Structure of PDB 5vyc Chain B4 Binding Site BS01

Receptor Information
>5vyc Chain B4 (length=214) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVS
LADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMME
IMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKK
PKFELGKLMELHGE
Ligand information
>5vyc Chain i4 (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)		F25 K28 C111 S112 V114 K115 K116 W117 M120 H124 R136 R146 N148 Q149 I150 R151 Y155 Q157 Q159 Q160 R162 R165 Q202 S203 I204 Y205 P206 K216
Binding residue
(residue number reindexed from 1)		F5 K8 C91 S92 V94 K95 K96 W97 M100 H104 R116 R126 N128 Q129 I130 R131 Y135 Q137 Q139 Q140 R142 R145 Q182 S183 I184 Y185 P186 K196
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0048027 mRNA 5'-UTR binding
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:0006413 translational initiation
GO:0030154 cell differentiation
GO:0042274 ribosomal small subunit biogenesis
GO:0043066 negative regulation of apoptotic process
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:0005925 focal adhesion
GO:0022626 cytosolic ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:0032040 small-subunit processome
GO:0045202 synapse
GO:0070062 extracellular exosome
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
UniProtP61247|RS3A_HUMAN Small ribosomal subunit protein eS1 (Gene Name=RPS3A)

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