Structure of PDB 5vyc Chain Y3 Binding Site BS01

Receptor Information
>5vyc Chain Y3 (length=131) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTT
PDVIFVFGFRTHFGGGKTTGFGMIYDSLDYAKKNEPKHRLARHGLYEKKK
TSRKQRKERKNRMKKVRGTAKANVGAGKKPK
Ligand information
>5vyc Chain i3 (length=1742) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgcuccucucccacuuggauaa
cugugguaauucuagagcuaauacaugccgacgggcgcugacccccuucg
cgggggggaugcgugcauuuaucaguggugacucuagauaaccucgggcc
gaucgcacgccccccguggcggcgacgacccauucgaacgucugcccuau
caacuuucgaugguagucgccgugccuaccauggugaccacgggugacgg
ggaaucaggguucgauuccggagagggagccugagaaacggcuaccacau
ccaaggaaggcagcaggcgcgcaaauuacccacucccgacccggggaggu
agugacgaaaaauaacaauacaggacucuuucgaggcccuguaauuggaa
ugaguccacuuuaaauccuuccgcgaggauccauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguugcu
gcaguuaaaaagcucguaguuggaucuugggagcgggcguccccgccgcc
ucucggccggggcccgaagcauuuacuuugaaaaaauuagaguguucaaa
gcaggcccgagccgccuggauaccgcagcuaggaauaauggaauaggacc
gcgguucuauuuuguugguuuucggaacugaggccaugauuaagagggac
ggccgggggcauucguauugcgccgcuagaggugaaauucuuggaccggc
gcaagacggaccagagcgaaagcauuugccaagaauguuuucauuaauca
agaacgaaagucggagguucgaagacgaucagauaccgucguaguuccga
ccauaaacgaugccgacuggcgaugcggcggcguuauucccaugacccgc
cgggcagcuuccgggaaaccaaagucuuuggguuccggggggaguauggu
ugcaaagcugaaacuuaaaggaauugacggaagggcaccaccaggagugg
agccugcggcuuaauuugacucaacacgggaaaccucacccggcccggac
acggacaggauugacagauugauagcucuuucucgauuccguggguggug
gugcauggccguucuuaguugguggagcgauuugucugguuaauuccgau
aacgaacgagacucuggcaugcuaacuaguuacgcgacccccgagcgguc
ggcgucccccaacuucuuagagggacaaguggcguucagccacccgagau
ugagcaauaacaggucugugaugcccuuagauguccggggcugcacgcgc
gcuacacugacuggcucagcgugugccuacccuacgccggcaggcgcggg
uaacccguugaaccccauucgugauggggaucggggauugcaauuauucc
ccaugaacgaggaauucccaguaagugcgggucauaagcuugcguugauu
aagucccugcccuuuguacacaccgcccgucgcuacuaccgauuggaugg
uuuagugaggcccucggaucggccccgccggggucggcccacggcccugg
cggagcgcugagaagacggucgaacuugacuaucuagaggaaguaaaagu
cguaacaagguuuccguaggugaaccugcggaaggaucauua
...<<<<<.[.((((>>>>><<<.<<<<<<...<.<<.........<<<.
<<<..<<....<<....<<..........>>...>>.>>......<<...
.....<<<......<<....<<<....................<<.....
<<.<<.......>>.>>......>>.........<<<<...<<<<.....
...>>>>...>>>><...<<<<<...<......>..>>>>>........>
..<<<<..<<........>>.>>>>....>>>...>>....>>>.<<<..
..<<<....<<<<<<<.........>>>>>>>>>>......>>>...<<<
.<<<<....>>>>....>>>.>>.<<.<<<..........>>>.>>.<.<
<....>>.>...>>>>>>.........<<<....<<<.....>>>..>>>
......>>.>.....<<.<<.<<..............>.>.>>..>>...
...<<..<...........>..>>.........<<<<<((......<<<<
.....<<..))>>.......>>>>.>>>>>..>>>>>>.>>>........
.<..((.....<.<<...<<<.<<..........................
.......................<<<<<.<.......<<...<.......
>..<<<.......>>>....>>......>.>>>..>>........<<.<.
.<<..<<.................>>..>>..>>>....>>....<<<<<
<..<...<<<<..<<..<<<<<<<<...<<<......>>>......>>>>
>>>.>.>>.......<<....>>...>>>>..>..>>>.>>>...>>>..
.>>.>....<<<<<<<...<...<<<<.<.....>.>>>>...>>>>>>>
>..........<<<.<<.<<<..<.<<<<<<.<<<<......>>>>>>>>
>>.>..>>>...<<..))>>...>>.....>>>...>.<<<......<<<
......>>>....>>>..)))).]<<<<<.<<<<<<<..<<..<<<<<..
<<<.<<<<........<<........>>........<.<<<.........
<<<<............<<........>>..........>>>>....<<.<
<<..<<.<<.<<<....<<<.<<<<<....>>>...<<<......>>>..
.>>.>>>....<<<...<...<<<<...<............<<......>
>............>..>>>>..>.....<<<<<.....>>>>>.......
.>>>....>>>..>>.....>>>>>>>.........>>>>.....>>>>.
>>>.....<<.<<<................<<<.<<<<....>>>>.>>>
..............>>>.>>......<..<<.<<<<<..........>>>
>>>>...>.....>>>>>.....<<<<<<<<.......>>>>>>>>....
..>>...>>>>>>>>>>.>>....<..<<.<..<<<..<<....<<<<<<
<<.<<<..<<<<.<<...<<<<<...........................
......>>>>>...>>.>>>>..>>>.>>>>>>>>...>>..>>>...>.
>>...>.....<<<<<<<<<....>>>>>>>>>.........
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5vyc Crystal Structure of the Human Ribosome in Complex with DENR-MCT-1.
Resolution6.0 Å
Binding residue
(original residue number in PDB)		R8 T9 R10 K11 F12 M13 T14 K32 A33 T34 P36 G59 F60 T62 H63 F64 G65 G66 H89 A92 R93 R104 K105 K108 K111 N112 K115 K116 G119 T120 A121
Binding residue
(residue number reindexed from 1)		R7 T8 R9 K10 F11 M12 T13 K31 A32 T33 P35 G58 F59 T61 H62 F63 G64 G65 H88 A91 R92 R103 K104 K107 K110 N111 K114 K115 G118 T119 A120
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0031369 translation initiation factor binding
Biological Process
GO:0002181 cytoplasmic translation
GO:0006364 rRNA processing
GO:0006412 translation
GO:0034101 erythrocyte homeostasis
GO:0042274 ribosomal small subunit biogenesis
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005829 cytosol
GO:0005840 ribosome
GO:0015935 small ribosomal subunit
GO:0016020 membrane
GO:0022626 cytosolic ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:0032040 small-subunit processome
GO:0044391 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:5vyc, PDBe:5vyc, PDBj:5vyc
PDBsum5vyc
PubMed28723557
UniProtP62847|RS24_HUMAN Small ribosomal subunit protein eS24 (Gene Name=RPS24)

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