Structure of PDB 5k0y Chain J Binding Site BS01

Receptor Information

>5k0y Chain J (length=53) Species: 9986 (Oryctolagus cuniculus)

QQLYWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKDIGFI
KLD

Ligand information

>5k0y Chain A (length=1776)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgcuccucuccuacuuggauaa
cugugguaauucuagagcuaauacaugccgacggcgcugacucccuuugu
gugggaugcgugcauuuaucagaucaaaaccaacccggucagcggcggcg
gcuuuggugacucuagauaaccucgggccgaucgcagcccuccguggcgg
cgacgacccauucgaacgucugcccuaucaacuuucgaugguagucgccg
ugccuaccauggugaccacgggugacggggaaucaggguucgauuccgga
gagggagccugagaaacggcuaccacauccaaggaaggcagcaggcgcgc
aaauuacccacucccgacccggggagguagugacgaaaaauaacaauaca
ggacucuuucgaggcccuguaauuggaaugaguccacuuuaaauccuuua
acgaggauccauuggagggcaagucuggucgcagcagccgcgguaauucc
agcuccaauagcguauauuaaaguugcugcaguuaaaaagcucguaguug
gaucuugagggcccgccccucggcgcccccucgaugugucccgcggggcc
cgaagcguuuacuuugaaaaaauuagaguguucaaagcaggcccgagccg
ccuggauaccgcagcuaggaauaauggaauaggaccgcgguucuauuuug
uugguuuucggaacugaggccaugauuaagagggacggccgggggcauuc
guauugcgccgcuagaggugaaauucuuggaccggcgcaagacggaccag
agcgaaagcauuugccaagaauguuuucauuaaucaagaacgaaagucgg
agguucgaagacgaucagauaccgucguaguuccgaccauaaacgaugcc
gacuggcgaugcggcggcguuauucccaugacccgccgggcagcuuccgg
gaaaccaaagucuuuggguuccggggggaguaugguugcaaagcugaaac
uuaaaggaauugacggaagggcaccaccaggaguggagccugcggcuuaa
uuugacucaacacgggaaaccucacccggcccggacacggacaggauuga
cagauugauagcucuuucucgauucugugggugguggugcauggccguuc
uuaguugguggagcgauuugucugguuaauuccgauaacgaacgagacuc
uggcaugcuaacuaguuacgcgacccccgagcggucggcgucccccaacu
ucuuagagggacaaguggcguucagccacccgagauugagcaauaacagg
ucugugaugcccuuagaugucggggcugcacgcgcgcuacacugacuggc
ucagcgugugccuacccuacgccggcaggcgcggguaacccguugaaccc
cauucgugauggggaucggggauugcaauuauuccccaugaacgaggaau
ucccaguaagugcgggucauaagcuugcguugauuaagucccugcccuuu
guacacaccgcccgucgcuacuaccgauuggaugguuuagugaggcccuc
ggaucggcccgccggggucggcccacggcccuggcggagcgcugagaaga
cggucgaacuugacuaucuagaggaaguaaaagucguaacaagguuuccg
uaggugaaccugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5k0y eIF3 Peripheral Subunits Rearrangement after mRNA Binding and Start-Codon Recognition.
• Resolution: 5.8 Å
• Binding residue (original residue number in PDB): Q4 Q5 L6 Y7 W8 H10 R12 K13 F14 G15 Q16 R19 R22 C24 N26 R27 H28 G29 L30 R32 K33 Y34 N37 R40 Q41 L55 D56
• Binding residue (residue number reindexed from 1): Q1 Q2 L3 Y4 W5 H7 R9 K10 F11 G12 Q13 R16 R19 C21 N23 R24 H25 G26 L27 R29 K30 Y31 N34 R37 Q38 L52 D53

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005791 rough endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5k0y, PDBe:5k0y, PDBj:5k0y
• PDBsum: 5k0y
• PubMed: 27373335
• UniProt: G1U7M4|RS29_RABIT Small ribosomal subunit protein uS14 (Gene Name=RPS29)