Structure of PDB 8scb Chain DD Binding Site BS01

Receptor Information

>8scb Chain DD (length=221) Species: 9986 (Oryctolagus cuniculus)

QISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVRTEIIILATRTQ
NVLGEKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLR
YKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGL
MIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPSGKIGPKKPLPD
HVSIVEPKDEILPTTPISEQK

Ligand information

>8scb Chain 9 (length=1692)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgccacuuggauaacugugguaauuc
uagagcuaauacaugccgacgggcgcugacccccuucgcgggggggaugc
gugcauuuaucaguggugacucuagauaaccucgggccgaucgcacgccc
cccguggcggcgacgaccauucgaacgucugcccuaucaacuuucgaugg
uagucgccgugccuaccauggugaccacgggugacggggaaucaggguuc
gauuccggagagggagccugagaaacggcuaccacauccaaggaaggcag
caggcgcgcaaauuacccacucccgacccggggagguagugacgaaaaau
aacaauacaggacucuuucgaggcccuguaauuggaaugaguccacuuua
aauccuuuaacgaggauccauuggagggcaagucuggugccagcagccgc
gguaauuccagcuccaauagcguauauuaaaguugcugcaguuaaaaagc
ucguaguuggaucuugggagcgggcguccccgccuuuacuuugaaaaaau
uagaguguucaaagcaggcccgagccgccuggauaccgcagcuaggaaua
auggaauaggaccgcgguucuauuuugguuuucggaacugaggccaugau
uaagagggacggccgggggcauucguauugcgccgcuagaggugaaauuc
uuggaccggcgcaagacggaccagagcgaaagcauuugccaagaauguuu
ucauuaaucaagaacgaaagucggagguucgaagacgaucagauaccguc
guaguuccgaccauaaacgaugccgacuggcgaugcggcggcguuauucc
caugacccgccgggcagcuuccgggaaaccaaagucuuuggguuccgggg
ggaguaugguugcaaagcugaaacuuaaaggaauugacggaagggcacca
ccaggaguggagccugcggcuuaauuugacucaacacgggaaaccucacc
cggcccggacacggacaggauugacagauugauagcucuuucucgauucc
gugggugguggugcauggccguucuuaguugguggagcgauuugucuggu
uaauuccgauaacgaacgagacucuggcaugcuaacuaguuacgcgaccc
ccgagcggucggcgucccccaacuucuuagagggacaaguggcguucagc
cacccgagauugagcaauaacaggucugugaugcccuuagauguccgggg
cugcacgcgcgcuacacugacuggcucagcgugugccuacccuacgccgg
caggcgcggguaacccguugaaccccauucgugauggggaucggggauug
caauuauuccccaugaacgaggaauucccaguaagugcgggucauaagcu
ugcguugauuaagucccugcccuuuguacacaccgcccgucgcuacuacc
gauuggaugguuuagugaggcccucggaucggccccgccggggugcccug
gcggagcgcugagaagacggucgaacuugacuaucuagaggaaguaaaag
ucguaacaagguuuccguaggugaaccugcggaaggaucauu

...<<<<<.[.((((>>>>><<<.<<<<<<...<.<<..<......<<<.
<<<..<<....<<....<<..........>>...>>.>>......<<...
.....<<<.<....<<....<<<<.......<<.....<<.<<<.....>
>>.>>......>>.........<<<<...<<<<<<....>>>>>>...>>
>>....<<<<<...<......>..>>>>>............<<<.<<<<.
.....>>>>>>>...>>>>...>>..>.>>>.<<<....<<<....<<<<
<<<.........>>>>>>>>>>......>>>...<<<.<<<<....>>>>
....>>>.>>.<<.<<<..........>>>.>>.<.<<....>>.>...>
>>>>>.........<<<....<<<<...>>>>..>>>..>...>>.>...
..<<.<<<<<<.<<<....>>>..>>>>>>..>>......<<..<.....
......>..>>.........<<<<<((......<<<<.....<<..))>>
.......>>>>.>>>>>..>>>>>>.>>>.........<.<((.....<.
<<...<<<.<<.....<<.<.<<....>>.>.>>.<<<<<<.<.......
<<...<.......>.<<<<.......>>>>...>>......>.>>>..>>
>.......<<.<..<<<<<<<............>>>>>>>.>.>>....>
>....<<<<<<..<...<<<<..<<..<<<<<<<<...<<<......>>>
......>>>>>>>>..>>.......<<....>>...>>>>..>..>>>.>
>>...>>>...>>.>....<<<<<<<...<...<<<<.<.....>.>>>>
...>>>>>>>>..........<<<.<<.<<<..<.<<<<<<.<<<.....
...>>>>>>>>>.>..>>>...<<..))>>...>>.....>>>.>.>.<<
<......<<<<....>>>>....>>>..)))).]<<<<<.<<<<<<<..<
<..<<<<<..<<<.<<<<<<......<<........>>..........<<
<<<.<....<<<..........<<.<<<........>>>.>>........
>>>...<<.<<<..<<<<<<<<<....<<<.<<<<<....>>>...<<<.
.....>>>...>>.>>>....<<<...<...<<<<..<<<.....<<<..
.<<<....>>>..>>>.....>>>..>>>>..>.....<<<<<.....>>
>>>........>>>....>>>.>>>...>.>>>>>>>.....>.>>>>>.
..>>.>>>>.>>>.....<<.<<<........<.......<<<.<<<<..
..>>>>.>>>....>.........>>>.>>......<...<.<<<<<...
.......>>>>>>....>.....>>>>>.....<<<<<<<<.......>>
>>>>>>......>>...>>>>>>>>>>.>>....<..<<.<..<<<<.<<
....<<<<<<<<.<<<..<<<<.<<...<<<<<<<<<<<<<<<..>>>>>
>>>>.>.>>>>>...>>.>>>>..>>>.>>>>>>>>...>>.>>>>...>
.>>...>.....<<<<<<<<<<..>>>>>>>>>>........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8scb Structure and consequences of eRF1 glued to the ribosomal decoding center
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): I5 S6 K7 K8 R9 S139 K141 R143 Q145 R146 A147 K151 L156 M157 I158 H159 S160 G161 D162 H174 L176 Q179 V181 G183 K185 P205 D206
• Binding residue (residue number reindexed from 1): I2 S3 K4 K5 R6 S133 K135 R137 Q139 R140 A141 K145 L150 M151 I152 H153 S154 G155 D156 H168 L170 Q173 V175 G177 K179 P199 D200

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:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• 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:0031334 positive regulation of protein-containing complex assembly
• GO:0051092 positive regulation of NF-kappaB transcription factor activity
• 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:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8scb, PDBe:8scb, PDBj:8scb
• PDBsum: 8scb
• PubMed: 38172604
• UniProt: G1TNM3|RS3_RABIT Small ribosomal subunit protein uS3 (Gene Name=RPS3)