Structure of PDB 3j7r Chain SD Binding Site BS01

Receptor Information
>3j7r Chain SD (length=227) Species: 9823 (Sus scrofa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIII
LATRTQNVLGEKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIA
QAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSM
KFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPTGKIGP
KKPLPDHVSIVEPKDEILPTTPISEQK
Ligand information
>3j7r Chain S2 (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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PDB3j7r Structure of the Mammalian ribosome-sec61 complex to 3.4 a resolution.
Resolution3.9 Å
Binding residue
(original residue number in PDB)
V3 Q4 I5 S6 K8 R9 R27 G140 K141 Q145 R146 A147 K151 L156 M157 I158 H159 S160 G161 D162 P163 V172 H174 L176 Q179 V181 G183 K185 P205 D206
Binding residue
(residue number reindexed from 1)
V3 Q4 I5 S6 K8 R9 R27 G140 K141 Q145 R146 A147 K151 L156 M157 I158 H159 S160 G161 D162 P163 V172 H174 L176 Q179 V181 G183 K185 P205 D206
Enzymatic activity
Enzyme Commision number 4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0016829 lyase activity
GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity
Biological Process
GO:0006281 DNA repair
GO:0006412 translation
GO:0006417 regulation of translation
GO:0006915 apoptotic process
GO:0051301 cell division
GO:2001235 positive regulation of apoptotic signaling pathway
Cellular Component
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005819 spindle
GO:0005840 ribosome
GO:0005856 cytoskeleton
GO:0015935 small ribosomal subunit
GO:0022626 cytosolic ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:0098556 cytoplasmic side of rough endoplasmic reticulum membrane
GO:1990904 ribonucleoprotein complex

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Molecular Function

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Biological Process

View graph for
Cellular Component
External links
PDB RCSB:3j7r, PDBe:3j7r, PDBj:3j7r
PDBsum3j7r
PubMed24930395
UniProtQ0Z8U2|RS3_PIG Small ribosomal subunit protein uS3 (Gene Name=RPS3)

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