucaaagucuuuggguucuggggggaguau
ggucgcaaggcugaaacuuaaaggaauugacggaagggcaccaccaggag
uggagccugcggcuuaauuugacucaacacggggaaacucaccaggucca
gacacaauaaggauugacagauugagagcucuuucuugauuuugugggug
guggugcauggccguucuuaguugguggagugauuugucugcuuaauugc
gauaacgaacgagaccuuaaccuacuaaauaguggugcuagcauuugcug
guuauccacuucuuagagggacuaucgguuucaagccgauggaaguuuga
ggcaauaacaggucugugaugcccuuagacguucugggccgcacgcgcgc
uacacugacggagccagcgagucuaaccuuggccgagaggucuugguaau
cuugugaaacuccgucgugcuggggauagagcauuguaauuauugcucuu
caacgaggaauuccuaguaagcgcaagucaucagcuugcguugauuacgu
cccugcccuuuguacacaccgcccgucgcuaguaccgauugaauggcuua
gugaggccucaggaucugggagaauuuggacaaacuuggucauuuagagg
aacuaaaagucguaacaagguuuccguaggugaaccugcggaaggaucau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4u4o ?
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): V86 Q87 K88 Q89 R91 A92 G93 R95 R97 K99 K116 K119 T159 K161 C162 G163 S164 R168 V179 A180 S181 Y197 T198 Q199 N201 K203 T204 R205 N209 K212 F224
• Binding residue (residue number reindexed from 1): V53 Q54 K55 Q56 R58 A59 G60 R62 R64 K66 K83 K86 T126 K128 C129 G130 S131 R135 V146 A147 S148 Y164 T165 Q166 N168 K170 T171 R172 N176 K179 F191

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0000054 ribosomal subunit export from nucleus
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042254 ribosome biogenesis
• GO:0045903 positive regulation of translational fidelity

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4u4o, PDBe:4u4o, PDBj:4u4o
• PDBsum: 4u4o
• PubMed: 25209664
• UniProt: P25443|RS2_YEAST Small ribosomal subunit protein uS5 (Gene Name=RPS2)